Monday, June 13, 2016

Capitalism will collapse because banks & political elite ‘allow poor to rot’

RT |  The banks behind politicians in the western world “have allowed the poor to rot,” and now the elites in those countries, especially the US, are facing a revolt, journalist and author Tariq Ali told RT America’s Chris Hedges in an exclusive interview. 

“The elites who have run the United States and western Europe have proven incapable of offering even the smallest palliatives to their populations. They have allowed the poor to rot ‒ regardless of skin color ‒ and grow,” Ali said. “And so what we have is a protest against this center elite, which I call the extreme center because whether it’s social democratic or conservative, they unite to crush.”

Presumptive Republican nominee Donald Trump has become a perfect example of this protest against the extreme center, he tells Hedges.

“They’ve found in Trump someone who airs their most crazed fantasies at the same time who attacks the banks, at the same time attacks these new treaties which are being carried through and promises some palliatives to the poorest section of the white working class,” Ali said.

The right and the far right are growing around the world, while the left has been weak. That is part of the reason that Democratic presidential candidate Bernie Sanders wasn’t able to succeed, even though he also offers an independent voice to the working class.

“I don’t think that there’s anything on the radical left at the moment ‒ of course, these things are volatile, things can happen,” he said.

Sunday, June 12, 2016

thought leadership

cbc |  Pat Kelly vividly remembers when he first knew he was a "thought leader":

"In 2005, I met another 'thought leader' and I asked him how he became a 'thought leader' and he said 'I don't know.' It was then that I knew I could be one too."

Kelly proved his skill at leading thoughts on the This Is That Talks stage this past April in Whistler, BC. As you can see in the video of his talk, Kelly confidently made grand statements, spoke with his hands, and had slides - all hallmarks of a true "thought leader" or "influencer."

"My talk was a big success: I said things and the audience nodded their heads."

Based on the success of his talk, Kelly hopes to appear on a number of podcasts about "big ideas."

are humans the only animals that mock one another?

telegraph |  Our animal ancestors, and most of their descendants, laughed simply because they were enjoying themselves, according to a new study. 

But over millions of years humans have perfected how to use the sound to wound as well.
Great apes which roamed the earth 16 million years ago are thought to be the first who developed the ability to laugh.
Modern-day Orangutans, the only species of Asian great ape, laugh when they are having fun, while African great apes, which include gorillas and chimpanzees, have learned that the sound can be used to influence others, but still only use laughter while playing.
However, human have gone much further, using laughter for a range of negative emotions, including to ridicule or sneer.

Saturday, June 11, 2016

ruthless conflation and exploitation of personal as political - hillBilly is the GOAT!!!

Haaretz |  "Religion ain’t bad; it’s people who are bad," he said. "You know the entire power structure is Zionist. They control America; they control the world. They are really against the Islam religion. So whenever a Muslim does something wrong, they blame the religion.”

Despite his frequent jabs at the Jewish community and Israel, Ali couldn't seem to alienate some of his most fervent Jewish admirers, among them Hollywood star Billy Crystal.

Crystal's 1977 impression of the boxing legend deciding to convert to Judaism and change his name to Izzy Yiskowitz became legendary on its own right. Fifteen years later, Ali had the pleasure of having Crystal perform at his 50th birthday party.

Sportscaster Howard Cosell, born Howard Cohen, was perhaps Ali's biggest defender. Unlike many others, Cosell immediately called Ali by his new, Islamic name after he changed it from Cassius Clay, and also stood up for his right to resist the draft. The Jewish journalist and the Muslim champion had a rapport that was evident in post-fight interviews, where they exchanged barbs and bantered, drawing in enchanted viewers.

triple-down on the faux identity-politics of Granny Goodness' faux populist VP...,

WaPo | The furor over Trump’s assaults on the impartiality of a Latino judge had just begun to subside when he lobbed two tweets Friday morning responding to Warren, who had lambasted him as a “thin-skinned, racist bully” in a speech the previous evening.

“Pocahontas is at it again!” Trump wrote in one. “Goofy Elizabeth Warren, one of the least productive U.S. Senators, has a nasty mouth.”

“No, seriously — Delete your account,” Warren tweeted back. One of the senator’s supporters secured and redirected it to Warren’s campaign site.

The real estate developer has repeatedly invoked the ­17th-century Native American figure to refer to Warren, an allusion to controversy about her heritage. The senator has said she grew up amid family stories about her Cherokee lineage, but that account has not been proved.

Trump began going after Warren’s claimed ancestry earlier this year, responding to the senator’s repeated slams of him as a “loser” and a bully. “Who’s that, the Indian?” he said at a March news conference when asked about Warren. “You mean the Indian?”

when passing out political favors is delegated to incompetent staff...,

abcnews |   Newly released State Department emails help reveal how a major Clinton Foundation donor was placed on a sensitive government intelligence advisory board even though he had no obvious experience in the field, a decision that appeared to baffle the department’s professional staff.

The emails further reveal how, after inquiries from ABC News, the Clinton staff sought to “protect the name” of the Secretary, “stall” the ABC News reporter and ultimately accept the resignation of the donor just two days later.

Copies of dozens of internal emails were provided to ABC News by the conservative political group Citizens United, which obtained them under the Freedom of Information Act after more the two years of litigation with the government.

A prolific fundraiser for Democratic candidates and contributor to the Clinton Foundation, who later traveled with Bill Clinton on a trip to Africa, Rajiv K. Fernando’s only known qualification for a seat on the International Security Advisory Board (ISAB) was his technological know-how. The Chicago securities trader, who specialized in electronic investing, sat alongside an august collection of nuclear scientists, former cabinet secretaries and members of Congress to advise Hillary Clinton on the use of tactical nuclear weapons and on other crucial arms control issues.

Friday, June 10, 2016

soul'd-out blonde-haired, blue-eyed devil pocahantas all-in for Granny Goodness

bostonglobe |  “I’m ready,” Warren said in an interview with The Globe. “I’m ready to jump in this fight and make sure that Hillary Clinton is the next president of the United States and be sure that Donald Trump gets nowhere near the White House.”

She added: “I’m supporting Hillary Clinton because she’s a fighter, a fighter with guts.”

Asked whether Clinton should release the transcripts of paid speeches she gave to Goldman Sachs, Warren said: “That’s for her to decide — there will be a whole lot of issues to talk about over the next several months.”

Sanders frequently calls on Clinton to release them.

She praised Sanders, saying that he has run an “incredible campaign.”

Warren, a champion of the left who passed up a presidential bid of her own, despite the urging of legions of followers, is uniquely positioned to serve as a bridge between the establishment candidacy of Clinton and Sanders supporters, who are being forced to come to terms with the Vermont senator’s loss.

Democrats view the freshman Massachusetts senator as a path of sorts to party unity, which helps explain an upsurge in buzz about Warren as a potential vice presidential pick. Senators and top staff say talking up Warren for vice president is a way to show Sanders and his millions of followers that the party establishment heard them loud and clear.

Warren and Clinton haven’t always been close — Warren called out Clinton in her book “The Two Income Trap” for switching her vote on legislation to overhaul bankruptcy laws when Clinton was in the Senate.

“Hillary Clinton could not afford such a principled position. Campaigns cost money, and that money wasn’t coming from families in financial trouble,” Warren wrote in a biting critique of the episode in which Clinton sided with the financial services sector and helped pass an industry-friendly overhaul of the bankruptcy laws.

Warren did not directly address the issue when asked about it Thursday. Instead, Warren told the Globe, “She’s someone who has had to take on a lot, and she’s going to fight back.”

bad fake indians

counterpunch |  JF: I notice you made no mention of public speaking. You used to do quite a lot of it, as I recall. Do you still?

WC: Nowhere near as much as I was doing prior to 2005. That, in part, is because I’ve been administratively blacklisted on campuses nationwide. There’ve been a fair number of instances in which I’ve been lined up by faculty and/or students to deliver a lecture and college or university presidents have directly intervened to prevent the event from happening. In a few cases, the organizers took such abridgments of their own intellectual rights seriously enough to force the issue and staged the events anyway, but usually not. The meekness with which tenured faculty members have typically submitted to administrative dictates in situations like this has been quite enlightening, and speaks volumes to the state of “academic freedom” in the contemporary U.S.

Both politically and psychologically, it’s of course been necessary that the folks I’ve just described, especially those claiming a liberal pedigree, advance some other, more palatable explanation of their behavior and its implications. Most often, this has taken the form of their citing some supposed defect in my scholarship and/or my “abrasive style,” either or both of which were ostensibly pointed out to them after their invitation was extended, causing them to rethink the propriety of offering me a forum in a campus setting imbued with such lofty standards of scholarship and collegiality as their own. In the name of something like “quality control,” then, preserving the “academic integrity” of their institutions leaves them no alternative but to concur—always with the utmost reluctance, of course—and only in this particular instance, mind you—with the administration’s preemption of students’ right to hear and assess whatever I might have to say and customary faculty prerogatives in the bargain.

The upshot is that not only has a decided majority of the liberal professoriate exposed itself as being guilty of the most craven sort of capitulation vis-à-vis the principles they espouse and are purportedly prepared to defend, but the manner in which they’ve sought to rationalize the capitulation has served to lend a completely unwarranted appearance of “left wing” validation to the welter of falsehoods promoted on the right for purposes of discrediting both me, personally, and, more importantly, the kind of work I’ve been doing over the past several decades. All of that nonsense about my having perpetrated “scholarly fraud” and the like has been long since and repeatedly disproven, both in court and elsewhere—that’s a matter of record, easily accessible to anyone who cares to look—but they simply ignore such facts in favor of the convenience embodied in regurgitating the same old lies as a pretext.

None of this is breaking news, of course, or at least it shouldn’t be. It’s how blacklisting has always worked. Which means, among other things, that being blacklisted is in no sense an experience unique to me, either currently or historically. A lot of people have been blacklisted for one reason or another and to a greater or lesser extent over the years, and, as is readily evidenced by the examples of Norman Finkelstein and a number of others, that’s still true. It just happens that among the recent cases, mine has been especially high-profile, and is thus rather useful for illustrative purposes. So I’ve run down this aspect of it mainly to demonstrate to anyone entertaining doubts on the matter that not much has really changed in these respects since, say, 1955.

good fake indians...,

politico |  Elizabeth Warren has pushed back hard on questions about a Harvard Crimson piece in 1996 that described her as Native American, saying she had no idea the school where she taught law was billing her that way and saying it never came up during her hiring a year earlier, which others have backed up.

But a 1997 Fordham Law Review piece described her as Harvard Law School's "first woman of color," based, according to the notes at the bottom of the story, on a "telephone interview with Michael Chmura, News Director, Harvard Law (Aug. 6, 1996)."

The mention was in the middle of a lengthy and heavily-annotated Fordham piece on diversity and affirmative action and women. The title of the piece, by Laura Padilla, was "Intersectionality and positionality: Situating women of color in the affirmative action dialogue."

"There are few women of color who hold important positions in the academy, Fortune 500 companies, or other prominent fields or industries," the piece says. "This is not inconsequential. Diversifying these arenas, in part by adding qualified women of color to their ranks, remains important for many reaons. For one, there are scant women of color as role models. In my three years at Stanford Law School, there were no professors who were women of color. Harvard Law School hired its first woman of color, Elizabeth Warren, in 1995."

Padilla, now at California Western School of Law, told POLITICO in an email that she doesn't remember the details of the conversation with Chmura, who is now at Babson College and didn't respond to a request for comment. It is unclear whether it was Padilla's language or Chmura's.

Thursday, June 09, 2016

corporate media complicity in western imperial crimes against humanity...,

medialens |  One of the essential functions of the corporate media is to marginalise or silence acknowledgement of the history – and continuation – of Western imperial aggression. The coverage of the recent sentencing in Senegal of Hissène Habré, the former dictator of Chad, for crimes against humanity, provides a useful case study.

The verdict could well have presented the opportunity for the media to examine in detail the complicity of the US, UK, France and their major allies in the Middle East and North Africa in the appalling genocide Habré inflicted on Chad during his rule – from 1982 to 1990. After all, Habré had seized power via a CIA-backed coup. As William Blum commented in Rogue State (2002: 152):
'With US support, Habré went on to rule for eight years during which his secret police reportedly killed tens of thousands, tortured as many of 200,000 and disappeared an undetermined number.'
Indeed, while coverage of Chad has been largely missing from the British corporate media, so too was the massive, secret war waged over these eight years by the United States, France and Britain from bases in Chad against Libyan leader Colonel Mu'ammar Gaddafi. (See Targeting Gaddafi: Secret Warfare and the Media, by Richard Lance Keeble, in Mirage in the Desert? Reporting the 'Arab Spring', edited by John Mair and Richard Lance Keeble, Abramis, Bury St Edmunds, 2011, pp 281-296.)

By 1990, with the crisis in the Persian Gulf developing, the French government had tired of Habré's genocidal policies while George Bush senior's administration decided not to frustrate France in exchange for co-operation in its attack on Iraq. And so Habré was secretly toppled and in his place Idriss Déby was installed as the new President of Chad.

Yet the secret Chad coups can only be understood as part of the United States' global imperial strategy. For since 1945, the US has intervened in more than 70 countries – in Africa, Eastern Europe, the Middle East, South America and Asia. Britain, too, has engaged militarily across the globe in virtually every year since 1914. Most of these conflicts are conducted far away from the gaze of the corporate media.

morality, stereotypes, and scientists—the anatomy of science denial

physorg |  Individuals tend to group others based on their perceived morality, often employing stereotypes to describe individuals or groups of people beliveved to have different morals or values. According to Fiske et al., stereotypes are well described using two dimensions: warmth and competence. Warmth (or lack of it) refers to the perceived positive/negative intent of another person, while competence refers to the other person's capacity to achieve their intent. Using this terminology, the ingroup, or the group that you belong to, is both warm and competent, and thus trustworthy. Stereotypes with high perceived competence and low perceived warmth, including stereotypically wealthy individuals, are often not trusted because perceived intent is either unknown or negative. Similarly, scientists have unclear intent due to their perceived amorality, and they are not trusted.

I believe that in order to incur more trust from the public, scientists must cultivate more warmth from the public.

I propose two ways to achieve this goal. First scientists need to make their intentions clear. Social psychologist Todd Pittinsky, mentioned in the introduction, has some terrific ideas on how to clarify intentions. One strategy is open access to data and methods, which is readily achieved through open access publishing. Scientists also need to treat misconduct by other scientists more seriously so that people don't, for example, deem that all vaccine science is fraud due to one case of misconduct. Finally, we need to treat science denial without disdain and acknowledge uncertainty properly when describing scientific results.

Second, scientists need to move into the ingroup sphere by imitating those already in the ingroup. Kahan et al. point out that an individual's established ideology greatly influences how they process new information. I would suggest scientists frame their findings in a way that fits with the audience's ideology, thus promoting "warmth". For example, the Pew report that reveals 37% of the public thinks that GMOs are not safe, which violates the individual foundations. Highlighting how certain crops can be genetically engineered for health (e.g. rice that is genetically engineered to produce beta carotene) shows how GMOs can be compatible with individual foundations. Behaving like an ingroup can then move scientists into the ingroup sphere.

Battling misinformation is definitely an uphill climb, but it is a climb scientists must endeavor to make. Climate change denial and the anti-vaccination movement threatens the future of scientific progress, and while the danger cannot be ignored, we should not belittle non-scientific ideas. Scientists can build goodwill through increased transparency and communicating the significance of their findings to the public. By taking other worldviews into account, we can find common ground and create open dialogue and perhaps find solutions to benefit everyone.

Wednesday, June 08, 2016

Hillary Clinton Talks About Inequality In Jacket That Cost More Than A New Car

theantimedia |  As someone who wants to give the appearance of knowing the hardships of common people, Hillary loves to bring up the topic of income inequality. In April, while giving a victory speech for her win in the New York primary, Hillary brought up that very subject — and then attempted to boast about her support among average Americans.

“I know how important it is that we get the campaign’s resources from people just like you, who go in and chip in $5, $25.  I am grateful to every one of you.

And she said every word of it while wearing a Giorgio Armani tweed jacket that cost a hefty $12,495.

At least lie to me Hillary — don’t pretend to be a champion against inequality while wearing an article of clothing that literally costs more than a new car. You lie about everything else, so rather than flouting your riches while championing the poor (and letting your riches show through the cracks), you might as well put on a cheap suit and give this ‘populist’ deception the effort you give your other ones.

Perfect End to Granny Goodness' Imperious Primary Fraud

theintercept |  Last night, the Associated Press — on a day when nobody voted — surprised everyone by abruptly declaring the Democratic Party primary over and Hillary Clinton the victor. The decree, issued the night before the California primary in which polls show Clinton and Bernie Sanders in a very close race, was based on the media organization’s survey of “superdelegates”: the Democratic Party’s 720 insiders, corporate donors, and officials whose votes for the presidential nominee count the same as the actually elected delegates. AP claims that superdelegates who had not previously announced their intentions privately told AP reporters that they intend to vote for Clinton, bringing her over the threshold. AP is concealing the identity of the decisive superdelegates who said this.

Although the Sanders campaign rejected the validity of AP’s declaration — on the ground that the superdelegates do not vote until the convention and he intends to try to persuade them to vote for him — most major media outlets followed the projection and declared Clinton the winner.

This is the perfect symbolic ending to the Democratic Party primary: The nomination is consecrated by a media organization, on a day when nobody voted, based on secret discussions with anonymous establishment insiders and donors whose identities the media organization — incredibly — conceals. The decisive edifice of superdelegates is itself anti-democratic and inherently corrupt: designed to prevent actual voters from making choices that the party establishment dislikes. But for a party run by insiders and funded by corporate interests, it’s only fitting that its nomination process ends with such an ignominious, awkward, and undemocratic sputter.

N.Y. Governor and Democrat Establishment Attack Free Speech to Protect Israel

theintercept |  One of the greatest free speech threats in the West is the growing, multi-nation campaign literally to outlaw advocacy of boycotting Israel. People get arrested in Paris — the site of the 2015 “free speech” (for Muslim critics) rally — for wearing pro-boycott T-shirts. Pro-boycott students on U.S. campuses — where the 1980s boycott of apartheid South Africa flourished — are routinely sanctioned for violating anti-discrimination policies. Canadian officials have threatened to criminally prosecute boycott advocates. British government bodies have legally barred certain types of boycott advocacy. Israel itself has outright criminalized advocacy of such boycotts. Notably, all of this has been undertaken with barely a peep from those who styled themselves free speech crusaders when it came time to defend anti-Muslim cartoons.

But now, New York’s Democratic Gov. Andrew Cuomo (above, in the 2016 Celebrate Israel Parade) has significantly escalated this free speech attack on U.S. soil, aimed at U.S. citizens. The prince of the New York political dynasty yesterday issued an executive order directing all agencies under his control to terminate any and all business with companies or organizations that support a boycott of Israel. It ensures that citizens who hold and express a particular view are punished through the denial of benefits that other citizens enjoy: a classic free speech violation (imagine if Cuomo issued an order stating that “anyone who expresses conservative viewpoints shall have all state benefits immediately terminated”).

Even more disturbing, Cuomo’s executive order requires that one of his commissioners compile “a list of institutions and companies” that — “either directly or through a parent or subsidiary” — support a boycott. That government list is then posted publicly, and the burden falls on them to prove to the state that they do not, in fact, support such a boycott. Donna Lieberman, executive director of the New York Civil Liberties Union, told The Intercept: “Whenever the government creates a blacklist based on political views it raises serious First Amendment concerns and this is no exception.” Reason’s Robby Soave denounced it today as “brazenly autocratic.”

To read the relevant provisions of Cuomo’s order is to confront the mentality of petty censoring tyranny, flavored with McCarthyite public shaming, in its purest form.

H.R.5181 Seeks to Establish an American Ministry of Truth

theantimedia |  In the true Orwellian fashion now typifying 2016, a bill to implement the U.S.’ very own de facto Ministry of Truth has been quietly introduced in Congress — its lack of fanfare appropriate given the bill’s equally subtle language. As with any legislation attempting to dodge the public spotlight, however, the Countering Foreign Propaganda and Disinformation Act of 2016 marks a further curtailment of press freedom and another avenue to stultify avenues of accurate information.
Introduced by Congressmen Adam Kinzinger and Ted Lieu, H.R. 5181 seeks a “whole-government approach without the bureaucratic restrictions” to counter “foreign disinformation and manipulation,” which they believe threaten the world’s “security and stability.”

“As Russia continues to spew its disinformation and false narratives, they undermine the United States and its interests in places like Ukraine, while also breeding further instability in these countries,” Kinzinger explained in a statement. “The United States has a role in countering these destabilizing acts of propaganda, which is why I’m proud to introduce [the aforementioned bill]. This important legislation develops a comprehensive U.S. strategy to counter disinformation campaigns through interagency cooperation and on-the-ground partnerships with outside organizations that have experience in countering foreign propaganda.”

Make no mistake — this legislation isn’t proposing some team of noble fact-finders, chiseling away to free the truth from the façades of various foreign governmental narratives for the betterment of American and allied populations. If passed, this legislation will allow cumbrously pro-‘American’ propaganda to infiltrate cable, online, and mainstream news organizations wherever the government deems necessary.

“From Ukraine to the South China Sea, foreign disinformation campaigns do more than spread anti-Western sentiments — they manipulate public perception to change the facts on the ground, subvert democracy and undermine U.S. interests,” Lieu explained. “In short, they make the world less safe.”

H.R. 5181 tasks the Secretary of State with coordinating the Secretary of Defense, the Director of National Intelligence, and the Broadcasting Board of Governors to “establish a Center for Information Analysis and Response,” which will pinpoint sources of disinformation, analyze data, and — in true dystopic manner — ‘develop and disseminate’ “fact-based narratives” to counter effrontery propaganda.

Tuesday, June 07, 2016

quantum criticality at the origin of life

arvix |  Why life persists at the edge of chaos is a question at the very heart of evolution. Here we show that molecules taking part in biochemical processes from small molecules to proteins are critical quantum mechanically. Electronic Hamiltonians of biomolecules are tuned exactly to the critical point of the metal-insulator transition separating the Anderson localized insulator phase from the conducting disordered metal phase. Using tools from Random Matrix Theory we confirm that the energy level statistics of these biomolecules show the universal transitional distribution of the metal-insulator critical point and the wave functions are multifractals in accordance with the theory of Anderson transitions. The findings point to the existence of a universal mechanism of charge transport in living matter. The revealed bio-conductor material is neither a metal nor an insulator but a new quantum critical material which can exist only in highly evolved systems and has unique material properties.

physorg |  Stuart Kauffman, from the University of Calgary, and several of his colleagues have recently published a paper on the Arxiv server titled 'Quantum Criticality at the Origins of Life'. The idea of a quantum criticality, and more generally quantum critical states, comes perhaps not surprisingly, from solid state physics. It describes unusual electronic states that are are balanced somewhere between conduction and insulation. More specifically, under certain conditions, current flow at the critical point becomes unpredictable. When it does flow, it tends to do so in avalanches that vary by several orders of magnitude in size.

In suggesting that biomolecules, or at least most of them, are quantum critical conductors, Kauffman and his group are claiming that their electronic properties are precisely tuned to the transition point between a metal and an insulator. An even stronger reading of this would have that there is a universal mechanism of charge transport in living matter which can exist only in highly evolved systems. To back all this up the group took a closer look at the electronic structure of a few of our standard issue proteins like myoglobin, profilin, and apolipoprotein E.

Monday, June 06, 2016

pseudoscience or a new kind of science?

theatlantic |   If his mushrooms could grow tailor-made weapons against any other types of fungi, would it be possible for them to do the same against any type of bacteria, too?

The rise of drug-resistant bacteria is sobering. Just last week, colistin-resistant E. coli––a “superbug” resistant to the antibiotic that’s considered the last resort for combatting particularly dangerous types of infections––landed in the U.S. Soon, public health officials anticipate, infections will be harder to stop; 10 million people could die of drug-resistant superbugs

It may be a long shot, but it’s conceivable that Cotter's process offers a new kind of hope. While scientists have been working on the problem of antibiotic resistance for many years—some are looking to harness the human immune system to better fight it; others are working on simply detecting the superbugs faster—his vision is to beat superbugs with medicine that actually adapts to destroy them. It’s not pharmaceuticals he has in mind; he's not planning to mass produce many different types of secondary metabolites. Rather, he believes it’s his unique style of co-culturing itself––the process of culturing two different microbes together to produce a defense entirely specific to the attacker––that may be able to create custom antibiotics that, at least in theory, could be inherently less susceptible to resistance.

His goal, in other words, is to grow mushrooms that are themselves medicine, because they could create whatever metabolites a sick person needs.

"The best situation I could describe is something everyone has gone through, like a strep throat culture,” Cotter says, imagining a scenario in which an infected patient walks into the doctor’s office, gets a throat swab, and then has the swab dropped into a specially designed module containing a fungus. That fungus would then sweat metabolites into a reservoir that would be naturally calibrated to combat the patient’s illness.

Cotter doesn’t know how the metabolites would be administered yet. A lollipop or throat spray for strep? Delivered topically for staph? His testing is still thoroughly ongoing. Should he receive the NIH grant he's applying for––a grant backed by a $1.2 billion White House Initiative to stop resistant diseases––answers could arrive rapidly. Analytical labs would go up, animal testing would begin, streptococcus lollipopus before we know it.

Sunday, June 05, 2016

the rise of artificial intelligence and the end of code

wired |  Artificial intelligence wasn’t supposed to work this way. Until a few years ago, mainstream AI researchers assumed that to create intelligence, we just had to imbue a machine with the right logic. Write enough rules and eventually we’d create a system sophisticated enough to understand the world. They largely ignored, even vilified, early proponents of machine learning, who argued in favor of plying machines with data until they reached their own conclusions. For years computers weren’t powerful enough to really prove the merits of either approach, so the argument became a philosophical one. “Most of these debates were based on fixed beliefs about how the world had to be organized and how the brain worked,” says Sebastian Thrun, the former Stanford AI professor who created Google’s self-driving car. “Neural nets had no symbols or rules, just numbers. That alienated a lot of people.”

The implications of an unparsable machine language aren’t just philosophical. For the past two decades, learning to code has been one of the surest routes to reliable employment—a fact not lost on all those parents enrolling their kids in after-school code academies. But a world run by neurally networked deep-learning machines requires a different workforce. Analysts have already started worrying about the impact of AI on the job market, as machines render old skills irrelevant. Programmers might soon get a taste of what that feels like themselves.

Of course, humans still have to train these systems. But for now, at least, that’s a rarefied skill. The job requires both a high-level grasp of mathematics and an intuition for pedagogical give-and-take. “It’s almost like an art form to get the best out of these systems,” says Demis Hassabis, who leads Google’s DeepMind AI team. “There’s only a few hundred people in the world that can do that really well.” But even that tiny number has been enough to transform the tech industry in just a couple of years.

These forces have led technologist Danny Hillis to declare the end of the age of Enlightenment, our centuries-long faith in logic, determinism, and control over nature. Hillis says we’re shifting to what he calls the age of Entanglement. “As our technological and institutional creations have become more complex, our relationship to them has changed,” he wrote in the Journal of Design and Science. “Instead of being masters of our creations, we have learned to bargain with them, cajoling and guiding them in the general direction of our goals. We have built our own jungle, and it has a life of its own.” The rise of machine learning is the latest—and perhaps the last—step in this journey.

NASA, Jesus, and Templeton...,

HuffPo |  More of NASA’s astrobiology strategy for the next decade can be found in its latest roadmap: Astrobiology Strategy 2015. Lindsay Hays of California Institute of Technology’s Jet Propulsion Laboratory is editor-in-chief. 

Microbes are given some attention in a section titled: “How Does Our Ignorance About Microbial Life on Earth Hinder Our Understanding of the Limits to Life?” Curiously, however, there’s not a word in the entire 256-page document (including the glossary) about the existence of viruses — the biggest part of the biosphere — let alone their consortial and persistent nature, when the new thinking in science is “virus first“ and that persistence may be just as crucial to life as replication.
Templeton last year also awarded $5.4 M for origin of life investigations to the Foundation for Applied Molecular Evolution, with funds being administered by FAME synthetic biologist Steve Benner (who once quipped, “If you don’t have a theory of life, you can’t find aliens — unless they shoot you in the leg with a ray gun.”) AND $5.6M to ELSI — the Japanese government’s earth science institute in Tokyo - for its ELSI Origins Network, headed by astrophysicist Piet Hut also of the Institute for Advanced Study in Princeton.
Steve Benner is listed as a reviewer on NASA’s latest roadmap and is on the editorial board of Astrobiology Journal whose senior editors include NAI’s new chief Penny Boston as well as ISSOL (International Society for the Study of Origin of Life) president Dave Deamer.

Astrobiology Journal is put together in the Kennewick, Washington home of Sherry Cady, a geologist who serves as editor in chief, and her husband Lawrence P. Cady, a fiction writer who serves as the journal’s managing editor and copy editor — according to LP Cady. The magazine is one of 80 of Mary Ann Liebert Inc.’s “authoritative” journals and has close ties to other NASA-funded scientists who serve as reviewers.
If anything substantive is likely to happen as a result of (or in spite of) Templeton funding on origin of life, I would expect it to come from Steve Benner’s project, which includes people like George E. Fox who collaborated early on with Carl Woese on Archaea, and Harry Lonsdale origin of life research funds recipient, Niles Lehman — plus Benner himself and eight others.
On the other hand, I have serious reservations about the NASA award of $1.1M of public funds to CTI. What ever happened to the separation of church and state?

Saturday, June 04, 2016

little things mean everything...,

thescientist |  Little things mean a lot. To any biologist, this time-worn maxim is old news. But it’s worth revisiting. As several articles in this issue of The Scientist illustrate, how researchers define and examine the “little things” does mean a lot.

Consider this month’s cover story, “Noncoding RNAs Not So Noncoding,” by TS correspondent Ruth Williams. Combing the human genome for open reading frames (ORFs), sequences bracketed by start and stop codons, yielded a protein-coding count somewhere in the neighborhood of 24,000. That left a lot of the genome relegated to the category of junk—or, later, to the tens of thousands of mostly mysterious long noncoding RNAs (lncRNAs). But because they had only been looking for ORFs that were 300 nucleotides or longer (i.e., coding for proteins at least 100 amino acids long), genome probers missed so-called short ORFs (sORFs), which encode small peptides. “Their diminutive size may have caused these peptides to be overlooked, their sORFs to be buried in statistical noise, and their RNAs to be miscategorized, but it does not prevent them from serving important, often essential functions, as the micropeptides characterized to date demonstrate,” writes Williams.

How little things work definitely informs another field of life science research: synthetic biology. As the functions of genes and gene networks are sussed out, bioengineers are using the information to design small, synthetic gene circuits that enable them to better understand natural networks. In “Synthetic Biology Comes into Its Own,” Richard Muscat summarizes the strides made by synthetic biologists over the last 15 years and offers an optimistic view of how such networks may be put to use in the future. And to prove him right, just as we go to press, a collaborative group led by one of syn bio’s founding fathers, MIT’s James Collins, has devised a paper-based test for Zika virus exposure that relies on a freeze-dried synthetic gene circuit that changes color upon detection of RNAs in the viral genome. The results are ready in a matter of hours, not the days or weeks current testing takes, and the test can distinguish Zika from dengue virus. “What’s really exciting here is you can leverage all this expertise that synthetic biologists are gaining in constructing genetic networks and use it in a real-world application that is important and can potentially transform how we do diagnostics,” commented one researcher about the test.

RNA-Targetting CRISPR

thescientist |  Much attention paid to the bacterial CRISPR/Cas9 system has focused on its uses as a gene-editing tool. But there are other CRISPR/Cas sytems. Researchers from MIT and the National Center for Biotechnology Information (NCBI) last year identified additional CRISPR proteins. One of these proteins, C2c2, seemed to be a putative RNA-cleaving—rather than a DNA-targeting—enzyme, the researchers reported at the time. Now, the same group has established that C2c2 indeed cleaves single-stranded RNA (ssRNA), providing the first example of a CRISPR/Cas system that exclusively targets RNA. The team’s latest results, published today (June 2) in Science, confirm the diversity of CRISPR systems and point to the possibility of precise in vivo RNA editing.

“This protein does what we expected, performing RNA-guided cleavage of cognate RNA with high specificity, and can be programmed to cleave any RNA at will,” study coauthor Eugene Koonin, of the NCBI and the National Library of Medicine, told The Scientist.

“I am very excited about the paper,” said Gene Yeo, an RNA researcher at the University of California, San Diego, who was not involved in the work. “The community was expecting to find native RNA CRISPR systems, so it’s great that one of these has now been characterized.”

non-coding rna not so non-coding...,

thescientist |  In 2002, a group of plant researchers studying legumes at the Max Planck Institute for Plant Breeding Research in Cologne, Germany, discovered that a 679-nucleotide RNA believed to function in a noncoding capacity was in fact a protein-coding messenger RNA (mRNA).1 It had been classified as a long (or large) noncoding RNA (lncRNA) by virtue of being more than 200 nucleotides in length. The RNA, transcribed from a gene called early nodulin 40 (ENOD40), contained short open reading frames (ORFs)—putative protein-coding sequences bookended by start and stop codons—but the ORFs were so short that they had previously been overlooked. When the Cologne collaborators examined the RNA more closely, however, they found that two of the ORFs did indeed encode tiny peptides: one of 12 and one of 24 amino acids. Sampling the legumes confirmed that these micropeptides were made in the plant, where they interacted with a sucrose-synthesizing enzyme.

Five years later, another ORF-containing mRNA that had been posing as a lncRNA was discovered in Drosophila.2,3 After performing a screen of fly embryos to find lncRNAs, Yuji Kageyama, then of the National Institute for Basic Biology in Okazaki, Japan, suppressed each transcript’s expression. “Only one showed a clear phenotype,” says Kageyama, now at Kobe University. Because embryos missing this particular RNA lacked certain cuticle features, giving them the appearance of smooth rice grains, the researchers named the RNA “polished rice” (pri).

Turning his attention to how the RNA functioned, Kageyama thought he should first rule out the possibility that it encoded proteins. But he couldn’t. “We actually found it was a protein-coding gene,” he says. “It was an accident—we are RNA people!” The pri gene turned out to encode four tiny peptides—three of 11 amino acids and one of 32—that Kageyama and colleagues showed are important for activating a key developmental transcription factor.4

Since then, a handful of other lncRNAs have switched to the mRNA ranks after being found to harbor micropeptide-encoding short ORFs (sORFs)—those less than 300 nucleotides in length. And given the vast number of documented lncRNAs—most of which have no known function—the chance of finding others that contain micropeptide codes seems high.

The hunt for these tiny treasures is now on, but it’s a challenging quest. After all, there are good reasons why these itty-bitty peptides and their codes went unnoticed for so long.

Friday, June 03, 2016

The Genome Project - Write

NYTimes |  “By focusing on building the 3Gb of human DNA, HGP-write would push current conceptual and technical limits by orders of magnitude and deliver important scientific advances,” they write, referring to three gigabases, the three billion letters in the human genome.

Scientists already can change DNA in organisms or add foreign genes, as is done to make medicines like insulin or genetically modified crops. New “genome editing” tools, like one called Crispr, are making it far easier to re-engineer an organism’s DNA blueprint.

But George Church, a professor of genetics at Harvard Medical School and one of the organizers of the new project, said that if the changes desired are extensive, at some point it becomes easier to synthesize the needed DNA from scratch.

“Editing doesn’t scale very well,” he said. “When you have to make changes to every gene in the genome it may be more efficient to do it in large chunks.”

Besides Dr. Church, the other organizers of the project are Jef Boeke, director of the Institute for Systems Genetics at NYU Langone Medical Center; Andrew Hessel, a futurist at the software company Autodesk; and Nancy J. Kelley, who works raising money for projects. The paper in Science lists a total of 25 authors, many of them involved in DNA engineering.

Autodesk, which has given $250,000 to the project, is interested in selling software to help biologists design DNA sequences to make organisms perform particular functions. Dr. Church is a founder of Gen9, a company that sells made-to-order strands of DNA.

Dr. Boeke of N.Y.U. is leading an international project to synthesize the complete genome of yeast, which has 12 million base pairs. It would be the largest genome synthesized to date, though still much smaller than the human genome.

Is Everything You Think You Know About AI Wrong?

WaPo |  consumers are already seeing our machine learning research reflected in the sudden explosion of digital personal assistants like Siri, Alexa and Google Now — technologies that are very good at interpreting voice-based requests but aren't capable of much more than that. These "narrow AI" have been designed with a specific purpose in mind: To help people do the things regular people do, whether it's looking up the weather or sending a text message.

Narrow, specialized AI is also what companies like IBM have been pursuing. It includes, for example, algorithms to help radiologists pick out tumors much more accurately by "learning" all the cancer research we've ever done and by "seeing" millions of sample X-rays and MRIs. These robots act much more like glorified calculators — they can ingest way more data than a single person could hope to do with his or her own brain, but they still operate within the confines of a specific task like cancer diagnosis. These robots are not going to be launching nuclear missiles anytime soon. They wouldn't know how, or why. And the more pervasive this type of AI becomes, the more we'll understand about how best to build the next generation of robots.

So who is going to lose their job?
Partly because we're better at designing these limited AI systems, some experts predict that high-skilled workers will adapt to the technology as a tool, while lower-skill jobs are the ones that will see the most disruption. When the Obama administration studied the issue, it found that as many as 80 percent of jobs currently paying less than $20 an hour might someday be replaced by AI.

"That's over a long period of time, and it's not like you're going to lose 80 percent of jobs and not reemploy those people," Jason Furman, a senior economic advisor to President Obama, said in an interview. "But [even] if you lose 80 percent of jobs and reemploy 90 percent or 95 percent of those people, it's still a big jump up in the structural number not working. So I think it poses a real distributional challenge."

Policymakers will need to come up with inventive ways to meet this looming jobs problem. But the same estimates also hint at a way out: Higher-earning jobs stand to be less negatively affected by automation. Compared to the low-wage jobs, roughly a third of those who earn between $20 and $40 an hour are expected to fall out of work due to robots, according to Furman. And only a sliver of high-paying jobs, about 5 percent, may be subject to robot replacement.

Those numbers might look very different if researchers were truly on the brink of creating sentient AI that can really do all the same things a human can. In this hypothetical scenario, even high-skilled workers might have more reason to fear. But the fact that so much of our AI research right now appears to favor narrow forms of artificial intelligence at least suggests we could be doing a lot worse.

Thursday, June 02, 2016


genes: convenient tokens of our time

ecodevoevo |  Our culture, like any culture, creates symbols to use as tokens as we go about our lives. Tokens are reassuring or explanatory symbols, and we naturally use them in the manipulations for various resources that culture is often about.  Nowadays, a central token is the gene.

Genes are proffered as the irrefutable ubiquitous cause of things, the salvation, the explanation, in ways rather similar to the way God and miracles are proffered by religion.  Genes conveniently lead to manipulation by technology, and technology sells in our industrial culture. Genes are specific rather than vague, are enumerable, can be seen as real core 'data' to explain the world.  Genes are widely used as ultimate blameworthy causes, responsible for disease which comes to be defined as what happens when genes go 'wrong'.  Being literally unseen, like angels, genes can take on an aura of pervasive power and mystery.  The incantation by scientists is that if we can only be enabled to find them we can even cure them (with CRISPR or some other promised panacea), exorcising their evil. All of this invocation of fundamental causal tokens is particulate enough to be marketable for grants and research proposals, great for publishing in journals and for news media to gawk at in wonder. Genes provide impressively mysterious tokens for scientists to promise almost to create miracles by manipulating.  Genes stand for life's Book of Truth, much as sacred texts have traditionally done and, for many, still do.

Genes provide fundamental symbolic tokens in theories of life--its essence, its evolution, of human behavior, of good and evil traits, of atoms of causation from which everything follows. They lurk in the background, responsible for all good and evil.  So in our age in human history, it is not surprising that reports of finding genes 'for' this or that have unbelievable explanatory panache.  It's not a trivial aspect of this symbolic role that people (including scientists) have to take others' word for what they claim as insights. 

genes without prominence...,

inference-review |  The cell is a complex dynamic system in which macromolecules such as DNA and the various proteins interact within a free energy flux provided by nutrients. Its phenotypes can be represented by quasi-stable attractors embedded in a multi-dimensional state space whose dimensions are defined by the activities of the cell’s constituent proteins.1
This is the basis for the dynamical model of the cell.

The current molecular genetic or machine model of the cell, on the other hand, is predicated on the work of Gregor Mendel and Charles Darwin. Mendel framed the laws of inheritance on the basis of his experimental work on pea plants. The first law states that inheritance is a discrete and not a blending process: crossing purple and white flowered varieties produces some offspring with white and some with purple flowers, but generally not intermediately colored offspring.2 Mendel concluded that whatever was inherited had a material or particulate nature; it could be segregated.3

According to the machine cell model, those particles are genes or sequences of nucleobases in the genomic DNA. They constitute Mendel’s units of inheritance. Gene sequences are transcribed, via messenger RNA, to proteins, which are folded linear strings of amino acids called peptides. The interactions between proteins are responsible for phenotypic traits. This assumption relies on two general principles affirmed by Francis Crick in 1958, namely the sequence hypothesis and the central dogma.4 The sequence hypothesis asserts that the sequence of bases in the genomic DNA determines the sequence of amino acids in the peptide and the three-dimensional structure of the folded peptide. The central dogma states that the sequence hypothesis represents a flow of information from DNA to the proteins and rules out a flow in reverse.

In 1961, the American biologist Christian Anfinsen demonstrated that when the enzyme ribonuclease was denatured, it lost its activity, but regained it on re-naturing. Anfinsen concluded from the kinetics of re-naturation that the amino acid sequence of the peptide determined how the peptide folded.5 He did not cite Crick’s 1958 paper or the sequence hypothesis, although he had apparently read the first and confirmed the second.

The central dogma and the sequence hypothesis proved to be wonderful heuristic tools with which to conduct bench work in molecular biology.

The machine model recognizes cells to be highly regulated entities; genes are responsible for that regulation through gene regulatory networks (GRNs).6 Gene sequences provide all the information needed to build and regulate the cell.

Both a naturalist and an experimentalist, Darwin observed that breeding populations exhibit natural variations. Limited resources mean a struggle for existence. Individuals become better and better adapted to their environments. This process is responsible for both small adaptive improvements and dramatic changes. Darwin insisted evolution was, in both cases, gradual, and predicted that intermediate forms between species should be found both in the fossil record and in existing populations. Today, these ideas are part of the modern evolutionary synthesis, a term coined by Julian Huxley in 1942.7 Like the central dogma, it has been subject to controversy, despite its early designation as the set of principles under which all of biology is conducted.8

The modern synthesis, we now understand, does not explain trans-generational epigenetic inheritance, consciousness, and niche construction.9 It is possible that the concept of the gene and the claim that evolution depends on genetic diversity may both need to be modified or replaced.

This essay is a step towards describing biology as a science founded on the laws of physics. It is a step in the right direction.

Wednesday, June 01, 2016

the constructal law in intelligence?

Stuart Kauffman's 1993 book, Origins of Order, is a technical treatise on his life's work in Mathematical Biology. Kauffman greatly extends Alan Turing 's early work in Mathematical Biology. The intended audience is other mathematical and theoretical biologists. It's chock full of advanced mathematics. Of particular note, Origins of Order seems to be Kauffman's only published work in which he states his experimental results about the interconnection between complex systems and neural networks.

Kauffman explains that a complex system tuned with particular parameters is a neural network.  I can not overstate the importance of the last sentence in the paragraph above. The implication is that one basis for intelligence, biological neural networks, can spontaneously self-generate given the correct starting parameters. Kauffman provides the mathematics to do this, discusses his experimental results, and points out that the parameters in question are an attractor state.

What's the meaning of life? Physics.

nationalgeographic |  According to your book, physics describes the actions or tendencies of every living thing—and inanimate ones as well. Does that mean we can unite all behavior under physics?

Absolutely. Our narrow definition of the discipline is something that’s happened in the past hundred years, thanks to the immense impact of Albert Einstein and atomic physics and relativity at the turn of the [20th] century.

But we need to go back farther. In Latin, nature—physics—means “everything that happens.”

One thing that came directly from Charles Darwin is that humans are part of nature, along with all the other animate beings. Therefore all the things that we make—our tools, our homes, our technologies—are natural as well. It’s all part of the same thing.

In your magazine and on your TV channel, we see many animals doing this—extending their reach with tools, with intelligence, with social organization. Everything is naturally interconnected.

Your new book is premised on a law of physics that you formulated in 1996. The Constructal Law says there’s a universal evolutionary tendency toward design in nature, because everything is composed of systems that change and evolve to flow more easily. That’s correct. But I would specify and say that the tendency is toward evolving freely—changing on the go in order to provide greater and greater ease of movement. That’s physics, stage four—more precise, more specific expressions of the same idea.

Flow systems are everywhere. They describe the ways that animals move and migrate, the ways that river deltas form, the ways that people build fires. In each case, they evolve freely to reduce friction and to flow better—to improve themselves and minimize their mistakes or imperfections. Blood flow and water flow essentially evolve the same way.

Why does life exist?

quantamagazine |  Popular hypotheses credit a primordial soup, a bolt of lightning and a colossal stroke of luck. But if a provocative new theory is correct, luck may have little to do with it. Instead, according to the physicist proposing the idea, the origin and subsequent evolution of life follow from the fundamental laws of nature and “should be as unsurprising as rocks rolling downhill.”

From the standpoint of physics, there is one essential difference between living things and inanimate clumps of carbon atoms: The former tend to be much better at capturing energy from their environment and dissipating that energy as heat. Jeremy England, a 31-year-old assistant professor at the Massachusetts Institute of Technology, has derived a mathematical formula that he believes explains this capacity. The formula, based on established physics, indicates that when a group of atoms is driven by an external source of energy (like the sun or chemical fuel) and surrounded by a heat bath (like the ocean or atmosphere), it will often gradually restructure itself in order to dissipate increasingly more energy. This could mean that under certain conditions, matter inexorably acquires the key physical attribute associated with life.

“You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant,” England said.

England’s theory is meant to underlie, rather than replace, Darwin’s theory of evolution by natural selection, which provides a powerful description of life at the level of genes and populations. “I am certainly not saying that Darwinian ideas are wrong,” he explained. “On the contrary, I am just saying that from the perspective of the physics, you might call Darwinian evolution a special case of a more general phenomenon.”

His idea, detailed in a recent paper and further elaborated in a talk he is delivering at universities around the world, has sparked controversy among his colleagues, who see it as either tenuous or a potential breakthrough, or both.

England has taken “a very brave and very important step,” said Alexander Grosberg, a professor of physics at New York University who has followed England’s work since its early stages. The “big hope” is that he has identified the underlying physical principle driving the origin and evolution of life, Grosberg said.

“Jeremy is just about the brightest young scientist I ever came across,” said Attila Szabo, a biophysicist in the Laboratory of Chemical Physics at the National Institutes of Health who corresponded with England about his theory after meeting him at a conference. “I was struck by the originality of the ideas.”