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Archive for November 20th, 2015

The Information Theory of Life

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Kevin Hartnett reports in Quanta:

There are few bigger — or harder — questions to tackle in science than the question of how life arose. We weren’t around when it happened, of course, and apart from the fact that life exists, there’s no evidence to suggest that life can come from anything besides prior life. Which presents a quandary.

Christoph Adami does not know how life got started, but he knows a lot of other things. His main expertise is in information theory, a branch of applied mathematics developed in the 1940s for understanding information transmissions over a wire. Since then, the field has found wide application, and few researchers have done more in that regard than Adami, who is a professor of physics and astronomy and also microbiology and molecular genetics at Michigan State University. He takes the analytical perspective provided by information theory and transplants it into a great range of disciplines, including microbiology, genetics, physics, astronomy and neuroscience. Lately, he’s been using it to pry open a statistical window onto the circumstances that might have existed at the moment life first clicked into place.

To do this, he begins with a mental leap: Life, he argues, should not be thought of as a chemical event. Instead, it should be thought of as information. The shift in perspective provides a tidy way in which to begin tackling a messy question. In the following interview, Adami defines information as “the ability to make predictions with a likelihood better than chance,” and he says we should think of the human genome — or the genome of any organism — as a repository of information about the world gathered in small bits over time through the process of evolution. The repository includes information on everything we could possibly need to know, such as how to convert sugar into energy, how to evade a predator on the savannah, and, most critically for evolution, how to reproduce or self-replicate.

This reconceptualization doesn’t by itself resolve the issue of how life got started, but it does provide a framework in which we can start to calculate the odds of life developing in the first place. Adami explains that a precondition for information is the existence of an alphabet, a set of pieces that, when assembled in the right order, expresses something meaningful. No one knows what that alphabet was at the time that inanimate molecules coupled up to produce the first bits of information. Using information theory, though, Adami tries to help chemists think about the distribution of molecules that would have had to be present at the beginning in order to make it even statistically plausible for life to arise by chance.

Quanta Magazine spoke with Adami about what information theory has to say about the origins of life. An edited and condensed version of the interview follows.

QUANTA MAGAZINE: How does the concept of information help us understand how life works?

CHRISTOPH ADAMI: Information is the currency of life. One definition of information is the ability to make predictions with a likelihood better than chance. That’s what any living organism needs to be able to do, because if you can do that, you’re surviving at a higher rate. [Lower organisms] make predictions that there’s carbon, water and sugar. Higher organisms make predictions about, for example, whether an organism is after you and you want to escape. Our DNA is an encyclopedia about the world we live in and how to survive in it.

Think of evolution as a process where information is flowing from the environment into the genome. The genome learns more about the environment, and with this information, the genome can make predictions about the state of the environment.

If the genome is a reflection of the world, doesn’t that make the information context specific?

Information in a sequence needs to be interpreted in its environment. Your DNA means nothing on Mars or underwater because underwater is not where you live. A sequence is information in context. A virus’s sequence in its context — its host — has enough information to replicate because it can take advantage of its environment.

What happens when the environment changes?

The first thing that happens is that stuff that was information about the environment isn’t information anymore. Cataclysmic change means the amount of information you have about the environment may have dropped. And because information is the currency of life, suddenly you’re not so fit anymore. That’s what happened with dinosaurs.

Once you start thinking about life as information, how does it change the way you think about the conditions under which life might have arisen? . . .

Continue reading.

Written by Leisureguy

20 November 2015 at 3:43 pm

Posted in Evolution, Math, Science

The FBI’s forensic “science” has put many innocent people in prison for decades

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Donald Gates, for example, whose 27 years in prison even though he was “stone-cold innocent” of the rape and murder of which he was accused—and of course the actual perpetrator was not caught (at least not for those crimes). You can read about it in this column by Radley Balko, in which Balko points out:

The case is as good an illustration as any that most fields of forensic “science” weren’t developed to find the truth but to aid police and prosecutors in convicting the person they already believe committed the crime. They aren’t neutral methods of analysis; they’re tools for the state. That doesn’t mean some fields don’t have some evidentiary value (though hair fiber analysis has very little). It just means that those that have some value should be considered and presented to juries for what they are. Too often, they’re presented as magical guilt/innocence divining rods.

There was also an informer who, return for $1,300, provided testimony to implicate the accused. Balko quotes from a report by Spencer Hsu, who notes:

Although it was not part of this month’s trial, Gates’s innocence triggered investigations that led to exonerations of four additional men in the District who had served up to 30 years for rape or murder since the 1980s based on flawed FBI forensic testimony about hairs.

The FBI in April acknowledged that for more than 20 years before 2000, nearly every member of an elite FBI forensic unit overreached by testifying to the near-certainty of hair matches without a scientific basis. Defendants are now being notified.

Written by Leisureguy

20 November 2015 at 2:57 pm

Misuse Rampant, Oversight Lacking at California’s Law Enforcement Network

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Giving law enforcement agencies (federal, state, county, or municipal)  unusual powers has a downside, well documented in Radley Balko’s column The Watch in the Washington Post. Dave Maass of the Electronic Frontier Foundation has a report at how California law enforcement has misused their law enforcement network:

Confirmed cases of misuse of California’s sprawling unified law enforcement information network have doubled over the last five years, according to records obtained by EFF under the California Public Records Act.

That adds up to a total 389 cases in which an investigation concluded that a user—often a peace officer—broke the rules for accessing the California Law Enforcement Telecommunications System (CLETS), such as searching criminal records to vet potential dates or spy on former spouses. More than 20 incidents since 2010 have resulted in criminal charges.


Unfortunately, those figures are only what was self-reported by government agencies to the California Attorney General. The actual number of misuse cases of CLETS are likely substantially higher since the California Attorney General’s Department of Justice (CADOJ) has let many agencies slide on their annual misuse disclosures. Among the delinquent are two of California’s largest law enforcement agencies: the Los Angeles Police Department (LAPD) and the Los Angeles County Sheriff’s Department.

What’s worse is the government body charged with overseeing disciplinary matters—the CLETS Advisory Committee (CAC)—seems to have taken no action to address the problem or ensure accountability from individual agencies.

Law enforcement abuse of confidential databases have been a growing concern for privacy and civil liberties groups like EFF. It occurs at all levels of government. In 2013, the NSA acknowledged that agents used intelligence systems to snoop on romantic interests (a practice dubbed “LOVEINT”). Last month, a Border Patrol supervisor was arrested and charged for allegedly manipulating a Homeland Security database to retaliate against a man who had made “child-rape” allegations against the supervisor’s brother.

Of the hundreds of cases of verified misuse of CLETS each year, only a handful of stories have reached the public, often years after the fact. Here are a few of the worst ways that police have abused the system in recent years:

  • In 2010, a Los Angeles Police officer used LAPD’s communications system, which is connected to CLETS, to pull information on witnesses who testified against his girlfriend’s brother in a murder case. Chief Charlie Beck told the press the department would “vigorously prosecute” the officer. Two years later, however, the Los Angeles County District Attorney dropped the case. By then, the officer had already resigned. (Los Angeles County District Attorney)
  • In the fall of 2010, an officer, who had been sending his estranged wife abusive text messages, used CLETS to dig up information on her new boyfriends. His wife complained to the police. The officer ultimately pled no contest to a misdemeanor harassment charge, but the charges for violating CLETS were dropped. He was also fired. (California Public Employee Relations Journal)
  • Two Fairfield Police officers were investigated for using CLETS to screen women from dating sites such as Tinder, eHarmony, and (Daily Republic)
  • Court records show that in 2009, a Westminster Police Officer was fired after accessing CLETS 96 times to gather information on 15 people for non-law enforcement purposes, such as meeting women and spying on his ex-wife and ex-girlfriends. In 2013, he pleaded guilty to domestic violence charges and unlawful disclosure of DMV records. (Orange County Register)
  • In 2013, the Madera County Sheriff’s Department of Corrections staff broke the rules by using a CLETS terminal at the county jail as a regular workstation. Consequently, officials failed to receive crucial communications, leading to the accidental release of a detainee. Days later, the released man was involved in a car chase that resulted in a crash that killed an innocent civilian. (Madera County Grand Jury)

EFF began investigating CLETS after reviewing official “misuse statistics” presented in public hearings that made little sense and did not seem to reflect misuse at all. Digging deeper, we learned the CLETS Advisory Committee has aggressively moved to expand the system’s capabilities, while more often than not turning a blind eye to the also-growing misuse.

What Is CLETS?

Think of CLETS as California’s law enforcement “cloud.”

CLETS links together more than 5,200 unique “points of presence,” such as dedicated office computers and mobile terminals in patrol cars. It’s a system so large that CADOJ told EFF it doesn’t even keep a master list of which agencies have signed agreements to access the system. In addition, many CLETS features are accessible through a web app called “SmartJustice.” The system also allows CLETS users to send millions of messages to each other every day, such as all-points-bulletins and Amber alerts.

CLETS users are granted access to whole universes of databases that don’t just contain information on Californians, but records from other states and the federal government.

If you’ve got a California-issued ID, registered a car in California, received a parking citation, have any kind of criminal history or protective order, or any kind of record in 11 other databases, then you likely have files that can be accessed from CLETS.

But that’s not all: . . .

Continue reading.

Written by Leisureguy

20 November 2015 at 2:48 pm

Saudi Arabia, an ISIS That Has Made It

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The NY Times has an interesting column by Kamel Daoud, which seems appropriate to the brutal and tyrannical theocratic government of Saudi Arabia:

Black Daesh, white Daesh. The former slits throats, kills, stones, cuts off hands, destroys humanity’s common heritage and despises archaeology, women and non-Muslims. The latter is better dressed and neater but does the same things. The Islamic State; Saudi Arabia. In its struggle against terrorism, the West wages war on one, but shakes hands with the other. This is a mechanism of denial, and denial has a price: preserving the famous strategic alliance with Saudi Arabia at the risk of forgetting that the kingdom also relies on an alliance with a religious clergy that produces, legitimizes, spreads, preaches and defends Wahhabism, the ultra-puritanical form of Islam that Daesh feeds on.

Wahhabism, a messianic radicalism that arose in the 18th century, hopes to restore a fantasized caliphate centered on a desert, a sacred book, and two holy sites, Mecca and Medina. Born in massacre and blood, it manifests itself in a surreal relationship with women, a prohibition against non-Muslims treading on sacred territory, and ferocious religious laws. That translates into an obsessive hatred of imagery and representation and therefore art, but also of the body, nakedness and freedom. Saudi Arabia is a Daesh that has made it.

The West’s denial regarding Saudi Arabia is striking: It salutes the theocracy as its ally but pretends not to notice that it is the world’s chief ideological sponsor of Islamist culture. The younger generations of radicals in the so-called Arab world were not born jihadists. They were suckled in the bosom of Fatwa Valley, a kind of Islamist Vatican with a vast industry that produces theologians, religious laws, books, and aggressive editorial policies and media campaigns.

One might counter: Isn’t Saudi Arabia itself a possible target of Daesh? Yes, but to focus on that would be to overlook the strength of the ties between the reigning family and the clergy that accounts for its stability — and also, increasingly, for its precariousness. The Saudi royals are caught in a perfect trap: Weakened by succession laws that encourage turnover, they cling to ancestral ties between king and preacher. The Saudi clergy produces Islamism, which both threatens the country and gives legitimacy to the regime.

One has to live in the Muslim world to understand the immense transformative influence of religious television channels on society by accessing its weak links: households, women, rural areas. Islamist culture is widespread in many countries — Algeria, Morocco, Tunisia, Libya, Egypt, Mali, Mauritania. There are thousands of Islamist newspapers and clergies that impose a unitary vision of the world, tradition and clothing on the public space, on the wording of the government’s laws and on the rituals of a society they deem to be contaminated.

It is worth reading certain Islamist newspapers to see their reactions to the attacks in Paris. The West is cast as a land of “infidels.” The attacks were the result of the onslaught against Islam. Muslims and Arabs have become the enemies of the secular and the Jews. The Palestinian question is invoked along with the rape of Iraq and the memory of colonial trauma, and packaged into a messianic discourse meant to seduce the masses. Such talk spreads in the social spaces below, while up above, political leaders send their condolences to France and denounce a crime against humanity. This totally schizophrenic situation parallels the West’s denial regarding Saudi Arabia.

All of which leaves one skeptical of Western democracies’ thunderous declarations regarding the necessity of fighting terrorism. Their war can only be myopic, for it targets the effect rather than the cause. Since ISIS is first and foremost a culture, not a militia, how do you prevent future generations from turning to jihadism when the influence of Fatwa Valley and its clerics and its culture and its immense editorial industry remains intact?

Is curing the disease therefore a simple matter? Hardly. Saudi Arabia remains an ally of the West in the many chess games playing out in the Middle East. It is preferred to Iran, that gray Daesh. And there’s the trap. Denial creates the illusion of equilibrium. Jihadism is denounced as the scourge of the century but no consideration is given to what created it or supports it. This may allow saving face, but not saving lives.

Daesh has a mother: the invasion of Iraq. But it also has a father: . . .

Continue reading.

Written by Leisureguy

20 November 2015 at 12:22 pm

BBS with the OneBlade

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SOTD 20 Nov 2015

I think I’ve finished the try-out of the OneBlade, and today I’m mailing it back to Mantic59. It’s been quite interesting, and also pleasing in how the shaves have steadily improved over the past 4 days. The second day I had a much better feel for the angle, and yesterday (the third day) I did get a BBS result. Today, with a new blade, the BBS result was even easier.

The blades, BTW, are thicker than DE blades (and thus require no bending to gain rigidity), much like standard single-edge blades (for the GEM, for example). And by yesterday I was able to complete a pass before rinsing, though it’s a bit iffy and sometimes an early rinse is needed.

Today’s lather was excellent. I used Floris No. 89 in deference to the new James Bond movie. (Floris No. 89 was favored by Bond, at least for a while.) The Copper Hat brush made a very fine lather. As you can see, the tub is very nearly full, so this is not a soap for those who cannot load the brush without making a mess and thus require soap containers that are half empty.

Three passes, with a good angle all the way, and then a good splash of Floris No. 89 aftershave.

A really nice shave. As I said yesterday, the OneBlade would indeed be a good razor for a well-heeled novice. The razor seems not to have a nick in it: extremely comfortable and, once you learn the angle (which takes about two shaves), it is quite efficient. It’s a little awkward under the nose because of the depth of the head behind the cutting edge, but by today I had mastered that (without conscious thought) and had no problems.

If having only one specific blade that works does not bother you, and the price of blade and razor is acceptable, then this is a very fine razor.

Thanks to Mantic59 and the entire Sharpologist team for giving me a chance to try it.

Written by Leisureguy

20 November 2015 at 8:59 am

Posted in Shaving

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