A Conversation With Nick Goldman: Using DNA to Store Digital Information

European Molecular Biology Laboratory

Nick Goldman, a molecular biologist at the European Bioinformatics Institute in Hinxton, England, used a technique with error-correction software to store and retrieve data in synthetic DNA molecules.

Last Wednesday, a group of researchers at the European Bioinformatics Institute reported in the journal Nature that they had managed to store digital information in synthetic DNA molecules, then recreated the original digital files without error.

The amount of data, 739 kilobytes all told, is hardly prodigious by today’s microelectronic storage standards: all 154 of Shakespeare’s sonnets, a scientific paper, a color digital photo of the researchers’ laboratory, a 26-second excerpt from the Rev. Dr. Martin Luther King Jr.’s “I have a dream” speech and a software algorithm. Nor is this the first time digital information has been stored in DNA.

But the researchers said their new technique, which includes error-correction software, was a step toward a digital archival storage medium of immense scale. Their goal is a system that will safely store the equivalent of one million CDs in a gram of DNA for 10,000 years.

If the new technology proves workable, it will have arrived just in time. The lead author, the British molecular biologist Nick Goldman, said he had conceived the idea with a colleague, Ewan Birney, while the two sat in a pub pondering the digital fire hose of genetic information their institute is now receiving — and the likelihood that it would soon outpace even today’s chips and disk drives, whose capacity continues to double roughly every two years, as predicted by Moore’s law.

The telephone interview with Dr. Goldman, from his laboratory in Hinxton, near Cambridge, has been edited and condensed.

Does your experiment suggest that DNA is a reasonable alternative for archiving digital information?

It’s too far beyond us at the moment because of the price. I don’t know if there are enough machines to write DNA in big quantities. I suspect not. The experiment we did converted about three-quarters of a megabyte of information off a hard disk drive into DNA. We showed it worked on a large scale, and part of what we published is an analysis of how that might scale up, at least theoretically. But we couldn’t do the scale-up experiments.

You’ve proved something. What’s next?

We’ve got a couple of ideas to pursue to make this a bit more likely to be something to turn up in the real world. One is to improve the coding and the decoding to see if we can get more information into the same amount of DNA. Hopefully if we can store twice as much information, that will halve our costs.

We were quite conservative in the approach we took. We really wanted to make sure that it worked, and so we used quite a lot of error-correction code. We could maybe sacrifice less to the error-correction part and use more actual information.

The other thing to make it work on a scale that the world would really be interested in is to automate and miniaturize. All the technologies exist — they’re all commercially available. But they’re not all in one place, and they’re not designed to work with each other as such.

If you wanted to do it properly you’d invest in the site, you’d have DNA synthesis at the site, you’d have the storage there, you’d have the reading back in one place, and you’d miniaturize it all. You’d have micro-fluidics to do what is currently lab science — even to the level of having robots to do the filing of the test tubes onto shelves. Robots are used in magnetic tape archive centers now, and you’d just want a smaller version of the same.

How similar is what you’ve done to what is involved in today’s gene-sequencing systems, which read and store the proteins in a DNA molecule?

The sequencing, or reading it back, that we did is exactly the same. We designed it that way. We designed it so that it would work in the standard protocols that we and our laboratory collaborators are familiar with, day in day out. It is really exactly the same process. We use an Illumina sequencing machine.

The writing of the information is a technology I’m a little bit less familiar with. But Agilent Technologies, whom we worked with, is one of the world leaders in developing this, and it is, I believe, very much like an inkjet printing system. But you’re not using colored dyes on paper — you’re using chemical solutions that include in them the nucleotides, the basis of DNA, fired very accurately onto a glass slide so that each little spot on the slide you build up is a separate sequence.

Is there a category of information you were most interested in archiving?

Read More..

Observatory: Viagra as Diet Pill?

New evidence suggests that the erectile-dysfunction drug Viagra might have another use: helping burn away excess fat.

The drug, generically known as sildenafil, helped convert undesirable white fat cells to energy-burning beige fat cells in laboratory mice, researchers at the University of Bonn in Germany report in The Journal of the Federation of American Societies for Experimental Biology.

It was already known that mice fed Viagra became less prone to obesity when fed a high-fat diet. What was not clear was why.

Dr. Alexander Pfeifer, director of the university’s Institute for Pharmacology and Toxicology, said he already had some clues: Viagra works by preventing the degradation of the intercellular messenger cGMP. Dr. Pfeifer has long been testing the effects of cGMP on fat cells.

So he fed the drug to mice for seven days and monitored their fat cells. As it turned out, the troublesome white fat cells, which are associated with human problems like the dreaded spare tire, were being converted to the beneficial type of fat cells at a higher rate than usual. Dr. Pfeifer called the results “very promising.”

Still, he cautions against taking the drug purely for dieting purposes. “The idea to have one pill and then obesity goes away, that is a dream, but not easy to come by,” he said. “What we are up to is basic research in mice. This pill is approved by the F.D.A. for a particular purpose for a reason.” DOUGLAS QUENQUA

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Observatory: Viagra as Diet Pill?

New evidence suggests that the erectile-dysfunction drug Viagra might have another use: helping burn away excess fat.

The drug, generically known as sildenafil, helped convert undesirable white fat cells to energy-burning beige fat cells in laboratory mice, researchers at the University of Bonn in Germany report in The Journal of the Federation of American Societies for Experimental Biology.

It was already known that mice fed Viagra became less prone to obesity when fed a high-fat diet. What was not clear was why.

Dr. Alexander Pfeifer, director of the university’s Institute for Pharmacology and Toxicology, said he already had some clues: Viagra works by preventing the degradation of the intercellular messenger cGMP. Dr. Pfeifer has long been testing the effects of cGMP on fat cells.

So he fed the drug to mice for seven days and monitored their fat cells. As it turned out, the troublesome white fat cells, which are associated with human problems like the dreaded spare tire, were being converted to the beneficial type of fat cells at a higher rate than usual. Dr. Pfeifer called the results “very promising.”

Still, he cautions against taking the drug purely for dieting purposes. “The idea to have one pill and then obesity goes away, that is a dream, but not easy to come by,” he said. “What we are up to is basic research in mice. This pill is approved by the F.D.A. for a particular purpose for a reason.” 

Read More..

A Conversation With Nick Goldman: Using DNA to Store Digital Information

European Molecular Biology Laboratory

Nick Goldman, a molecular biologist at the European Bioinformatics Institute in Hinxton, England, used a technique with error-correction software to store and retrieve data in synthetic DNA molecules.

Last Wednesday, a group of researchers at the European Bioinformatics Institute reported in the journal Nature that they had managed to store digital information in synthetic DNA molecules, then recreated the original digital files without error.

The amount of data, 739 kilobytes all told, is hardly prodigious by today’s microelectronic storage standards: all 154 of Shakespeare’s sonnets, a scientific paper, a color digital photo of the researchers’ laboratory, a 26-second excerpt from the Rev. Dr. Martin Luther King Jr.’s “I have a dream” speech and a software algorithm. Nor is this the first time digital information has been stored in DNA.

But the researchers said their new technique, which includes error-correction software, was a step toward a digital archival storage medium of immense scale. Their goal is a system that will safely store the equivalent of one million CDs in a gram of DNA for 10,000 years.

If the new technology proves workable, it will have arrived just in time. The lead author, the British molecular biologist Nick Goldman, said he had conceived the idea with a colleague, Ewan Birney, while the two sat in a pub pondering the digital fire hose of genetic information their institute is now receiving — and the likelihood that it would soon outpace even today’s chips and disk drives, whose capacity continues to double roughly every two years, as predicted by Moore’s law.

The telephone interview with Dr. Goldman, from his laboratory in Hinxton, near Cambridge, has been edited and condensed.

Does your experiment suggest that DNA is a reasonable alternative for archiving digital information?

It’s too far beyond us at the moment because of the price. I don’t know if there are enough machines to write DNA in big quantities. I suspect not. The experiment we did converted about three-quarters of a megabyte of information off a hard disk drive into DNA. We showed it worked on a large scale, and part of what we published is an analysis of how that might scale up, at least theoretically. But we couldn’t do the scale-up experiments.

You’ve proved something. What’s next?

We’ve got a couple of ideas to pursue to make this a bit more likely to be something to turn up in the real world. One is to improve the coding and the decoding to see if we can get more information into the same amount of DNA. Hopefully if we can store twice as much information, that will halve our costs.

We were quite conservative in the approach we took. We really wanted to make sure that it worked, and so we used quite a lot of error-correction code. We could maybe sacrifice less to the error-correction part and use more actual information.

The other thing to make it work on a scale that the world would really be interested in is to automate and miniaturize. All the technologies exist — they’re all commercially available. But they’re not all in one place, and they’re not designed to work with each other as such.

If you wanted to do it properly you’d invest in the site, you’d have DNA synthesis at the site, you’d have the storage there, you’d have the reading back in one place, and you’d miniaturize it all. You’d have micro-fluidics to do what is currently lab science — even to the level of having robots to do the filing of the test tubes onto shelves. Robots are used in magnetic tape archive centers now, and you’d just want a smaller version of the same.

How similar is what you’ve done to what is involved in today’s gene-sequencing systems, which read and store the proteins in a DNA molecule?

The sequencing, or reading it back, that we did is exactly the same. We designed it that way. We designed it so that it would work in the standard protocols that we and our laboratory collaborators are familiar with, day in day out. It is really exactly the same process. We use an Illumina sequencing machine.

The writing of the information is a technology I’m a little bit less familiar with. But Agilent Technologies, whom we worked with, is one of the world leaders in developing this, and it is, I believe, very much like an inkjet printing system. But you’re not using colored dyes on paper — you’re using chemical solutions that include in them the nucleotides, the basis of DNA, fired very accurately onto a glass slide so that each little spot on the slide you build up is a separate sequence.

Is there a category of information you were most interested in archiving?

Read More..

Egypt’s Morsi Declares State of Emergency

CAIRO (AP) — Egypt's president declared a state of emergency and curfew in three Suez Canal provinces hit hardest by a weekend wave of unrest that left more than 50 dead, using tactics of the ousted regime to get a grip on discontent over his Islamist policies and the slow pace of change.

Angry and almost screaming, Mohammed Morsi vowed in a televised address on Sunday night that he would not hesitate to take even more action to stem the latest eruption of violence across much of the country. But at the same time, he sought to reassure Egyptians that his latest moves would not plunge the country back into authoritarianism.

"There is no going back on freedom, democracy and the supremacy of the law," he said.

The worst violence this weekend was in the Mediterranean coastal city of Port Said, where seven people were killed on Sunday, pushing the toll for two days of clashes to at least 44. The unrest was sparked on Saturday by a court conviction and death sentence for 21 defendants involved in a mass soccer riot in the city's main stadium on Feb. 1, 2012 that left 74 dead.

Most of those sentenced to death were local soccer fans from Port Said, deepening a sense of persecution that Port Said's residents have felt since the stadium disaster, the worst soccer violence ever in Egypt.

At least another 11 died on Friday elsewhere in the country during rallies marking the second anniversary of the anti-Mubarak uprising. Protesters used the occasion to renounce Morsi and his Islamic fundamentalist group, the Muslim Brotherhood, which emerged as the country's most dominant political force after Mubarak's ouster.

The curfew and state of emergency, both in force for 30 days, affect the provinces of Port Said, Ismailiya and Suez. The curfew takes effect Monday from 9 p.m. to 6 a.m. every day.

Morsi, in office since June, also invited the nation's political forces to a dialogue starting Monday to resolve the country's latest crisis. A statement issued later by his office said that among those invited were the country's top reform leader, Nobel peace Laureate Mohammed ElBaradei, former Arab League chief Amr Moussa and Hamdeen Sabahi, a leftist politician who finished third in last year's presidential race.

The three are leaders of the National Salvation Front, an umbrella for the main opposition parties.

Khaled Dawoud, the Front's spokesman, said Morsi's invitation was meaningless unless he clearly states what is on the agenda. That, he added, must include amending a disputed constitution hurriedly drafted by the president's Islamist allies and rejected by the opposition.

He also faulted the president for not acknowledging his political responsibility for the latest bout of political violence.

"It is all too little too late," he told The Associated Press.

In many ways, Morsi's decree and his call for a dialogue betrayed his despair in the face of wave after wave of political unrest, violence and man-made disasters that, at times, made the country look like it was about to come unglued.

A relative unknown until his Muslim Brotherhood nominated him to run for president last year, Morsi is widely criticized for having offered no vision for the country's future after nearly 30 years of dictatorship under Mubarak and no coherent policy to tackle seemingly endless problems, from a free falling economy and deeply entrenched social injustices to surging crime and chaos on the streets.

Reform of the judiciary and the police, hated under the old regime for brutality, are also key demands of Morsi's critics.

Morsi did not say what he plans to do to stem the violence in other parts of the country outside those three provinces, but he did say he had instructed the police to deal "firmly and forcefully" with individuals attacking state institutions, using firearms to "terrorize" citizens or blocking roads and railway lines.

There were also clashes Sunday in Cairo and several cities in the Nile Delta region, including the industrial city of Mahallah.

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Unboxed: Literary History, Seen Through Big Data’s Lens

ANY list of the leading novelists of the 19th century, writing in English, would almost surely include Charles Dickens, Thomas Hardy, Herman Melville, Nathaniel Hawthorne and Mark Twain.

But they do not appear at the top of a list of the most influential writers of their time. Instead, a recent study has found, Jane Austen, author of “Pride and Prejudice, “ and Sir Walter Scott, the creator of “Ivanhoe,” had the greatest effect on other authors, in terms of writing style and themes.

These two were “the literary equivalent of Homo erectus, or, if you prefer, Adam and Eve,” Matthew L. Jockers wrote in research published last year. He based his conclusion on an analysis of 3,592 works published from 1780 to 1900. It was a lot of digging, and a computer did it.

The study, which involved statistical parsing and aggregation of thousands of novels, made other striking observations. For example, Austen’s works cluster tightly together in style and theme, while those of George Eliot (a k a Mary Ann Evans) range more broadly, and more closely resemble the patterns of male writers. Using similar criteria, Harriet Beecher Stowe was 20 years ahead of her time, said Mr. Jockers, whose research will soon be published in a book, “Macroanalysis: Digital Methods and Literary History” (University of Illinois Press).

These findings are hardly the last word. At this stage, this kind of digital analysis is mostly an intriguing sign that Big Data technology is steadily pushing beyond the Internet industry and scientific research into seemingly foreign fields like the social sciences and the humanities. The new tools of discovery provide a fresh look at culture, much as the microscope gave us a closer look at the subtleties of life and the telescope opened the way to faraway galaxies.

“Traditionally, literary history was done by studying a relative handful of texts,” says Mr. Jockers, an assistant professor of English and a researcher at the Center for Digital Research in the Humanities at the University of Nebraska. “What this technology does is let you see the big picture — the context in which a writer worked — on a scale we’ve never seen before.”

Mr. Jockers, 46, personifies the digital advance in the humanities. He received a Ph.D. in English literature from Southern Illinois University, but was also fascinated by computing and became a self-taught programmer. Before he moved to the University of Nebraska last year, he spent more than a decade at Stanford, where he was a founder of the Stanford Literary Lab, which is dedicated to the digital exploration of books.

Today, Mr. Jockers describes the tools of his trade in terms familiar to an Internet software engineer — algorithms that use machine learning and network analysis techniques. His mathematical models are tailored to identify word patterns and thematic elements in written text. The number and strength of links among novels determine influence, much the way Google ranks Web sites.

It is this ability to collect, measure and analyze data for meaningful insights that is the promise of Big Data technology. In the humanities and social sciences, the flood of new data comes from many sources including books scanned into digital form, Web sites, blog posts and social network communications.

Data-centric specialties are growing fast, giving rise to a new vocabulary. In political science, this quantitative analysis is called political methodology. In history, there is cliometrics, which applies econometrics to history. In literature, stylometry is the study of an author’s writing style, and these days it leans heavily on computing and statistical analysis. Culturomics is the umbrella term used to describe rigorous quantitative inquiries in the social sciences and humanities.

“Some call it computer science and some call it statistics, but the essence is that these algorithmic methods are increasingly part of every discipline now,” says Gary King, director of the Institute for Quantitative Social Science at Harvard.

Cultural data analysts often adapt biological analogies to describe their work. Mr. Jockers, for example, called his research presentation “Computing and Visualizing the 19th-Century Literary Genome.”

Such biological metaphors seem apt, because much of the research is a quantitative examination of words. Just as genes are the fundamental building blocks of biology, words are the raw material of ideas.

“What is critical and distinctive to human evolution is ideas, and how they evolve,” says Jean-Baptiste Michel, a postdoctoral fellow at Harvard.

Mr. Michel and another researcher, Erez Lieberman Aiden, led a project to mine the virtual book depository known as Google Books and to track the use of words over time, compare related words and even graph them.

Google cooperated and built the software for making graphs open to the public. The initial version of Google’s cultural exploration site began at the end of 2010, based on more than five million books, dating from 1500. By now, Google has scanned 20 million books, and the site is used 50 times a minute. For example, type in “women” in comparison to “men,” and you see that for centuries the number of references to men dwarfed those for women. The crossover came in 1985, with women ahead ever since.

In work published in Science magazine in 2011, Mr. Michel and the research team tapped the Google Books data to find how quickly the past fades from books. For instance, references to “1880,” which peaked in that year, fell to half by 1912, a lag of 32 years. By contrast, “1973” declined to half its peak by 1983, only 10 years later. “We are forgetting our past faster with each passing year,” the authors wrote.

JON KLEINBERG, a computer scientist at Cornell, and a group of researchers approached collective memory from a very different perspective.

This article has been revised to reflect the following correction:

Correction: January 27, 2013

An earlier version of this article misstated Matthew L. Jockers’s age. He is 46, not 48. 

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Brain Aging Linked to Sleep-Related Memory Decline

Scientists have known for decades that the ability to remember newly learned information declines with age, but it was not clear why. A new study may provide part of the answer.

The report, posted online on Sunday by the journal Nature Neuroscience, suggests that structural brain changes occurring naturally over time interfere with sleep quality, which in turn blunts the ability to store memories for the long term.

Previous research had found that the prefrontal cortex, the brain region behind the forehead, tends to lose volume with age, and that part of this region helps sustain quality sleep, which is critical to consolidating new memories. But the new experiment, led by researchers at the University of California, Berkeley, is the first to directly link structural changes with sleep-related memory problems.

The findings suggest that one way to slow memory decline in aging adults is to improve sleep, specifically the so-called slow-wave phase, which constitutes about a quarter of a normal night’s slumber.

Doctors cannot reverse structural changes that occur with age any more than they can turn back time. But at least two groups are experimenting with electrical stimulation as a way to improve deep sleep in older people. By placing electrodes on the scalp, scientists can run a low current across the prefrontal area, essentially mimicking the shape of clean, high-quality slow waves.

The result: improved memory, at least in some studies. “There are also a number of other ways you can improve sleep, including exercise,” said Ken Paller, a professor of psychology and the director of the cognitive neuroscience program at Northwestern University, who was not involved in the research.

Dr. Paller said that a whole array of changes occurred across the brain during aging and that sleep was only one factor affecting memory function.

But Dr. Paller said the study told “a convincing story, I think: that atrophy is related to slow-wave sleep, which we know is related to memory performance. So it’s a contributing factor.”

In the study, the research team took brain images from 19 people of retirement age and from 18 people in their early 20s. It found that a brain area called the medial prefrontal cortex, roughly behind the middle of the forehead, was about one-third smaller on average in the older group than in the younger one — a difference due to natural atrophy over time, previous research suggests.

Before bedtime, the team had the two groups study a long list of words paired with nonsense syllables, like “action-siblis” and “arm-reconver.” The team used the nonwords because one type of memory that declines with age is for new, previously unseen information.

After training on the pairs for half an hour or so, the participants took a test on some of them. The young group outscored the older group by about 25 percent.

Then everyone went to bed — and bigger differences emerged. For one, the older group got only about a quarter of the amount of high-quality slow-wave sleep that the younger group did, as measured by the shape and consistency of electrical waves on an electroencephalogram machine, or EEG. It is thought that the brain moves memories from temporary to longer-term storage during this deep sleep.

On a second test, given in the morning, the younger group outscored the older group by about 55 percent. The estimated amount of atrophy in each person roughly predicted the difference between his or her evening and morning scores, the study found. Even seniors who were very sharp at night showed declines after sleeping.

“The analysis showed that the differences were due not to changes in capacity for memories, but to differences in sleep quality,” said Bryce A. Mander, a postdoctoral fellow at Berkeley and the lead author of the study. His co-authors included researchers from the California Pacific Medical Center in San Francisco; the University of California, San Diego; and the Lawrence Berkeley National Laboratory.

The findings do not imply that medial prefrontal atrophy is the only age-related change causing memory problems, said Matthew P. Walker, a professor of psychology and neuroscience at Berkeley and a co-author of the study.

“Essentially, with age, you lose tissue in this prefrontal area,” Dr. Walker said. “You get less quality deep sleep, and have less opportunity to consolidate new memories.”

Read More..

Brain Aging Linked to Sleep-Related Memory Decline

Scientists have known for decades that the ability to remember newly learned information declines with age, but it was not clear why. A new study may provide part of the answer.

The report, posted online on Sunday by the journal Nature Neuroscience, suggests that structural brain changes occurring naturally over time interfere with sleep quality, which in turn blunts the ability to store memories for the long term.

Previous research had found that the prefrontal cortex, the brain region behind the forehead, tends to lose volume with age, and that part of this region helps sustain quality sleep, which is critical to consolidating new memories. But the new experiment, led by researchers at the University of California, Berkeley, is the first to directly link structural changes with sleep-related memory problems.

The findings suggest that one way to slow memory decline in aging adults is to improve sleep, specifically the so-called slow-wave phase, which constitutes about a quarter of a normal night’s slumber.

Doctors cannot reverse structural changes that occur with age any more than they can turn back time. But at least two groups are experimenting with electrical stimulation as a way to improve deep sleep in older people. By placing electrodes on the scalp, scientists can run a low current across the prefrontal area, essentially mimicking the shape of clean, high-quality slow waves.

The result: improved memory, at least in some studies. “There are also a number of other ways you can improve sleep, including exercise,” said Ken Paller, a professor of psychology and the director of the cognitive neuroscience program at Northwestern University, who was not involved in the research.

Dr. Paller said that a whole array of changes occurred across the brain during aging and that sleep was only one factor affecting memory function.

But Dr. Paller said the study told “a convincing story, I think: that atrophy is related to slow-wave sleep, which we know is related to memory performance. So it’s a contributing factor.”

In the study, the research team took brain images from 19 people of retirement age and from 18 people in their early 20s. It found that a brain area called the medial prefrontal cortex, roughly behind the middle of the forehead, was about one-third smaller on average in the older group than in the younger one — a difference due to natural atrophy over time, previous research suggests.

Before bedtime, the team had the two groups study a long list of words paired with nonsense syllables, like “action-siblis” and “arm-reconver.” The team used the nonwords because one type of memory that declines with age is for new, previously unseen information.

After training on the pairs for half an hour or so, the participants took a test on some of them. The young group outscored the older group by about 25 percent.

Then everyone went to bed — and bigger differences emerged. For one, the older group got only about a quarter of the amount of high-quality slow-wave sleep that the younger group did, as measured by the shape and consistency of electrical waves on an electroencephalogram machine, or EEG. It is thought that the brain moves memories from temporary to longer-term storage during this deep sleep.

On a second test, given in the morning, the younger group outscored the older group by about 55 percent. The estimated amount of atrophy in each person roughly predicted the difference between his or her evening and morning scores, the study found. Even seniors who were very sharp at night showed declines after sleeping.

“The analysis showed that the differences were due not to changes in capacity for memories, but to differences in sleep quality,” said Bryce A. Mander, a postdoctoral fellow at Berkeley and the lead author of the study. His co-authors included researchers from the California Pacific Medical Center in San Francisco; the University of California, San Diego; and the Lawrence Berkeley National Laboratory.

The findings do not imply that medial prefrontal atrophy is the only age-related change causing memory problems, said Matthew P. Walker, a professor of psychology and neuroscience at Berkeley and a co-author of the study.

“Essentially, with age, you lose tissue in this prefrontal area,” Dr. Walker said. “You get less quality deep sleep, and have less opportunity to consolidate new memories.”

Read More..

Exam Finds Nothing Unusual About a Second Boeing 787 Battery

WASHINGTON — Although a fire destroyed one of two big batteries on a Boeing 787 parked at Logan Airport in Boston three weeks ago, a quick examination of the second battery found “no obvious anomalies,” the National Transportation Safety Board said on Sunday.

The second battery was of identical design but used for a different purpose than the first, the agency said. Its report added scattered details to what is known about the incident, one of two battery problems that led to the grounding of all 50 of the 787s in airline service.

The board said that its laboratory was continuing to study the destroyed battery, whose function was to start the auxiliary power unit, a small jet engine used mostly on the ground. The battery, which was not being charged or discharged, caught fire on Jan. 7 while the plane was empty.

The undamaged battery on which the board reported Sunday was a backup for cockpit instruments, located near the nose. The board has released photos of the damaged and undamaged batteries.

On Jan. 16, on a different 787 on a domestic flight in Japan, the main battery began belching smoke a few minutes after takeoff, forcing an emergency landing. Investigators have not said whether it was being charged at the time. The planes were grounded shortly afterward.

The batteries use a lithium-ion chemistry, which has been in use for many years in many applications but is new in airplanes. Investigators say the problem could be the batteries or with the associated electronics used to manage them.

The board said Sunday that at the time of the fire at Logan, the plane, which belonged to Japan Airlines, had completed 22 flights and 169 flight hours.

The board’s update also said that investigators had completed a review of two systems associated with the auxiliary power unit, at two locations in Arizona, and found no problems.

The board said it had sent two additional investigators to Seattle, where the board was working with the Federal Aviation Administration to review work at Boeing. One investigator will work with a group reviewing Boeing’s corrective actions, and the other will work on how the lithium-ion batteries were approved by the F.A.A.

The safety board is an advisory body with no regulatory authority — that belongs to the F.A.A. — but it is in charge of safety investigations.

A team led by the safety board also examined circuit boards used to monitor the battery in the in-flight incident in Japan, the board said. The circuit boards were damaged in the incident, “which limited the information that could be obtained from tests,” the board said. It added that the team “found no significant discoveries.”

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The Saturday Profile: Leading the Tunisian Agency That Once Jailed Him

TUNIS — It was the first time Ali Laarayedh had inspected a prison cell, but even then, as the interior minister, his old instincts kicked in.

“I turned around to see who would shut the cell door on me,” he said in his quiet manner.

But no one bolted the door. For Mr. Laarayedh had experienced a profound reversal of fortune, mirroring that of the Islamist political party that he helped found. Jailed numerous times in the Interior Ministry as a political prisoner, he now runs the very security agency that once sent him to death row.

His memory of the cells remains vivid. “Even though they are on the ground floor,” he said, “once you are inside them you have the impression that you have entered a cave.”

Mr. Laarayedh, 57, speaking in his office at a considerable distance above the cells, argued that his grueling prison experiences make him a better minister, sensitive to the abuse of power and the need for not just Tunisia, but all Arab states, to bend their omnipotent secret police to the rule of law.

Others are not convinced of his commitment to the law, at least not in the Western style. Mr. Laarayedh was imprisoned repeatedly, including all the years from 1990 to 2004, for being a founding member of the Renaissance Party, or Ennahda in Arabic, the Islamist political party that dominates Tunisia’s first elected post-revolutionary government.

Many in the opposition suspect that when men like Mr. Laarayedh talk about the rule of law, they mean Shariah, or Islamic law, a Koran-based code that is often at odds with Western standards of justice. The minister has also been widely criticized for the level of violence the police still unleash to squelch protests.

The interior minister is one of at least eight cabinet ministers, about one-third of the total, who spent significant chunks of their adult lives behind bars, often in solitary confinement. Some Tunisians believe that a country struggling with unemployment and political upheaval would be better off run by technocrats rather than veteran prisoners lacking real-world experience.

After one notorious episode on Sept. 14, when the American Embassy was sacked, critics mocked Mr. Laarayedh mercilessly for saying essentially that security forces had protected the embassy’s front door, but unfortunately the marauders entered through the back. Since that melee, which left four people dead, the police have been unable to apprehend Seifallah Ben Hassine, the leader of the puritanical Salafi movement, who is wanted for helping to inspire it.

In the interview, the minister said his forces were overwhelmed that day by a lack of equipment, including armored vehicles needed to protect the police. On the larger issue of governance, he argued that Tunisia was better off in the hands of those who sacrificed for change.

“We have to choose people who can break with the past and put the country on the path to democracy and a state of law,” said Mr. Laarayedh. “If we go back to the old, to the people with experience, nothing will change.”

He prefers not to detail his own imprisonment, saying that political detainees of all stripes had to endure the same terrible physical and mental torture. Many died or lost their minds, he said; as for himself, his physical scars are not visible, so it is better to focus on the revolution. When pressed, however, he revealed some contained anger.

“One of the worst forms of torture is when they leave you all alone,” he said. “When you pound on the iron door, if you are sick or you need something, and you can pound all night and they do not respond. Believe me, that is the worst contempt and the worst violence that I experienced. They take you for a mouse or a fly, or for nothing at all. You do not exist. You are not even worth being beaten. Do you understand? You are not even worth being beaten.”

He can put that behind him, he said, mostly because the revolution succeeded. “I realized all my objectives — a dictator fell, a democracy for which I gave my life was born and Tunisians are masters of their own destiny,” he said.

Mr. Laarayedh said he worried more about the effect his long absences had on his wife, a medical technician, and his three children, as he dedicated his life to political activism.

After obtaining a degree in maritime engineering in 1980, he worked for the government for only a year before going underground. He had odd jobs like teaching math in private schools, and he even got married in 1983 while on the run. His long years in and out of prison began around 1987.

Those years instilled in him the need for Tunisia to reach an equilibrium, he said, for a government able to curb the excesses of both the religious zealots and the liberals. Each camp accuses him of coddling the other.

“I don’t want the state to be hostage to either of these extremist tendencies,” he said.

He denied that the Renaissance Party worked in collusion with the more puritanical Salafis, who have staged a series of violent protests against art galleries and other liberal institutions. “We try to compromise between modernity, with all its values, and our own authenticity, our Arab Muslim identity,” he said, whereas the Salafis create “an antagonism between the present and the past.”

Some activists, particularly women, remain skeptical. Tunisia had perhaps the most progressive Arab gender laws for decades, and they believe that the Renaissance Party is shrinking the public space for women. They had hoped for something different given that while underground, the Islamists had emphasized the universal rights of man.

Olfa el-Alem, a political organizer, noted that despite repeated promises to investigate police violence against demonstrators, no results had been publicized.

“I thought the day they gained their liberty they would let others have their freedom as well,” said Ms. Alem, referring to the Renaissance leaders.

Mr. Laarayedh and other Renaissance leaders suggested that they lack full control over the levers of state. Mr. Laarayedh said Tunisians cannot yet take their nascent democracy for granted.

“This used to be Ben Ali’s desk!” he said, beaming, as he showed a visitor his office. Zine el-Abidine Ben Ali, the leader deposed by the January 2011 revolution, was prime minister when he seized the presidency in a bloodless 1987 coup.

Perhaps the best testament to the fact that democracy will emerge from Tunisia’s ferment, Mr. Laarayedh said, is that he now sits at that desk.

“It is a miracle,” he said. “If you want to look for irrefutable evidence that there was a revolution here, it is that someone condemned to death by this very ministry has become the minister.”

This article has been revised to reflect the following correction:

Correction: January 26, 2013

An earlier version of this article misidentified the title held by Zine el-Abidine Ben Ali when he seized the presidency in 1987. He was prime minister, not interior minister.

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