The Historic Interpreter
“It is only the enlightened ruler and the wise general who will use the highest intelligence of the army for the purposes of spying, and thereby they achieve great results. Spies are a most important element in war, because on them depends an army’s ability to move.” – Sun Tzu
“No war can be conducted successfully without early and good intelligence.” – John Churchill, The first Duke of Marlborough
Intelligence activities at the national level first developed during the middle ages in diplomatic circles, with espionage being one of the fundamental duties of ambassadors and envoys. The first English monarch known to place a heavy emphasis on espionage was Henry VII, who in the late fifteenth century employed agents to track the activities of his enemies both domestically and abroad. Prior to assuming the throne, it was only through employment of personal agents that Henry avoided death…
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A very good sign if the LAPD and other big city police forces think of themselves as not only guardians against criminals and terrorists but as guardians against government as well.
A very good sign, I think. Kate Mather reports in the LA Times:
For years, Los Angeles police officers have worked under the shadow of the department’s dark past.
The LAPD of the 1970s and ’80s acted as a hard-charging, occupying force that raided poor neighborhoods and rounded up anyone in sight. Police stormed suspected crack houses, tearing down walls with a tank-like battering ram. Officers of that era were trained to think of themselves as soldiers in a never-ending war on crime.
But now the department is using that notorious history as a crucial lesson for its officers.
“We were warriors,” Deputy Chief Bill Scott recently told a room filled with LAPD rank-and-file officers, a group of fresh-faced rookies watching from the front.
Now, he said, officers need to think of themselves as guardians watching over communities — not warriors cracking down on them.
“That means if we’ve…
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The Historic Interpreter
“Tell me Mr. Robertson, are you a man of courage?” “Try me Sir Arthur.” “That, is what we mean to do” – Conversation between Sir Arthur Wellesley and Father James Robertson (Longford, 1969)
“The French armies have no communications and one army has no knowledge of the position or of the circumstances in which the others are placed, whereas I have knowledge of all that passes on all sides.” – Sir Arthur Wellesley (Esdaile, 2004)
Civilian Sources of Military Intelligence
During the French Revolutionary/Napoleonic period, there were a number of churchmen who served as agents for the British military. During the Revolution, the French Republicans adopted policies, targeting the Church, attempting to de-Christianize the country. These included:
- Confiscation of Church lands, which were to be the security for the new Assignat currency
- Destruction of statues, plates and other iconography from places of worship
- Destruction of crosses, bells and other…
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The XX Committee
Hillary Rodham Clinton’s effort to quash the rising scandal over her misuse of email when she was secretary of State has so far backfired spectacularly. Instead of cutting the story short, she has fanned the flames, and now even some of her backers in the Democratic Party are worried about the trajectory of this drama, which threatens to derail her presidential candidacy.
For readers who’ve mostly ignored emailgate — assuming it would disappear — and now feel the need to catch up, here’s a primer on why it matters.
It’s difficult to avoid the suspicion that Clinton, after the scandals that rocked her husband’s presidency during the 1990s, simply did not want to leave behind a paper trail (or e-trail). And so, as secretary of State, she tried to skirt federal records law by employing her own IT systems and servers, and by exclusively using a personal email address.
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Amelia's Networked Culture
Todays Lecture talked about the history of the Internet, focusing on World War 2 and moving forward from there. It was really interesting to see the development of these networks and the impact they have had on the world.
World War 2 saw the use of mass air warfare to destroy enemies, targeting specifically countries centre bases (nodes). This war was about destruction, focusing its efforts on bombing and air attacks creating more efficient and strategic attacks. By striking not only the enemy’s centres of information but also their weapon manufacturers and warehouses, an upper hand in the war was achieved. The war forced people to invent, kicking technology advancement into gear to beat opponents in the fight for survival. The Internet was developed out of this fear, particularly towards nuclear weapons.
At the end of World War 2 many of the German rocket scientists moved to America and the Soviet Union…
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So, about a month agoe I got the Garmin Epix. I had been droling over it since it was first announced, some time agoe.
I have to admit that I was really unsure before buying it. First of all because I thought the Fenix 3 looked cooler, second because I read about all the complaints about the Epix having a lot of software bugs.
But in the end I thought that the software stuff would be sorted out in time. The hardware with having a map on your wrist at all time was the thing that made me buy it in the end.
Price and alternatives
This is an expensive watch priced at $550. It’s suppose to do everything the Fenix 3 does but adding the mapping feature.
This is not true. As I understand, the Fenix 3 has indeed a support for Wifi, which sounds kind of clever…
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Mount Gravatt Environment Group
Bush monsters on top of mountain
By: Michael Fox
Fearsome bush monsters joined us for bushcare on Tuesday afternoon.
Three members of the famous Geocaching Woods family joined Marshal and I at Fox Gully Bushcare.
Bush re-generator Eloise in action
Bush monsters Eloise and Lincoln are very passionate about the bush and enthusiastic about bush restoration.
Investigator Lincoln hunting for bugs
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Wendy and John's Travel Adventures
Yesterday, after packing a few boxes for Andrew and Lynley to help for their impending shift, we jumped on a couple of trains and went out to Crystal Palace, home of the football team. There is a very attractive park out there which was set up in 1852 by Professor Richard Owen who was the person to categorise the giant lizards as a new scientific group and named them ‘ Dinosaurs’. In and around the lake are models of different dinosaurs, amphibians, pterosaurs, marine reptiles. There is a trail to follow and information boards along the way.
The sculptures are huge and were produced at the dawn of Palaeontology, using fossils from the Natural History Museum and introduced the controversial idea that animals existed millions of years ago. This park predated Darwin’s theory of the origin of the species by 7 years.
Along the way we managed to find a geocache, the first…
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So I’ve spent exactly 2 weeks in China. So much has happened that it would take me pages and pages to write about everything and I’m pretty lazy. So instead I’ll bullet point some highlights and include pictures and I’ll go into more details about individual things later.
I spent a total of 26 hours traveling from Toledo, Ohio to Ningbo, China. My longest flight was 11 hours. We traveled with the sun and it was really weird to spend the entire 11 hour flight in sunlight. After arriving I was definitely jet lagged for several days.
I’m all moved into my apartment. I live on the ninth floor of a hotel (the top floor is all apartments.) I have a studio apartment with a lofted bedroom and a great view of the city! Unfortunately, I also have a couple of pink walls and I haven’t decided if they are…
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This spot in my home has been a place where I’ve experienced the most joy & pain, where I’ve learnt the power of music and how it can capture and understand me, in every season, in every moment. I have sat on this spot so many times, discovering what it is to commit to something, practicing for hours and desiring to be the best I possibly can be. It was in this spot that I discovered that I love to write music, and where it first was a 7 year old me playing what I thought to be symphonies, to where my parents would listen to my first attempts to music that captured my heart.
It was in this spot where I met God in worship. Where I would sing to Him and get lost in His presence. Where music became a spiritual experience, filled with hope, grace and love…
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Winds & Waves
For my senior thesis project, I have decided that I will probably be focusing on the role of food, feasting, and memory in the Odyssey, although exactly where I am going with this idea is still to be determined. To get me started, my thesis advisor recommended several sources, including an essay entitled Banter and Banquets for Heroic Death by Pietro Pucci from his book The Song of the Sirens: Essays on Homer because of its possible connection to my topic.
It focuses on the Iliad, not the Odyssey, but what it says about banquets may still be useful to me. The main argument of the essay, as far as I understood it, is that the Iliad is a self-reflective text that points to the inherent instability of the kleos, or fame/rumor, which is represented by the very genre of epic poetry of which the Iliad itself is a…
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Footsteps In The Deep
On Sunday, the 16th of June, 1935, in the town of Maglavit, a seventeen-year-old, poor shepherd with a speech impediment finally worked up enough courage to announce to his church a short message he claimed came directly from God the Father, whom he swore had visited him in the form of an old man while he was tending sheep. His message, a stereotypical Old Testament “turn or burn” indictment of his people, was met with both obvious incredulity and a similarly expected enthusiasm. Both those in favor and those against the happenings in Maglavit, and especially those hoping to profit from the events, spread the news far and wide. Newspapers were full of stories of miracles, healings, and prophecies as excitement over the shepherd boy who had seen God spread. In time, over two million people would take part in the spectacular events of Maglavit. Today, much of…
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Undergoing repairs at the 82nd Shipyard in Roslyakovo, Murmansk region since May, the flagship of the Russian Navy is now set to return to its home port in Severomorsk, outside the port city of Murmansk.
“Logistical support forces of the Northern Fleet and workers of the 82nd Shipyard in Roslyakovo (Murmansk region) launched a joint operation to bring the flagship of the Russian Navy, the heavy aircraft-carrying missile cruiser, Admiral of the Fleet of the Soviet Union Kuznetsov, out of the floating dock. The bulk of the repair work on the aircraft carrier has been completed,” Luzik reported, according to Russia’s RIA Novosti.
The Navy spokesman explained that during the three months of servicing and repairs, the Admiral Kuznetsov saw repairs…
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“Action in The Slot” by Tom Freeman
PT boat report for 10/11 January – The Slot action at Guadalcanal: The Japanese ships came in under the cover of a rain squall and the 2 US scout groups missed them. The first contact was made by strike group-1, spotting 3 destroyers off the Guadalcanal coast. The 3 boats attacked the enemy ships but the enemy sank PT-112 and damaged PT-43 so badly, it was abandoned. IJN destroyer Hatasukaze was hit by a torpedo, killing 8 and wounding 23, and retired to Shortland Island. PT-43 was later sighted on the Japanese-held portion of the island and was destroyed by gunfire from a New Zealand corvette.
P-38 Lightning in Alaska
12-19 January – 2,000 American troops, in an amphibious landing on Amchitka Island in the Aleutians, started their operations to take back the enemy held areas in Alaska. The USS Worden was sunk…
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I’ve long suspected something like this… and I don’t see at all how it could be a surprise, after all it is readily available raw material, just not always actualized or properly arranged material.
It is a lot easier than seeking out and incorporating alien or foreign genetic material.
Genes, like people, have families — lineages that stretch back through time, all the way to a founding member. That ancestor multiplied and spread, morphing a bit with each new iteration.
For most of the last 40 years, scientists thought that this was the primary way new genes were born — they simply arose from copies of existing genes. The old version went on doing its job, and the new copy became free to evolve novel functions.
Certain genes, however, seem to defy that origin story. They have no known relatives, and they bear no resemblance to any other gene. They’re the molecular equivalent of a mysterious beast discovered in the depths of a remote rainforest, a biological enigma seemingly unrelated to anything else on earth.
The mystery of where these orphan genes came from has puzzled scientists for decades. But in the past few years, a once-heretical explanation has quickly gained momentum — that many of these orphans arose out of so-called junk DNA, or non-coding DNA, the mysterious stretches of DNA between genes. “Genetic function somehow springs into existence,” said David Begun, a biologist at the University of California, Davis.
This metamorphosis was once considered to be impossible, but a growing number of examples in organisms ranging from yeast and flies to mice and humans has convinced most of the field that these de novo genes exist. Some scientists say they may even be common. Just last month, research presented at the Society for Molecular Biology and Evolution in Vienna identified 600 potentially new human genes. “The existence of de novo genes was supposed to be a rare thing,” said Mar Albà, an evolutionary biologist at the Hospital del Mar Research Institute in Barcelona, who presented the research. “But people have started seeing it more and more.”
Researchers are beginning to understand that de novo genes seem to make up a significant part of the genome, yet scientists have little idea of how many there are or what they do. What’s more, mutations in these genes can trigger catastrophic failures. “It seems like these novel genes are often the most important ones,” said Erich Bornberg-Bauer, a bioinformatician at the University of Münster in Germany.
The Orphan Chase
The standard gene duplication model explains many of the thousands of known gene families, but it has limitations. It implies that most gene innovation would have occurred very early in life’s history. According to this model, the earliest biological molecules 3.5 billion years ago would have created a set of genetic building blocks. Each new iteration of life would then be limited to tweaking those building blocks.
Yet if life’s toolkit is so limited, how could evolution generate the vast menagerie we see on Earth today? “If new parts only come from old parts, we would not be able to explain fundamental changes in development,” Bornberg-Bauer said.
The first evidence that a strict duplication model might not suffice came in the 1990s, when DNA sequencing technologies took hold. Researchers analyzing the yeast genome found that a third of the organism’s genes had no similarity to known genes in other organisms. At the time, many scientists assumed that these orphans belonged to families that just hadn’t been discovered yet. But that assumption hasn’t proven true. Over the last decade, scientists sequenced DNA from thousands of diverse organisms, yet many orphan genes still defy classification. Their origins remain a mystery.
In 2006, Begun found some of the first evidence that genes could indeed pop into existence from noncoding DNA. He compared gene sequences from the standard laboratory fruit fly, Drosophila melanogaster, with other closely related fruit fly species. The different flies share the vast majority of their genomes. But Begun and collaborators found several genes that were present in only one or two species and not others, suggesting that these genes weren’t the progeny of existing ancestors. Begun proposed instead that random sequences of junk DNA in the fruit fly genome could mutate into functioning genes.
Yet creating a gene from a random DNA sequence appears as likely as dumping a jar of Scrabble tiles onto the floor and expecting the letters to spell out a coherent sentence. The junk DNA must accumulate mutations that allow it to be read by the cell or converted into RNA, as well as regulatory components that signify when and where the gene should be active. And like a sentence, the gene must have a beginning and an end — short codes that signal its start and end.
In addition, the RNA or protein produced by the gene must be useful. Newly born genes could prove toxic, producing harmful proteins like those that clump together in the brains of Alzheimer’s patients. “Proteins have a strong tendency to misfold and cause havoc,” said Joanna Masel, a biologist at the University of Arizona in Tucson. “It’s hard to see how to get a new protein out of random sequence when you expect random sequences to cause so much trouble.” Masel is studying ways that evolution might work around this problem.
Another challenge for Begun’s hypothesis was that it’s very difficult to distinguish a true de novo gene from one that has changed drastically from its ancestors. (The difficulty of identifying true de novo genes remains a source of contention in the field.)
Ten years ago, Diethard Tautz, a biologist at the Max Planck Institute for Evolutionary Biology, was one of many researchers who were skeptical of Begun’s idea. Tautz had found alternative explanations for orphan genes. Some mystery genes had evolved very quickly, rendering their ancestry unrecognizable. Other genes were created by reshuffling fragments of existing genes.
Then his team came across the Pldi gene, which they named after the German soccer player Lukas Podolski. The sequence is present in mice, rats and humans. In the latter two species, it remains silent, which means it’s not converted into RNA or protein. The DNA is active or transcribed into RNA only in mice, where it appears to be important — mice without it have slower sperm and smaller testicles.
The researchers were able to trace the series of mutations that converted the silent piece of noncoding DNA into an active gene. That work showed that the new gene is truly de novo and ruled out the alternative — that it belonged to an existing gene family and simply evolved beyond recognition. “That’s when I thought, OK, it must be possible,” Tautz said.
A Wave of New Genes
Scientists have now catalogued a number of clear examples of de novo genes: A gene in yeast that determines whether it will reproduce sexually or asexually, a gene in flies and other two-winged insects that became essential for flight, and some genes found only in humans whose function remains tantalizingly unclear.
The Odds of Becoming a Gene
Scientists are testing computational approaches to determine how often random DNA sequences can be mutated into functional genes. Victor Luria, a researcher at Harvard, created a model using common estimates of the rates of mutation, recombination (another way of mixing up DNA) and natural selection. After subjecting a stretch of DNA as long as the human genome to mutation and recombination for 100 million generations, some random stretches of DNA evolved into active genes. If he were to add in natural selection, a genome of that size could generate hundreds or even thousands of new genes.
At the Society for Molecular Biology and Evolution conference last month, Albà and collaborators identified hundreds of putative de novo genes in humans and chimps — ten-fold more than previous studies — using powerful new techniques for analyzing RNA. Of the 600 human-specific genes that Albà’s team found, 80 percent are entirely new, having never been identified before.
Unfortunately, deciphering the function of de novo genes is far more difficult than identifying them. But at least some of them aren’t doing the genetic equivalent of twiddling their thumbs. Evidence suggests that a portion of de novo genes quickly become essential. About 20 percent of new genes in fruit flies appear to be required for survival. And many others show signs of natural selection, evidence that they are doing something useful for the organism.
In humans, at least one de novo gene is active in the brain, leading some scientists to speculate such genes may have helped drive the brain’s evolution. Others are linked to cancer when mutated, suggesting they have an important function in the cell. “The fact that being misregulated can have such devastating consequences implies that the normal function is important or powerful,” said Aoife McLysaght, a geneticist at Trinity College in Dublin who identified the first human de novo genes.
De novo genes are also part of a larger shift, a change in our conception of what proteins look like and how they work. De novo genes are often short, and they produce small proteins. Rather than folding into a precise structure — the conventional notion of how a protein behaves — de novo proteins have a more disordered architecture. That makes them a bit floppy, allowing the protein to bind to a broader array of molecules. In biochemistry parlance, these young proteins are promiscuous.
Scientists don’t yet know a lot about how these shorter proteins behave, largely because standard screening technologies tend to ignore them. Most methods for detecting genes and their corresponding proteins pick out long sequences with some similarity to existing genes. “It’s easy to miss these,” Begun said.
That’s starting to change. As scientists recognize the importance of shorter proteins, they are implementing new gene discovery technologies. As a result, the number of de novo genes might explode. “We don’t know what things shorter genes do,” Masel said. “We have a lot to learn about their role in biology.”
Scientists also want to understand how de novo genes get incorporated into the complex network of reactions that drive the cell, a particularly puzzling problem. It’s as if a bicycle spontaneously grew a new part and rapidly incorporated it into its machinery, even though the bike was working fine without it. “The question is fascinating but completely unknown,” Begun said.
A human-specific gene called ESRG illustrates this mystery particularly well. Some of the sequence is found in monkeys and other primates. But it is only active in humans, where it is essential for maintaining the earliest embryonic stem cells. And yet monkeys and chimps are perfectly good at making embryonic stem cells without it. “It’s a human-specific gene performing a function that must predate the gene, because other organisms have these stem cells as well,” McLysaght said.
“How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”