I subscribe to Wired Magazine, but am sometimes frustrated by the nature of its content which can drift off into the nonsensical. Just when I am ready to give up on the publication, it prints something that renews my interest.

The March 2010 issue has an article by Jordan Ellenberg, a mathematician at the University of Wisconsin, “F_ll _n t_e Bl_nks”  about the mathematical concepts of sparsity and compressed sensing. I will not spoil the article but he begins the article by describing an MRI scan of a young child at Lucille Packard Children’s Hospital at Stanford. The pediatricians needed a high resolution scan of the child’s liver. If the doctors were to get the scan they needed, the child would have to remain perfectly still for two minutes. If the doctors gave the child enough anesthesia to stop his breathing for that period of time, they could place him in grave danger.

The solution lay in an algorithm for compressed sensing discovered by Emmanuel Candes, an applied mathematician, then at Caltech now at Stanford, in 2004. As Jordan Ellenberg explains Candes,center photo, was looking at a image called the Shepp-Logan Phantom, shown on the left, used by computer scientists to work on imaging algorithms. The image replicates the fuzzy one doctors might get if they had insufficient time to do an MRI. Candes applied an algorithm called l one minimization to the image by the press of a computer key. To his amazement the image appeared in perfect definition.

He consulted a colleague at UCLA, Terry Tao, and they developed an explanation of what might have happened. As a consequence of this research MRI machines can now produce images in seconds that used to take up to an hour to produce. The National Science Foundation awarded Candes the $ 500,000 Waterman Prize, its highest honor, for the work in 2006.

Ellenberg gives a commonsense explanation. Suppose one takes a digital image of an object that is composed of one million pixels. In compressed sensing or CS instead of measuring all one million of the pixels, one measure “only” 100.000 pixels leaving an infinite number of ways the remaining 900,000 pixels could be filled in. Candes and Tao turned to the mathematical notion of sparsity. They noted that a picture is made up of a few understandable elements of wiggly lines and blocks of color. In mathematical terms it is sparse in the way a random collection of dots on a page is not.

But Candes and Tao realized that the sparsest image is the one with the fewest number of building blocks and that they could use the l one minimization algorithm to find it quickly.The algorithm takes the blank space and starts trying to fill them in with with large blocks of color. Ellenberg notes that if the algorithm sees a cluster of green pixels it will fill the space between them with a large green rectangle. In areas of different colors it puts down smaller and smaller rectangles or other shapes to fill in the colors. At the end of the process the algorithm creates an image with the smallest possible combination of building blocks whose one million pixels have all been filled in with color. The Wired article, available on the magazine site on the Internet, has an interesting graphic showing the application of the algorithm to a grainy picture of President Obama.

The article notes that Candes and Tao have shown mathematically that the chance the image will be wrong is infinitesimally small. If it is off a bit, a mathematician can tweak the image on a laptop instead of shutting down the young patient’s lungs for an extra minute to keep his breathing still. Ellenberg notes that every interesting signal is sparse, he uses the example of a piano chord, if one can only discern the way to define it. Take what you have and then use l one minimization algorithim to fill in the blanks.

CS also addresses a growing problem, what do we do with all the information that is being accumulated? The February 24 th edition of the Economist has a 14 page supplement on “The Data Deluge.” In a sidebar entitled ” All Too Much, Monstrous Amounts of Data.” the magazine notes that the amount of information is growing at a annual compound rate of 60 %. It cites a study which notes that in 2010 1,200 exabytes of data will be generated. One exabyte is the number two to the power of sixty or ten billion copies of the one hundred and two page magazine. The Large Hadron Collider at CERN generates 40 terabytes of digital data per second. All the catalogued books in the Library of Congress contain fifteen terabytes. In other words, the information generated is more than can be stored or analyzed, so the scientists collect what they can and let the rest disappear. These numbers are beyond normal human comprehension.

Candes sees the use of CS to lighten this load. Compression and decompression algorithms will steadily improve. Perhaps in the future we will store only twenty per cent of the pixels from an audio visual image and then use the algorithms to produce the original should it be needed.

In a sense everything old is new again. In the current movie “The Last Station,” Helen Mirren plays Tolstoy’s ( played by Christopher Plummer) wife. She had worked with him for years on his novels and was able to anticipate his thought processes. In one scene she recounts how he gave her only two letters from a paragraph he was working on and exxpains how using those two letters she was able to construct the entire paragraph, a human sparsity algorithm at work.

Tags: Compressed Sensing

I grew up in Sacramento, and I read an inscription in the State Capitol Building that I subliminally internalized, “Bring me men to match my mountains.” I was born in Nevada which is the most mountainous state in the lower 48 states, measured in the number of mountain chains. My mother was born in Reno, and we travelled across the Sierra Nevada ( the Snowy Mountains) to visit our cousins and grandparents in Reno. So early on I became fascinated by the mountains.

The Sierra Club had a rock climbing section, so I joined members for a few sessions on Indian Rock in Berkeley, and made the hike to the top of Mt. Shasta slightly over 14,000 feet and succeeded in climbing one of the peaks in the Pinnacles region of the Southern Sierra outside of Independence. The banner of my blog shows my summit picture on Mt. Kilimanjaro, the highest point in Africa at a little over 19,000 feet. I joined my friend Perry Massa on an attempt on Mt. Rainier and fell short although Perry, who I refer to as the Shasta Mule because he lives in Redding and frequently climbs on Mt. Shasta, made it.

The wonderful Wikipedia identified the quote for me. Sam Walter Foss was born in Candia, New Hampshire and graduated from Brown University. He became the librarian of the Somersville, Massachusetts Public Library and wrote a poem a day for local newspapers. The “men and mountains” quote comes from a poem he wrote for the Fourth of July 1894 entitled “The Coming American.”

Bring me men to match my mountains

Bring me men to match my plains

Men with empires in their purpose

And new eras in their brains

All of this came back when I read the review of a German movie,  The North Face, which opened this week in the Bay Area. The North Face is the North Face of the Eiger, a climb so sheer and dangerous, that mountaineers refer to the North Face, Norwand in German, as the Morwand, or the Murder Wall. The North Face has received a warm reception in Germany where it revives the classic film tradition of the bergfilme or mountain film, a kind of German equivalent to the American Western.

The Wikipedia states that the first mountain film released in 1903 depicted the ascent of Mt. Blanc by the American climber Frank Ormiston-Smith. But the most important director in the genre was Dr. Arnold Fanck. He made his first motion picture in 1913 and after World War I service purchased a rare Ernemann camera which shot 500 frames per second. He taught himself to shoot on location on an expedition to climb the Jungfrau which he edited on his mother’s kitchen table. He released the film with the title The Wonders of Skiing in 1919, and it became an instant success. The director films a bergfilme on location under actually climbing conditions, variable temperatures and weather and the inherent danger of the mountain climbing environment.

Leni Riefenstahl, a young interpretive dancer, was enamoured by Franck’s 1924 film, Mountain of Destiny, and she convinced him to make her one of the stars of his bergfilme classic, The Holy Mountain, made in 1926. He wrote the film in three days but took over a year to shoot it on location in the Alps. This was the beginning of Riefenstahl’s own film career. Her 1932 film Blue Light caught the attention of Adolf Hitler. She filmed Triumph of the Will in 1934 which is a glorification of National Socialism based on the theme of the return of Germany to the world stage as a world power with Hitler as the True German Leader.

Despite the fact that the film is pure propaganda film critics today still regard it as one of the greatest films in history. Riefenstahl blended music and cinematography, moved the camera, aerial photography, and used telephoto lens to distort perspective. Ironically the bergfilme languished and fell out of favor as World War II approached.

The Eiger is in the Bernese Alps of Switzerland and rises to an elevation of 13,025 and has a railroad tunnel running through it. Two internal railroad station provide mountain viewing. The Swiss guides Christian Almer and Peter Bohren accompanied by the Irishman Charles Barrington climbed the west flank on August 11, 1858. But the piece de resistance of the Eiger is the sheer north wall which rises 5,900 feet over the valley below it. The Wikipedia article notes that since 1935 at least 64 climbers have died on the face earning it the nickname of the Morwand, in German the Murder Wall.

The first ascent of the North Face was made by a four man Austrian-German team of Anderl Heckmair, Ludwig Vorg, Heinrich Harrer, and Fritz Kasparek in July 1938. One of the upper pitches of the climb consists of snow-filled cracks radiating from an ice field that resembles a spider and is referred to as the White Spider. Harrer used this as the title of his still very readable and exciting account of the ascent.

Phillip Stolzl directed the North Face which is the story of a 1936 German expedition to climb the Morwand. In 1936 the Alpinists considered the Eiger North Face to be the “last problem of the Western Alps. The Nazis wanted Germans to scale the peak as propaganda coup for the upcoming Berlin Olympics. The peak conquerors would appear at the Olympics as tangible symbols of Aryan supremacy. The challenge was taken or forced upon two young German soldiers who were lifelong climbers from Berchtesgarden, Toni Kurtz and Andi Hinterstoisser. The two reached the mountain only to find a team of rival Austrian climbers and the German press in place. A portion of the climb shown in the picture at the left is today known as the Hinterstossier Traverse and graphically illustrates the difficulty of the climb.

I will not spoil the movie by revealing the story. I have not yet seen the movie myself. But one sentence from a review establishes the theme of the movie for me”…(B)ut when they bust out their period gear (pitons, ancient canvas bivvy sacks, natural-fiber ropes) they seem convincing in their use of ancient techniques. Relying entirely on an arsenal of knots and hip belays, you realize how soft these old-school hardmen make modern climbers look.” Today the slopes of Mt. Everest can be as crowded as the Santa Monica Freeway at rush hour populated by climbers who have paid thousands of dollars to guides to get them up the mountain with maximum use of technical gear and oxygen tanks. I am looking forward to this acclaimed movie version of the battle of man and Nature set against the backdrop of the looming World War.

While a new ballot initiative that was the subject of my February 14, 2010 post poses a challenge to California’s movement to alternative fuels, a smaller state in the mid-Pacific is making great strides toward that goal with its own program. On a trip to the Big Island in November I made a visit to the National Energy Research Laboratory of Hawaii Authority located on 877 acres near the Kona Airport. The operators of the facility now carefully choose among the private venturers who propose to use some of the remaining acreage.

An article in the Los Angeles Times reports that some 42 green private-sector business now call the Lab home. These ventures range from a business devoted to making bio fuel from algae to solar mirrors to wind turbines whose blades spin parallel to the ground.

Hawaii has even more ambitious green goals than California. The state has pledged to obtain 40 % of its energy from renewable sources and to obtain another 30 % from energy efficiency sources by 2030 which contrasts with California’s goal of getting one-third of its energy from renew-ables by 2020. Hawaii may have a more doable program. The state already has high energy costs,so the price of renewable energy sources may be competitive with existing sources. The state gets virtually all of its energy from the importation of 51 million barrels of oil annually. Any rise in sea level from climate change would endanger part of the islands as would more violent storms brought on by climate variability, so climate change poses a direct threat.

The Hawaiian Islands are home to 1.3 million people so the “greening” of Hawaii will not make a great dent in the world’s carbon emissions. But the Islands have ample solar, geothermal, wind, and wave resources. The pictures above show a solar facility at the lab and wind turbines on the Parker Ranch that occupies a large area of the Parker Ranch on the Big Island. So Hawaii may be able to provide an example of what can be done at an economically reasonable cost.

In previous posts I have made it clear that I believe global warming is a reality that must be confronted. But this has been a difficult week for those who share my view. On February 11 there was snow on the ground someplace in all of the 50 states except Hawaii, and a group constructed the igloo shown in the picture on Capitol Hill. Does all that snow mean that global warming is a fraud?

No. An article in the Los Angeles Times notes that the scientifically verified warming over the last century was one degree Fahrenheit which is not enough to eradicate snow in the mid-Atlantic states. As I have noted in previous posts, weather in not climate. Weather is variable. There would be extreme highs and lows even within a general warming trend.

Many climate models also suggest an increase in snowfall. There is more moisture in the atmosphere. Water vapor is a greenhouse gas. This fact will lead to more rain in warmer conditions and more snow in colder conditions. The article quotes Jay Gulledge, the senior scientist for the Pew Center on Global Climate Change. He notes that snow is produced when cold air and moisture meet, something that should happen with increasing frequency as the world warms.

In California the climate wars dramatically escalated this week. Perhaps the landmark achievement of Governor Schwarzenegger is AB 32 (Assembly Bill 32) designed to decrease the emission of greenhouse gases by a variety  of means including an increasing reliance on clean, non fossil fuels. Last week a group of Republican politicians  and conservative activists launched a campaign to put a measure on the ballot which would suspend the implementation of the bill until unemployment in California fell to 5.5 %, a level last seen in California in 2007. The current rate is 12.4 %, one of the highest in the nation.

The prospects for the success of the iniative seem high. A survey by the Pew Reseach Center shows that the percentage of the public that considers global warming to be a high stands at 28 %, a drop of ten points from 2007. The survey found that people are most concerned about jobs and the economy. The two GOP gubernatorial candidates, Meg Whitman and Steve Poizner, support the initiative, in alliance with Tea Party organizers who paint the legislation as job killing interference in the economy. The Wall Street Journal has also endorsed the measure.

The real problem, I believe, is that the debate will be uniformed and dyspeptic. California’s non-partisan Legislative Analyst reported that the rollback would increase short-term profits for some businesses but would dampen investments in clean technology and green jobs. In a study done last December the San Francisco think tank Next 1o reported that jobs in California green businesses increased 36 % from 1995 to 2008 while total employment increased 13 %. The East Bay cities of Fremont and Milpitas present the dilemma in microcosm. Solyndra is building a $ 535 million dollar plant with a Department of Energy guarantee in Fremont to build solar panel. The NUMMI auto plant in Milpitas, formerly a joint venture of Toyota and General Motors and the last remaining auto manufacturing plant in California, is closing. There is nothing to indicate that the suspension of AB 32 would preserve this or other traditional “smokestack” industries.

Mary Nichols, the chairwoman of the California Air Resources Board, says that passage of the initiative would “…put all our efforts at energy efficiency and renewable energy in the deep freeze for a long time.” But the article quotes two Los Angeles talk radio show hosts as characterizing AB 32 as the “global warming final solution act” promoted by “fascist, Nazi” officials. Assemblyman Dan Logue (R-Marysville), one of the initiatives sponsors is quoted as stating,”We are on fire.”

Unfortunately the issues are complex and require study and evalutaion to make an informed decision. But as most ballot initiatives, this one will likely be decided on the basis of overly simplistic television sound bytes.

I like to quickly leaf through each new weekly edition of Nature when I receive it. In the February 4, 2010 issue a picture of an attractive woman on page 610 and a mid article color picture of human cells caught my eye, so I read the book review by Steve Silberman, who writes for the New Yorker and Wired, of a new book by science writer, Rebecca Skloot, The Immortal Life of Henrietta Lacks. The book tells one of the most amazing science stories that I have “never heard.”

I went to my local library to check the book out. The library had ordered five copies, a large number for a science book, and the computer told me that I was 62 in line to receive one of the five copies which indicated to me that other people were as intrigued as I. Ms. Skloot bases her book on an article she wrote for John Hopkins Magazine in April 2000, “Henrietta’s Dance.”

The attractive woman in the picture was, and in a certain sense still is, Henrietta Lacks, who was born Henrietta Pleasant on August 18, 1920 in Roanoke, Virginia. She married her first cousin David Lacks  and the couple moved in 1943 to Baltimore County, Maryland where the couple had five children. As Ms. Skloot relates in the article, in February 1951 Henrietta found blood on her underwear and went to Hopkins Hospital for treatment. The attending physician, Howard Jones, found a supple tumor on her cervix which bled when he touched it. He cut out a quarter sized piece of the tumor and sent it to the lab and Henrietta home.

The lab reported that the tumor was malignant and Henrietta returned to the hospital eight days later. The Hopkins’ physicians attempted to kill the growth by coating it with radium, but before they did that they took another another sample which they sent to the hospital tissue lab where it reached Howard Gey, the head of tissue research, and his wife Margaret. The Geys had been looking for cells that would live indefinitely outside the human body to continue their cancer research. They had met failure for two decades when Richard TeLinde, the Hopkins head of Gynecology, suggested that they look at cervical cells which he also wanted for his own research.

When Howard Gey received the cell sample from Henrietta Lacks, medicine changed dramatically. Her cells stuck to the sides of the test tube and consumed the medium in which they were placed and became thicker and thicker. But this research miracle was also a human tragedy. The cells overwhelmed Henrietta’s body in the same manner they took over the test tube. Within months the cells coated every organ in her body, and she died on October 4, 1951. On that very day George Gey appeared on television with a vial of her cells, and announced that with the help of the cells for research he and his colleagues hoped to find a cure for cancer.

Her family returned Henrietta’s body to Lackstown in the town of Clover in Halifax County, Virginia in a family cemetery. The Lacks family had received the land from the family of which they had been slaves. Henrietta’s mother is the only family member in the cemetery whose grave is marked with a headstone. Henrietta’s grave did not receive a headstone although the family believes that she was buried within a few feet of her mother’s grave.

Gey and his colleagues used the test cells to grow strains of the polio virus and identified the strain that was causing polio or infantile paralysis. Jonas Salk and his researchers developed a vaccine and the National Foundation for Infantile Paralysis mass produced the cells for testing the vaccine before it was used on humans.

Gey sent samples of the cells to researchers around the world for use in research on leukemia, radiation, and genetic mutation. Ms. Skloot notes ironically that although Henrietta never travelled farther than from Virginia to Baltimore her cells travelled to nuclear test sites throughout the world and even multiplied in test tubes in a space shuttle above the earth.

The story does take a darker turn. The researchers had asked her husband David if they could take a sample and he let them do it. His understanding was that the researchers would use the cells to determine if his and Henrietta’s children were susceptible to cancer. But the family had no idea of the uses to which the cells had been put or even knew that they were alive until Henrietta’s daughter in law heard about the cells by chance from a scientist at a dinner party some 24 years after Henrietta’s death There is also some evidence that the scientists attempted to preserve Henrietta’s anonymity by referring to the cells as “Helen Lane” or “Helen Larson” cells.

In another bit of irony the very strength of the HeLa cells,they reproduce an entire generation every 24 hours, has proved an impediment to biological science. The HeLa cells have contaminated other cell cultures.

In a February 18, 2009 blog post on the blog “Darwin’s Students” Jo Kirkham notes a pair of ethical dilemma’s raised by the HeLa cells. One issue is whether David Lacks gave anything resembling what we would no recognize as informed consent based on the very limited information he was given about what would be done with the sample. The second is whether the family should have in any way shared in the proceeds from the commercial use of Henrietta’s cells. The Wikipedia article on the HeLa cells notes that in the California Supreme Court case of Moore v. Regents of the University of California, the California Supreme Court held that a person’s discarded cells and tissue are not their property and can be commercialized.

Mr. Silberman ends his review with a poignant vignette from the book. Ms.Skloot apparently became close to Henrietta’s daughter Deborah, who was able to view some of the cells under a microscope at Hopkins. He relates that when Deborah looked at the cells she whispered,” They’re beautiful.” I shall await my turn to read the book. Ms. Skloot is scheduled to appear at the Buhler Alumni Center at UC Davis on April 24 at four in the afternoon. You can find the details of her extensive book tour on her website www.rebeccaskloot.com.

Tags: Medecine, Rebecca Skloot

In June I did a post on the National Ignition Facility (NIF) at the Livermore National Laboratory where scientists have built the world’s most powerful laser. The laser is in a building the size of three football fields and ten stories high. Inside the building the Livermore scientists have used hundreds of optical amplifiers, beam splitters, and other devices to split a normal laser beam 192 ways and to boost the power of the combined  beams to 1.8 megajoules. The joule is a unit of energy equal to .2388 calories or .0009481 British thermal units. One British thermal unit is the approximate equivalent of the energy in a single match head.

The 192 beams are fired at a “nut” in the form of a sphere of beryllium the size of a peppercorn. In later experiments the sphere will contain small amounts of the isotopes of hydrogen, deuterium and tritium (D-T). The power of the laser will heat the capsule so quickly that it will explode propelling the D-T mixture inward to the center crushing it to a temperature and pressure greater than that found in the core of the sun. As the nuclei in the very center fuse, the energy will cause all the D-T mixture to burn in a flash of energy which will hopefully produce more energy than was placed into the capsule in the first place.

In an online study published in Science scientists describe shots of 0.7 megajoules about 40 % of the beam’s capacity. The team must focus the power of the beam on the capsule symmetrically so it explodes implodes evenly. The laser output is in the ultraviolet spectrum but to get the best implosion the scientists need x-rays. To do this they focus the beams into the center of a gold cylinder about the size of a pencil eraser called a hohlraum. By shining the beams through holes in the end of the hohlraum, they make its inner surface hot enough to produce x-rays which cause the capsule to implode. In the experiments they produced a temperature inside the hohlraum of 3.3 million kelvins which was exactly what their models had predicted.

There is a peril in this method. The gold atoms kicked off the wall of the hohlraum can create a plasma that interferes with the incoming beams in unpredictable ways. The NIF team tuned the beams to successfully keep these laser-plasma reactions at an acceptable level.

The next problem to be faced by the NIF team is to ensure that the implosion of the fuel will be smooth and symmetrical. This problem has yet to be addressed because the first shots have been at empty capsules. As of yet, the team has not machined the capsule to the same precision as will be used for ignition shots. The team has currently stopped experiments at the NIF in preparation for an ignition campaign to begin in May. If the campaign goes well, the scientists will decide in July whether to go for ignition in October. One of the scientists, Dr. Robert McCrory of the Laboratory for Laser Energetics at the University of Rochester does not rule out the possibility of successful ignition this year but deems it unlikely.

Tags: Ignition Fusion

One of the conceits of the Back to the Future film series was that the protagonist played by Michael J. Fox could use a time machine to return to the past and take actions which would alter the future. This idea is expressed in these lines of doggerel:

There once was a young lady named Bright

Who travelled at the speed of light

She left home one day in a relative way

And returned the previous night.

But could the nearly superluminal  Ms. Bright really change the day she left if in fact she arrived back at the day before? The Rubaiyat of Omar Khayyam would say no:

The Moving Finger writes;and having writ,

Moves on: nor all the Piety nor Wit

Shall lure it back to cancel half a Line,

Nor all thy Tears wash out a Word of it.

Why does time appear to us to move only in a single direction? This is the subject of a new book by Sean Carroll, a theoretical physicist at Cal Tech, From Eternity to Here: The Quest for the Ultimate Theory of Time, and he resorts to the concept of the Arrow of Time. The Wikipedia attributes this term to the British astronomer Arthur Eddington. He explained the flow of time in terms of the study of atoms, molecules, and bodies. Carroll uses the example of an egg and an omelet. We can turn an egg into an omelet but we cannot return the omelet back into the eggs that compose it.

The scientific name for this phenomenon as expressed by the Second Law of Thermodynamics is entropy, or the degree of disorderliness of a system. Carroll uses the example of neatly stacked pile of papers. The pile is orderly,so it has low entropy. If I scatter the pile across my desk it has a higher state of entropy of disorderliness. The macroscopic world is characterized by irreversibility. Heat does not flow spontaneously from cold to hot objects. The Second Law of Thermodynamics in its simplest form holds that the entropy of any system left to its own devices will either increase or remain the same. The Arrow of Time comes down to the fact that the past is characterized by lesser  entropy and that the future is characterized by greater entropy. The disorderliness of the universe increases and in physical terms is described in a decrease in the amount of usable energy. The ultimate outcome is a cold lifeless universe.

This is the T.S. Eliot view of a world that ends with a whimper, and not a bang. The Motion Picture Academy of Arts and Sciences announced the 2009 Academy Award nominations this week. As I have in previous posts I would note a movie that illustrates some of these concepts, in this case the 2000 psychological thriller Memento. Lennie, the protagonist of the film has anterograde amnesia, which impairs his ability to remember recent events as the consequence of a physical attack. Two men attack and kill his wife. He kills one of the attackers but the other strikes him and the trauma results in the amnesia. Lenny has to take notes to himself to remember what he is learning and observing as he tracks down the other killer.

The film uses two sets of alternating time frames. The black and white frames progress from the future to the past, and the color sequences go in reverse order from the future to the past. In the opening black and white frame Lenny displays the photo of a man shot in the head. The color sequences describe the investigation that has led Lenny to identify the man who attacked him and to kill him by shooting him in the head. The two sequences end at the same point. The audience gets to see the Arrow of Time pointing in two directions and to follow the Arrow in both directions as it tells one common story.

I liked the movie because of its originality even though I admit that I did not completely understand it. I have reproduced the chart from the Wikipedia that contrasts the sequences and which would make the film more understandable on a second viewing.

Tags: Entropy, Sean Carroll

I have posted on Barsoom, which is the word that Edgar Rice Burroughs used for Mars. This is an example of a constructed language or a “conlang.” A conlang, per the Wikipedia, is one whose phonology, grammar, and or vocabulary have been consciously devised by an individual or group, instead of having developed naturally. Two recent events have sparked a new interest in conlangs. The first is a charming extremely readable book by Arika Okrent, In the Land of Invented Languages, Esperanto Rock Stars, Klingon Poets, Loglan Lovers, and the Mad Dreamers Who Tried to Build a Perfect Language. The second is the blockbuster movie by James Cameron, Avatar, which features the conlang, Na’vi, a product of the USC linguistic professor  Paul R. Frommer for use not on one of the planets in our solar system such as Mars but the exoplanet Pandora.

Colangs have long had a place in the media. J.R. Toliken created the Elvish language for use in the Lord of the Rings trilogy. Linguist Mark Okrand created Klingon for use in the movie Star Trek III. Ms. Okrent notes that there is a Klingon Language Instiute on the internet and that one can take classes and the Institute will certify learners in various levels of proficiency. The Wickipedia describes a German Trekie who calls himself Klenginem who has posted Klingon versions of Eminem rap songs on You Tube.

I just viewed Avatar and was quite surprised. It is a good movie driven by what drives all good movies a great story. The visual effects add to the enjoyment of the movie, but without a good story visual effects can be wasted pyrotechnics. The most interesting thing about the Pandaroans’ use of Na’vi is that it works. The language is not jarring and seems natural. Cameron wisely limits its use. At most two or three sentences at a time will appear as subtitles. When the hero, Jake Sully, makes a speech to the Pandorans in one of the climactic scenes, he speaks in English and the Pandoran leader translates into Na’vi so the audience does not have to read large chunks of subtitles which would slow the action at a critical point.

In a Los Angeles Times article, Frommer says that when Cameron approached the USC linguistic department, Cameron had already formulated about thirty Na’vi words to give the linguists an idea of what he was looking for. Frommer prepared five sets of sound palattes of words and phrases which had no meaning but had the cadence and feel of languages. Cameron picked one of the palattes that without tonal differences or variations in vowel length.

Frommer excluded the sounds buh,duh,guh,chu, and su. He added ejectives or popping sounds found in North American languages and languages in parts of Africa and Central Asia. In the article Frommer says that what one leaves out of a language can be as important as what he puts in. The absences can sometimes define a language. Based on his work on the film and an accompanying video game, Frommer has created about 1000 words and will continue expanding and building upon the language. There is a quick flash in the film of a book that looks something like a Lonely Planet volume that has the title Na’vi.

Frommer said that actress Zoe Saldana was particularly adept at picking up the language but that other actors struggled with it. Since it is clear that there will be a second movie, one expects that the Na’vi dialogue will be expanded in the second film and that a coterie of the film’s fans will know the language well enough to dispose with the subtitles. Perhaps there should be a special category in this year’s Academy Awards for Best Motion Picture colang.

Tags: Constructed Language, Linguistics

The Wikipedia says that the Polish geneticist Waclaw Szybalski first used the term “synthetic biology” in 1974. He wrote a comment in the journal Gene in 1978 about the award of the Nobel Prize in Physiology or Medicine in which he noted “…the new era of synthetic biology where not only existing genes are described and also analyzed but new gene arrangements can be constructed and evaluated.”

On January 27, 2010 the Lawrence Berkeley National Laboratory announced that a team  of scientists lead by chemical engineer Jay Keasling of the University of California at Berkeley  had engineered a strain of the common Escherichia coli ( E. coli) bacterium to make bio diesel directly from biomass with no other chemical modification at the Lab’s Joint BioEnergy Institute in Emeryville. The team manipulated the genes of E. coli to chew up plant derived sugar to produce diesel and other hydrocarbons directly. The E. coli secretes the bio diesel which floats to the top of a fermentation vat so their is no need for distillation or any other purification process or any need, such as when algae is used, to break the cell to get the oil out.

The team cloned genes from Clostridium stercorarium and Bacteroides ovatus which thrive in the soil and in the guts of plant eating animals. These bacterium produce enzymes which break down cellulose. They added short bits of genetic code in the form of amino acid sequences that instruct the E. coli to break down the plant cellulose to turn it to sugar. The E. coli then turns the sugar into bio diesel. The process can be used to produce hydrocarbons with 12 carbon atoms in them but cannot yet produce the shorter chain hydrocarbons of gasoline which has 8 carbon atoms. That work is continuing.

E.coli is hardy, fast growing, and tolerates genetic changes easily. Ideally a producer will ferment a batch of bio fuel from one colony of E. coli and then dispose of the colony and start anew. This minimizes the chance of mutations which might occur from continuous sub culturing of the microbe. But there are problems. E. coli is not the most efficient producer of bio fuel, producing only about 10 % of the theoretical maximum yield from sugar. Keasling would like to reach 80 to 90 % and use a large scale production porcess such as 100,000 litre tanks to make the process commercially viable.

A September 28,2009 article in the New Yorker, A Life of Its Own,” chronicles the way in which Keasling started his work by using synthetic biology to create artememisinin, an anti- malarial drug produced from the sweet wormword herb. His team dismantled several different organisms and then cobbled together portions of their genes to create a custom built package of DNA for producing the drug. He created a new company, Amyris Biotechnologies,  to refine the organism. Within a decade Amyris had increased the amount of artememisinin a single cell could produce by a factor of a million and brought down the cost of a course of treatment from ten dollars to less than a dollar.

Keasling and his team have successfully translated this process into the production of a bio fuel with a simple bacterium. However, synthetic biology is not universally triumphant as noted by science writer Roberta Kwok in a News Feature in the January 21, 2010 edition of Nature entitled “Five Hard Truths for Synthetic Biology. ” She notes that the analogies between biology and hardware engineering can be exaggerated. She quotes Rob Carlson of Biodesic in Seattle who notes, ‘ There are very few molecular operations that you understand in the way that you understand a wrench or a screwdriver or a transistor.’

Ms. Kwok lists her five hard truths:

1. Many of the parts are undefined- She notes that a “gene part” can be anything from a DNA sequence that encodes a specific protein to a promoter that facilitates the expression of a gene. Many of these parts have not been tested and even if they have their performance can change in different cell types or under different laboratory conditions. She notes that the frequent depiction of the process as equivalent to the assembly of Lego blocks is a great simplification.
2. The circuitry is unpredictable-Even if the scientists know the function of each part the parts may not work as expected when put together. Computational modelling may be of assistance in predicting cell behavior. But the cell is a complex, evolving thing very different from a transistor.
3. The complexity is unwieldy-As the biological circuits grow, the process of constructing and testing them gets more difficult. She notes that Keasling estimates that it has taken about 150 person-years of work to take the E. coli process to where it is.
4. Many of the parts are incompatible-Synthetic genetic circuits can have unintended effects on their host cells such as making them sick or slowing their growth.
5. Variability crashes the system-The new genetic circuits must function reliably, but molecular activities in cells are prone to random fluctuations and over the long term random genetic mutations may kill a cell’s function altogether.

Despite achievements like that of Keasling’s team, Ms. Kwok concludes that synthetic biology may have been overhyped. She notes that the field has yet to produce much of practical use. She observes that some scientists believe that as more people tinker with biological parts the field could progress faster, but ends her article with another quote from Rob Carlson,’ It’s a question of whether the complexity of biology yields to that kind of  an effort.”

Tags: Synthetic Biology

Anyone who reads articles related to global warming and climate science will come across this large word,”anthropogenic.” The term anthropogenic designates an effect or object resulting from human activity. The term was first introduced as “anthropocene” in the mid-1970s by the atmospheric scientist Paul Crutzen.

In previous blog posts I have written about “climate-gate.” Someone leaked one thousand e-mails last November from the Climate Research Unit of the University of East Anglica. Critics of the idea of global warming and climate change took comments from some of these e-mails out of context and arranged them in a way to suggest that the proponents of global warming and climate change and global warming were hiding or misrepresenting data that would disprove these ideas. Again in an early post I noted that several reporters from the Associated Press reread all of the e-mails and concluded that in their totality the e-mails established the reality of anthropogenic change, global climate change induced by human activity.

The January 21, 2010 issue of the science journal Nature has an instructive News Feature entitled “The Real Holes in Climate Science” that candidly deals with the problems of climate science but which at the same time notes that these difficulties do not rebut the conclusion that climate change is happening and is having unwelcome effects on the habitability of the planet and needs to be dealt with.  The four areas of difficulty are regional climate prediction, precipitation, aerosols, and paleoclimatology.

Regional Climate Prediction

Scientists use general circulation models (GCM) that represent the physical processes in the atmosphere, oceans, ice sheets, and land surfaces. These models have a resolution of about 1 to 3 degrees in longitude and latitude, which means that they are too coarse to give guidance in many cases. A climate scientist at the University of Arizona might use a climate model which would be quite accurate with respect to the American Southwest as a whole, New Mexico, Arizona, Southern California, and Southern Nevada, but might not be of great assistance in forecasting climate changes in a specific location within that area such as Yuma, Arizona.

Scientists can try to extrapolate from the larger models to these specific areas, but as the article notes, zooming in from the GCMs creates the risk of magnifying any weakness in these models. The downscaled models have difficulty in dealing with areas of complex topography such as where mountains create a wall between two distinct climate zones. In the fifty miles that separate Lake Tahoe and Carson City, Nevada the Sierra Nevada Mountains create a rain shadow that differentiates an alpine climate from a desert climate.

Climate models also make different assumptions about greenhouse gas emissions. The climatic model of California will be much different if the state transitions successfully to alternative energy sources and reduces the carbon footprint of its residents by greater reliance on public transportation than if increased power demands are met by  construction of more fossil fuel power plants and the use of the gasoline powered automobile continues as the main form of transportation.

The article notes that regional simulations are not useless as long as researchers recognize their limitations as they improve their methodologies.

Precipitation

Rising global temperatures will accelerate the hydrological cycle. This change will dry subtropical areas and increase precipitation at higher latitudes. All the models draw this conclusion, but the models diverge wildly on their predictions of future precipitation, especially winter precipitation from which most water supplies are replenished. The existing models also seem to underestimate the amount of precipitation change which has already occurred, making future prediction more difficult. To improve predictions in this area scientists are trying to improve their simulation of climate variable such as the formation and dynamics of cloud formation. They are also using high resolution satellite observations to validate and improve the realism of their models.

Aerosols in the Atmosphere

Despite decades of research climate scientists are not clear on the effect that aerosols have had on temperature and rainfall. Aerosols can have different effects. Black carbon absorbs sunlight and has a warming effect that can also inhibit rainfall.Sulphates reflect sunlight and have a cooling effect, so the net effect of aerosols is not known. Aerosols may also alter the formation and lifetime of low level clouds which reflect sunlight and cool the planet’s surface. NASA will launch the Glory satellite in October which will have a solar- irradiance monitoring capability that will greatly increase the amount of available data.

Paleoclimatology

Reliable temperature records for most locations go back at the most 15o years. For previous time scientists must rely on data from sources such as tree rings, coral reefs, lake sediments, glacial movements, and historical accounts. Growing trees develop rings that reflect temperature and moisture patterns. Critics have decried the use of these proxy records. One issue that has arisen is “divergence.” In a few northern sites in the Northern Hemisphere scientists have tracked tree ring growth with temperature records. For most of the Twentieth Century these methods agreed. But during recent decades there has been an unexplained divergence. The article speculates that when temperatures reach a certain threshold tree growth responds differently. However, the “divergence” problem is restricted to a few northern locations and is not ubiquitous there.

The main point of the article is that the conclusion of the Intergovernmental Panel on Climate Change that most of the global warming observed since the mid-twentieth century is very likely to be caused by human caused increases in greenhouse-gas emissions is based not a single piece of evidence but multiple lines of evidence.

The article also contains a text box setting forth what it calls Enduring Climate Myths:

• Climate models cannot provide useful information about the real world-The article describes the uncertainties in such models. But existing models can provide useful general information, and they unconditionally predict a warmer world.
• Global warming stopped ten years ago-Weather is not climate. Natural variations can cause temperatures to vary from year to year. Although the mean global temperature did not rise as rapidly in the last decade as in past decades,the decade just ended was the warmest on record.
• Temperatures were higher in pre-industrial times-Proxy records indicate that the second half of the twentieth century was warmer than any other half century in more than a millennium. There were warmer periods in the past of the planet do to orbital and geological conditions but the warm spells in the past cannot be attributable to human activity as the present one can.
• A few degrees of warming is not a big deal-While Earth may not have an optimum temperature, modern societies are adapted to the weather patterns and sea levels of the past Milena. Increases in sea levels and draconian changes in growing and precipitation patterns brought on by global warming will create at the very least severe adaptation problems for human societies.
• Measured increases in temperatures really reflect the growth of cities around weather stations-Climate researchers have taken great care to correct for variables arising from temperatures taken at rural and local locations. But some of the most dramatic climate change has taken place in the most isolated areas such as the Arctic and the Antarctic Peninsula. Measurements also show temperature increases on the ocean surface and in the deeper marine layers.

The evidence is unequivocal that if changes are not made in half a century there will be a “Hot Time on the Old Planet Today” and that will not necessarily mean that the human race and the planet are enjoying a festive party.

Tags: Climate Change, Global Warming