Monday, October 25, 2010

Newspaper Circulation figures

Media circulation figures out today, October 25, 2010, indicate the Wall Street Journal led the country in increasing circulation numbers. Only the Dallas Morning News also increased circulation numbers in "recent months." Most newspaper declined in circulation. However all the major New York City newspapers posted strong circulation numbers. The New York Times was number 3. I can't tell if the Dallas paper is behind a pay wall, or not. January the NYT is going behind a paywall, though not utterly.  We'll see how that works out. I may have to start getting my local news from another country (The Guardian, for instance.) Of course the WSJ is already behind a paywall. 


In today’s Media Decoder section, Jeremy W. Peters of NYTimes.com shared some promising news for Wall Street Journal readers: WSJ was just one of two major newspapers in the nation to improve daily circulation in recent months. The Audit Bureau of Circulations reported a 5 percent drop in weekday circulation for over 600 newspapers from April to September,however The Journal witnessed a 1.8 percent rise in circulation and an average weekday distribution of more than two million (including 450,000 digital subscriptions). According to a company press release, The Journal upped circulation revenue by 7 percent compared to the April-September 2009 period.

While The Journal boasted the top weekday readership totals in the country, some other New York-based titles maintained high circulation numbers despite the slow decline of newspaper industry in the U.S. Other than WSJ, The New York Times (third), New York Daily News (sixth), and New York Post (seventh) ranked among the country’s top seven papers in terms of weekday circulation. Although these newspapers — along with other heavyweights like USA Today and Los Angeles Times — sold plenty of issues over the past six months, The Journal was joined only by The Dallas Morning News in posting distribution growth since this past spring.

Friday, October 22, 2010

Mysteries of Planetary Evolution

Here is a lovely glimpse of the kinds of issues involved in modeling a history of our own solar system. I could hardly bear to excerpt it, from the current Sky and Telescope online issue. (Nov. 2010). The article purports to answer some dilemmas. For some the interest in is the problems we did not know existed.

Our "New, Improved" Solar System

...
NASA's solar system
As portrayed on the home page for the NASA/JPL Photojournal, our solar system is an orderly arrangement of planets orbiting the Sun.
NASA / JPL
Compared with the systems of planets being found around other stars, our solar system is an orderly place, with each planet tracking around the Sun in a stable, roughly circular orbit. For centuries, the planets' long-term stability has been taken as evidence that they formed where they are now, sucking up gas, dust, and larger building blocks from the protoplanetary disk around them until reaching their final sizes.

But dig a little deeper, and you find serious problems with that simplistic view. For example, Uranus and Neptune should have ended up much smaller and less massive, because billions of miles from the infant Sun the protoplanetary pickings were slim and the assembly process too slow. Conversely, Mars formed in the fat of the disk and should have ended up at least 10 times more massive than it is today. And no one really understands the asteroid belt's existence — particularly why it's crudely divided into rocky bodies (called S types) nearer the Sun and dark, carbon-dominated hunks (C types) farther out.

Dynamicists solved the Uranus-Neptune dilemma several years ago by positing that the four giant planets were initially a much closer-knit family, coming together in a cozy zone 5 to 12 astronomical units from the Sun.

Evolution of outer planets' orbits
Computer models suggest that the outer planets formed within a narrow range of heliocentric distances, 5 to 12 a.u. from the Sun (vertical scale, lower left). After about 2 million years, however, the orbit of Saturn entered a 5:3 orbital resonance with Jupiter and became more eccentric. Neptune, which formed closer in than Uranus did, has repeated close encounters with all three of the other planets and is eventually ejected outward to its present location.
A. Morbidelli & others / Astronomical Journal
The Big Four coexisted peacefully at first, but after a couple of million years things got ugly. Jupiter's gravity jostled Saturn into an unstable, wide-swinging orbit, triggering a chain reaction of close encounters that ultimately threw Neptune and Uranus out to the distant depths of interplanetary space they now occupy.

Theorists now have computer models that get the outer solar system to come out right, more or less, but they're still vexed by the inner planets. The thorny problems of a too-small Mars and a compositionally stratified asteroid belt remain.

Worse, discoveries of other solar systems were revealing radically different inner-planet architectures: "hot Jupiters" whirling so close to their suns that a year for them is just days long, and massive planets in orbits so wildly out of round that any lesser worlds they encountered would have been tossed out. Given all the disorder so common among the exoplanets, it's remarkable that the Sun ended up with any small, close-in worlds at all.

But there's been a breakthrough in modeling our solar system's formation, details of which emerged at last week's meeting of the American Astronomical Society's Division for Planetary Sciences. It turns out that getting four right-size terrestrial planets and the right kind of asteroid belt is a snap — but it requires dramatic new thinking about the path Jupiter (and Saturn) took getting to their current locations.

Pulsar planet
Nobody really knows what the planet system orbiting pulsar B1257+12 would look like if viewed up close, but here's a plausible depiction. Three terrestrial-mass planets orbit the pulsar at close range; an asteroid-mass object (not pictured here) orbits much farther out. Click on the image for a larger view.
Robert Hurt
Solving for Mars

The stage for this revolution was actually set last year, when Brad Hansen (University of California, Los Angeles) tried assembling the inner solar system an entirely new way. He took a cue from the one other place known to have close-in, Earth-size planets: the system surrounding the millisecond pulsar B1257+12. Discovered in 1991, these pulsar planets are often overlooked because their host "star" is so extreme.

Prior computer simulations assumed that the inner planets accreted from a dense, massive belt of mile-wide planetesimals extending almost out to Jupiter. But invariably the outcome was a too-massive Mars and jumbled mess in the asteroid belt. However, Hansen realized that PSR B1257+12's planets must have assembled from a limited disk of hot material closely surrounding the pulsar.

Modeling the inner planets
By assembling the terrestrial planets from a narrowly confined disk (gray band), simulations yield a distribution of inner planets (open circles from 23 computer runs) that closely matches the actual arrangement (colored dots). Mercury's upper value assumes the planet formed with the same iron abundance as other terrestrial planets'.
Brad Hansen / Astrophysical Journal
When he tried that approach withour solar system, starting with a disk confined to just 0.7 to 1.0 astronomical unit from the Sun,voilà! — his computer runs routinely coughed up sets of planets with bigger ones (think "Earth" and "Venus") in the middle and smaller ones ("Mercury" and "Mars") near the inner and outer edges.

So why should Earth and its immediate neighbors have formed from such a limited disk? Hansen had no clue when he published his resultslast year. "In my paper I freely admit the choice was ad hoc," he allows. But it worked — far better, in fact, than any of the previous trials.

Meanwhile, the outer-planet crowd had wondered how Jupiter managed to avoid becoming a close-in captive of the Sun, as so many other beefy exoplanets had. On paper, tidal interactions between the King of Planets and the Sun's protoplanetary disk should have drawn Jupiter inward to its doom, or nearly so.

As early as 1999, however, theorists Frederic Masset and Mark Snellgrove (then at Queen Mary College) showed that Jupiter would have indeed migrated inward — but only until it linked up with Saturn in a 3:2 resonance, that is, with the two spaced such that Jupiter completed three orbits for every two of Saturn's. At that point the pair would have reversed direction and headed outward. ...
Hansen's shot-in-the-dark simulations, combined with the realization that the gas giants could have migrated both inward and outward, gave solar-system modelers a "Eureka!" moment. What would have happened, they wondered, if young Jupiter had ventured much closer to the Sun than where it finally ended up?

Jupiter and Saturn on the move
This simplified sequence shows how the in-and-out migration of Jupiter and Saturn early in solar-system history could have created a truncated disk of material from which the inner planets formed. Their movement also created overlapping zones of rocky (S) and carbonaceous (C) bodies in the asteroid belt.
Kevin Walsh / SWRI
The amazing answers came to light at last week's meeting. Kevin Walsh, who'd worked this problem with Alessandro Morbidelli while post-docing at Côte d'Azur Observatory in France, ran computer simulations that put Jupiter initially 3½ a.u. from the Sun and allowed it to creep inward to 1½ a.u. (about where Mars orbits now). The results were remarkable in their breadth and significance.

First, Jupiter's gravity would have forced the small stuff in its path inward too, creating a perturbation-driven snowplow that piled all the rocky planetesimals into a mini-disk with an outer edge 1 a.u. from the Sun. According to presenterDavid O'Brien (Planetary Science Institute), a member of Walsh's team, Jupiter took only 100,000 years to drive inward to 1½ a.u.and another 500,000 years to reach its current orbit, 5.2 a.u. from the Sun.

Second, the new computer runs confirmed what Hansen had already shown: a mini-disk of rocky material extending only to 1 a.u. provided just what's needed to assemble four terrestrial planets — and a Mars that's not too big.

At the meeting, David Minton and Hal Levison (Southwest Research Institute) described their own simulations using a truncated mini-disk, and they come to much the same conclusions. One key variation is that, in the Minton-Levison runs, Mars forms well within the disk and migrates to its outer edge and beyond.

This could be a good thing, because a moving Mars would provide the gravitational perturbations needed to kick iron-rich planetesimals out of the disk and into the inner asteroid belt, where they're commonly found today. "The original locations of Mars in the [disks] I calculated were quite variable," Hansen comments. "The outward migration was driven by scattering, so things shake up quite a bit."

Third, Jupiter probably would likely have come in even closer, perhaps sliding all the way into the Sun, had not Saturn (already in tow via the 3:2 resonance) grown massive enough to hit the tidal brakes and reverse both planets' movement. In this sense, the formation and survival of the terrestrial planets hinged not on Jupiter's existence but on Saturn's.

Fourth, Jupiter's inward trek would have completely swept clear the asteroidal region from 2 to 4 a.u. Most of the objects there were lost completely, but roughly 15% ended up scattered into a disk beyond Saturn. After reversing course and moving outward, the two planets scattered some of those previously displaced objects again, this timeinward, returning them to what's now the inner asteroid belt.

Fifth, as Saturn and Jupiter continued outward to their final orbits, they encountered another group of asteroids. Unlike the rocky bodies that had boomeranged out and back, these were carbon- and water-rich objects that had formed 6 to 9 a.u. from the Sun. Tossed inward by perturbations from the dynamic duo, they formed most of what's now the outer asteroid belt.

Sun and forming planets
If recent computer simulations are correct, the Sun's innermost planets assembled from a narrow disk of rocky rubble that was only about 30 million miles wide. Such a tightly confined disk yields a Mars that's not too big — a failing of previous modeling.
NASA / JPL / T. Pyle (SSC)
A New Paradigm?

To recap: in one sweeping narrative, these theorists propose solutions for both a minimalist Mars and a stratified asteroid belt with a rock-rich inner region and a carbonaceous, water-harboring outer belt. As a bonus, the new mindset leads naturally to a set of four inner planets (correct sizes, correct orbits) that assembled on the right time scale (within about 30 million years of the Sun's formation). It even provides a source of water for Earth (C-type asteroids) and a near-Earth environment conducive to the presumed giant impact that formed the Moon.

This radical scenario represents "a paradigm shift in our understanding of the evolution of the inner solar system," says Walsh. That's an understatement! It all seems hauntingly Velikovskian to me, except that these folks have clearly done their homework.

Will "Jupiter's Grand Tack" (as Morbidelli dubs it) hold up to further scrutiny? Walsh and his team have submitted a fuller treatment toNature for publication, but other dynamicists are already weighing in based on the presentations heard last week. "Many aspects of their model look good to me," observes SwRI officemate William Bottke, "but lots of first-order things have to be tested before they can declare victory on all fronts."

For example, it's now widely accepted that most of Earth's water was imported from the outer asteroid belt. Yet Bottke thinks the scenario envisioned by Walsh, Morbidelli, O'Brien, and others would require a vast reservoir of water-rich (C-type) bodies, totaling hundreds of times the mass of the current asteroid belt. "We need to vet these models with more physics and more cosmochemistry," he says. Also, the depth of Jupiter and Saturn's inward penetration would have depended critically on how fast Saturn grew to nearly full size and when. The broader the range of initial conditions that "work," the more confidence there'll be that this scenario is the right one.

Morbidelli remains confident that they're onto something profound. "We consider ourselves celestial geologists," he quips. "We're now able to 'read' the current solar-system arrangement well enough to figure out what the early planets did."

Tuesday, October 19, 2010

Mysteries of vertebrate origins (even of spineless commenters)

The following article is excerpted from Wired (under the headline Hagfish opens major gap in tree of life). Wired picked it up, according to this citation: “microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate.” By Alysha M. Heimberg, Richard Cowper-Sallari, Marie Sémon, Philip C. J. Donoghue, and Kevin J. Peterson. Proceedings of the National Academy of Sciences, Vol. 107 No. 42, October 19, 2010. You should check out the original Wired article; not only have I excerpted it but the article has neat pictures, and really interesting comments. Really interesting. But onward with a story about how there is this gap  between vertebrate life and invertebrate life,---looking at the fossil record there is no immediate intermediary species that would form a link between say jelly fish, and people. 
Now, from the article The origin of all living vertebrates just got more mysterious.

Since the 1970s, many evolutionary biologists have considered an eel-like, deep-sea-dwelling creature called the hagfish to be the closest extant relative of a last common ancestor for all backboned creatures.

That made the hagfish a stand-in for a transitional species between invertebrates and higher animals, spanning a leap as dramatic as any in evolutionary history. But a new family tree based on high-powered molecular analysis lumps hagfish together with lampreys, a jawless fish that’s primitive, but very much a vertebrate.

“It removes hagfish from representing the intermediate step, and makes the jump from invertebrates to vertebrates all the more formidable,” ...

Donoghue’s study,[quoted above and] co-authored with Dartmouth College biologist Kevin Peterson and published October 19 in the Proceedings of the National Academy of Sciences, is the latest in a series of attempts to arrange hagfish and lampreys in the tree of life.

Prior to the 1970s, researchers extrapolated their trees from comparisons of physical characteristics. On this basis, hagfish resembled lampreys. But when scientists used genetic analysis to revisit those comparisons, they found major genetic differences between the two species. Since hagfish have a skull but no backbone and only a rudimentary nervous system, they were interpreted as resembling an earlier, pre-lamprey evolutionary stage.

The new study goes beyond genes to the level of microRNA — molecular snippets that help turn genes on and off and seem to play a crucial role in allowing basic genetic components to be configured and reconfigured in ever-more-complex ways. As a guide for determining relationships between species, they’re more reliable than genes. And they suggest that hagfish really are close relatives of lampreys...

Without hagfish, evolutionary biologists are left with a gap between complex invertebrates like sea squirts..., and simple vertebrates like lampreys. Whatever went between them, “we don’t even know what sort of sensory organs they had, how they made their living feeding, and so on,” said Donoghue. The invertebrates provide little guidance. ...

[C]omparisons have already shown the jump from invertebrate to vertebrate was attended by a duplication of every gene in the genome, and an explosion in new types of microRNA. “There are more microRNAs acquired at the origin of vertebrates than at any other time in animal evolutionary history,” said Donoghue. “It was just bizarre.”

Read More http://www.wired.com/wiredscience/2010/10/vertebrate-origins/#ixzz12qxd4YVK

Monday, October 18, 2010

The Other Guy (as in guy-wire) part 2

The following article  forms a counter balance to the first story, just preceding this, about an American millionaire. This is all part of a necessary, greater machinery. Both stories are about helpless people who are part of a greater system they have not clue about. In this of course they are typical of everyone (everyone statistically speaking, anyway). Weep perhaps, then turn away. The emotional outrage is not a profitable reaction for someone struggling to understand their own situation. Envy, or anger, only hurts the person with an aim.  Smile perhaps a wee bit at the fact one is named trump, the other little, which I just now noticed myself.

By Andria Simmons, The Atlanta Journal-Constitution, 11:30 p.m. Wednesday, October 13, 2010

A mentally ill North Carolina man is suing the federal government for deporting him to Mexico, where he was left penniless and forced to fend for himself for four months without even the slightest grasp of the Spanish language.
The ACLU on Wednesday filed a lawsuit on behalf of Mark Lyttle, who settled near Atlanta after returning to the United States last year.
Lyttle's troubles began when he was misidentified as an illegal immigrant in September 2008 while serving a 100-day sentence at a North Carolina prison. He was there on a misdemeanor assault charge for inappropriately touching a female orderly at a psychiatric hospital where he received treatment.
A spokesman for the North Carolina Department of Corrections (DOC) said Lyttle reported his place of birth was Mexico City when he was booked into the prison.
"That brought him to the attention of ICE," said Keith Acree, public affairs director for the North Carolina DOC. "When he finished his prison sentence, he ultimately did get deported.
...
Lawyers for Lyttle claim he had trouble communicating because he has several problems that rendered him "mentally disabled," including bipolar disorder, a history of physical abuse and emotional problems. Lyttle and three of his siblings were removed from their biological parents' home when he was 7 and placed in foster care. They were eventually adopted by a Rowan County, N.C. , family. As a teenager, Lyttle was institutionalized several times at various psychiatric hospitals....
ICE agents investigating Lyttle's immigration status searched criminal and other databases which showed Lyttle had a Social Security number and was a U.S. citizen, according to the lawsuit.
However, Lyttle signed several documents that cemented his impending deportation, including an acknowledgment that he was a citizen of Mexico and an agreement to be voluntarily removed to Mexico. Lyttle said he didn't understand the paperwork and he was confused because he is bipolar.
While he is of Puerto Rican descent, Lyttle was born in Rowan County, N.C., Aug. 2, 1977, and had never traveled outside of the United States before he was deported.
"They didn't believe anything I was saying and I told them numerous times I was an American citizen," Lyttle said.
Lyttle's lawyers claim he was coerced into approving the documents.
After Lyttle's prison term expired on Oct. 28, 2008, he was transferred to ICE custody and spent six weeks at the Stewart Detention Center in Lumpkin, Ga. He went before an immigration judge on Dec. 9, 2008. The judge ordered Lyttle to be removed to Mexico.
Lyttle was put on a plane to Hidalgo, Texas, on Dec. 18, 2008, and dropped off at the Mexican border. Authorities sent him packing with $5 in his pocket and nothing but a prison-issued jumpsuit on his back.
Relatives say they were never notified of what happened to Lyttle after he left prison.
"It was like he vanished, and for a couple Christmases and holidays I wondered where he was at and why he wouldn't contact me," said Lyttle's brother, David Lyttle, reached by phone Tuesday at his home in Conway, S.C. "Something wasn't right and I couldn't put my finger on it."
...
Lyttle spent eight days begging and sleeping on the streets before he tried to re-enter the country. However, he was rebuffed by border patrol agents who searched their computerized database and found his immigration status to be that of a "prior deported alien," according to the lawsuit.
Lyttle says he spent the next four months on an odyssey through Mexico, Honduras, Nicaragua and Guatemala. He alternated between homelessness, living in shelters and incarceration in foreign jails. He did not remember his relatives' phone numbers, which he usually kept written down in his wallet, according to his brother.
Because Lyttle lacked proper identification, Mexican officials deported him to Honduras. Honduran officials held Lyttle in an immigration camp, then tossed him in jail, and finally shipped him off to Guatemala.
He finally convinced a U.S. embassy official in Guatemala to contact his two brothers who were serving in the U.S. military. Thanks to the efforts of his brothers and the embassy official, a passport was issued to him within 24 hours.
Yet even after making arrangements to return to the United States, Lyttle was re-arrested at Hartsfield-Jackson International Airport and detained for six more days. Then, in a motion to terminate deportation efforts, the Department of Homeland Security finally acknowledged that Lyttle was "not a Mexican citizen, and, in fact, is a citizen of the United States."
Jacqueline Stevens, a professor of political science at Northwestern University in Evanston, Ill., researches the deportation of American citizens. She said Lyttle's case is similar to others she has seen, where someone in a legally fragile position coming out of prison is somehow diverted into the immigration system.
"They don't have contact with their families, and they get thrown into detention centers in the middle of nowhere," Stevens said. "There is no requirement for a bond hearing there. So people just get fed up with being locked up for so long and figure the only way I am going to get out of here is if they sign this paper saying I'm deportable."
Lyttle settled in Griffin, Ga., and works as a landscaper now, but it he says he still has nightmares about his ordeal.
"They took my freedom from me, they took my dignity from me," Lyttle said. "I'm going to do to them what they did to me."
The lawsuit in U.S. District Court, Northern District of Georgia, seeks unspecified damages from the federal government and additional safeguards to protect the rights of American citizens and persons with mental disabilities who are subject to potential deportation. The Department of Homeland Security, Immigration and Customs Enforcement, and top officials from those agencies are named in the lawsuit. The suit also targets Corrections Corporation of America, a Nashville-based private company that runs the Stewart Detention Center in Lumpkin, Ga. 
This excerpted article can be seen in full at this link:
http://www.ajc.com/news/north-carolina-man-sues-681887.html

A Tale of Two Guys (as in guy-wires) Part 1

http://www.scotsman.com/news/39Government-told-me-I39d-win39.6585005.jp 
is the link for a story about not local politics, but, perhaps, just "politics." The story is set in Scotland, involving an American millionaire and how he got permission to build what he calls a world class golf course, in an area many locals felt should be protected for environmental and historical reasons. I have another story, quite different, but again, illustrating how the official rules are not the real story.  That other story says part 2 in the title. Below is an article, slightly excerpted, from

'Government told me I'd win' – Donald Trump

Published Date: 17 October 2010
By Eddie Barnes
Political Editor

DONALD Trump has made the "explosive admission" the Scottish Government called him after his golf course plan was rejected by councillors to urge him to press on, assuring him "you'll win".

In new revelations, the US tycoon – whose £750 million development at Menie estate, north of Aberdeen, is already under construction after getting subsequent government approval– reveals details of contacts he had with government after the course's original rejection.
In November 2007, it was turned down by a committee of Aberdeenshire councillors, in a move which scuppered the proposal. But the billionaire businessman claims he was then called by the government and urged to keep his interest alive.
In an interview with Scotland on Sunday, the 66-year- old tycoon claims: "I give the Executive (Scottish Government] a lot of credit. They called me and really wanted me to continue going forward. I said are you kidding? I just lost. I don't like to lose. They said no, you'll win. They didn't want me to leave."
Four days after the rejection, the Scottish Government "called in" the application, on the grounds the decision put the integrity of the planning process in jeopardy. It then went to a public inquiry before being approved by finance secretary John Swinney.
The revelation has brought calls for a new inquiry into the chain of events that preceded that decision.
Labour MSP Duncan McNeil, who led a Holyrood local government committee inquiry into the affair two years ago, said: "This is an explosive admission from Donald Trump. In many ways he has let the cat out of the bag and raises serious questions. The Scottish Government cannot form an impartial view on a planning application that has been called in if they have given secret guarantees to one side. There is now a case for reviewing the evidence in light of this new information."
Trump's plans to create a huge golfing resort on environmentally-protected coastal dunes north of Aberdeen were originally rejected by the council sub-committee on the casting vote of the chairman. Despite that rejection, the full council, following the move to call the project in, later voted for it. Following a public inquiry, which also backed the plan, Swinney approved it in November 2008.
Trump's claim that the Scottish Government offered him its support following the rejection is significant as it is supposed to remain impartial. Officials strongly denied his claims last night.

Parliamentary questions over the issue began after it emerged First Minister Alex Salmond met Trump's representatives after the rejection by the infrastructure services committee of Aberdeenshire Council. He said he was entitled to do so because, as
MSP for Gordon, he is the local parliamentarian. He then set up a meeting between Trump officials and Scotland's chief planner, Jim Mackinnon. Mackinnon and Swinney then took the decision to "call in" the development, removing the council from the process.
In the interview, Trump said the government was backing him all the way during the tortuous planning process.
He said: "They knew what we were doing was right, that it was going to create a lot of jobs and maybe, most importantly, that it was going to be great in terms of the psyche of Scotland because it's going to be really special."
Asked about Salmond's involvement, he added: "I have a lot of respect for Alex Salmond. He's a strong man who loves Scotland above all else. I know he wanted the project to happen because it was good for Scotland."
Giving evidence to MSPs in 2008, the First Minister said he had met Trump aides to urge them to keep going with their application because of fears its rejection would give out the message that Scotland was "not open for business." Ministers insisted calling in the plans had been motivated by concerns that its rejection presented "a threat to the integrity of the planning system" and that the development was "of national significance".
At the inquiry in 2008, Mackinnon said the decision to call in the plans was "not about expediting" the development. He told MSPs: "There is no presumption in favour of, or against, the development; there is a presumption in favour of ensuring that the processes are fair."
Aberdeenshire councillor Martin Ford, the committee chair who voted against the development in 2007, said last night: "This is an extraordinary claim by Mr Trump. If what he says is true, it is a serious matter for the Scottish Government. This was a planning application and there was a process to be followed designed to ensure fairness and proper consideration of the issues before a decision was reached."
Asked whether anyone from government assured Trump he "would win", a government spokesman said: "No, this is not correct. No person in the Scottish Government expressed such a view."
He added: "The issue was determined according to the due process of the public local inquiry, which followed John Swinney's decision to call in the application on 4 December 2007.
"The PLI was announced on 28 February 2008, the independent reporter recommended outline planning permission be granted, and Mr Swinney granted this on 3 November 2008."
He said: "This procedure was totally robust, and was all gone into in the Local Government and Communities Committee Report of 14 March 2008, which said: 'The committee notes that the chief planner and the planning minister (Cabinet secretary for finance and sustainable growth], John Swinney acted in accordance with planning laws when issuing the decision to call in the application'."

Thursday, October 14, 2010

Genome mysteries

Here is part of an article from Wired about how little we know about the human genome. I thought boy, this will be an interesting read (and it is) but bottom line, what the teaser meant was we don't even know the number of genes in people. Nothing conceptually surprising, except our ignorance about our ignorance. My thought was they would delve into the mysteries about how genes work together, but no---that is not what this article is about.  
...
Exactly how many genes make up the human genome remains a mystery, even though scientists announced the completion of the Human Genome Project a decade ago. The project to decipher the genetic blueprint of humans was supposed to reveal all of the protein-producing genes needed to build a human body.

“Not only do we not know what all the genes are, we don’t even know how many there are,” Steven Salzberg of the University of Maryland in College Park said October 11 during a keynote address at the Beyond the Genome conference, held in Boston. Most estimates place the human gene count in the neighborhood of 22,000 genes, which falls between the number of genes in a chicken and the number in a grape.

Grape plants have 30,434 genes, by the latest count. Chickens have 16,736 genes, a number Salzberg said will likely grow as scientists put the finishing touches on the chicken genome. As in humans, the gene totals for each species are not as precise as they seem and are subject to revision.
...
...[D]isparate numbers [suggested as possible totals] stem from the fact that genes comprise only about 1 percent of the 3 billion As, Ts, Gs and Cs that make up the human genetic instruction book. And the genes aren’t conveniently laid out as single, continuous stretches of genetic code. Instead, human genes are found in protein-encoding pieces called exons, interspersed with stretches of DNA that don’t make protein. These spacers are called introns.

To make matters worse, each exon in a gene codes for only a portion of a protein. Cells can mix and match different combinations of exons to make various proteins.

Traditionally, scientists have used computer programs to sift through billions of DNA letters and pinpoint the locations of genes. The programs have improved over the years, but they still aren’t as good as people at plucking exons from the sea of introns and figuring out how those protein-encoding segments are spliced together, said Clara Amid, a computational biologist at the Wellcome Trust Sanger Institute in Hinxton, England.

Amid is involved in the Gencode project, an effort to identify all the human genes and the many permutations of those genes that can lead to a dizzying number of proteins. She and her colleagues pick out genes the old-fashioned way — by hand. The researchers get plenty of clues where genes are from computerized gene-finders, studies that sequence RNA produced by genes, and from comparisons of human DNA to the genomes of other animals. Synthesizing all that information allows people to accurately find and mark the locations of genes, a process scientists call annotation. “The best computerized methods could replicate the manual annotation only 40 to 50 percent of the time,” Amid said October 12 at the Beyond the Genome conference.

The Gencode team isn’t finished with its work; several chromosomes still need the human touch. Gencode’s current count is 21,671 human genes. “The number will go up, definitely,” Amid said. Already the team has located several new genes on chromosome 4 thanks to data from RNA-sequencing projects, she said.
...
The Mammalian Gene Collection, one effort to catalog all of the full-length RNA versions of genes, lists 18,877 human genes. That number is likely to represent the lower boundary of the gene count, Salzberg said.

If new RNA sequencing methods detect the same proportion of new genes in people as were found in fruit flies, the human genome could gain about 3,000 more genes in addition to those already confirmed by RefSeq. “That would be an exciting result,” Salzberg said. “I’d be surprised, but we like surprises in science.”

Read More http://www.wired.com/wiredscience/2010/10/human-genome-still-chock-full-of-mysteries/#ixzz12NwSR1gc

Tuesday, October 5, 2010

When Snakes Fly

Some snakes can fly. Okay, glide, from tree branches, like flying squirrels, and they are called flying snakes. Here's the National Geographic link.. They are not in North America, they are in south Asia. Now.