Dino-plasty?

Guambat is sure somewhere there must be someone, maybe on one of those planets they've been discovering that "could" support life -- as we know it, complete with shopping malls, who finds the following article more useful than a snout on a chicken.

Tweaking the beak: Retracing the bird’s beak to its dinosaur origins, in the laboratory

Scientists have successfully replicated the molecular processes that led from dinosaur snouts to the first bird beaks.

Using the fossil record as a guide, a research team led by Yale paleontologist and developmental biologist Bhart-Anjan S. Bhullar and Harvard developmental biologist Arhat Abzhanov conducted the first successful reversion of a bird’s skull features. The scientists replicated ancestral molecular development to transform chicken embryos in a laboratory into specimens with a snout and palate configuration similar to that of small dinosaurs such as Velociraptor and Archaeopteryx.

“The beak is a crucial part of the avian feeding apparatus, and is the component of the avian skeleton that has perhaps diversified most extensively and most radically — consider flamingos, parrots, hawks, pelicans, and hummingbirds, among others,” Bhullar explained. “Yet little work has been done on what exactly a beak is, anatomically, and how it got that way either evolutionarily or developmentally.”

The team looked at gene expression in the embryos of emus, alligators, lizards, and turtles. The researchers discovered that both major living lineages of birds (the common neognaths and the rarer paleognaths) differ from the major lineages of non-bird reptiles (crocodiles, turtles, and lizards) and from mammals in having a unique, median gene expression zone of two different facial development genes early in embryonic development. This median gene expression had previously only been observed in chickens.

Using small-molecule inhibitors to eliminate the activity of the proteins produced by the bird-specific, median signaling zone in chicken embryos, the researchers were able to induce the ancestral molecular activity and the ancestral anatomy. Not only did the beak structure revert, but the process also caused the palatine bone on the roof of the mouth to go back to its ancestral state. “This was unexpected and demonstrates the way in which a single, simple developmental mechanism can have wide-ranging and unexpected effects,” Bhullar said.

Bhullar noted that this same approach could be used to investigate the underlying developmental mechanisms of a host of great evolutionary transformations. “Our goal here was to understand the molecular underpinnings of an important evolutionary transition, not to create a ‘dino-chicken’ simply for the sake of it,” said Bhullar, lead author of the study, published online May 12 in the journal Evolution.

Guambat reckons there's a new reality show in the works.

So, who are we to believe?

Who ya gonna believe: some dayem scientist or the Texas Board of Education? OK, that's a bit cheeky; opposition to science extends far beyond the halls of the Texas "school" system, as we see below (which bears passing similarity to the actual article).

Views on evolution among the public and scientists

Whereas nearly all scientists say that humans and other living things have evolved over time, only two thirds of the public agrees, according to a new report from the Pew Research Center.

Asked which comes closer to their view, "Humans and other living things have evolved over time" or "Humans and other living things have existed in their present form since the beginning of time," 98% of scientists responding chose the "evolved-over-time" option and only 2% chose the "since the beginning-of-time" option.

65% of the public respondents chose the "since the beginning-of-time" option, and 31% chose the "evolved-over-time" option. 4% perhaps responded, "huh?". 66% of the public, however, believed scientists generally agree that humans evolved over time.

Digging deeper, those who chose the "evolved-over-time" option were then asked whether they preferred "Humans and other living things have evolved due to natural processes such as natural selection" or "A supreme being guided the evolution of living things for the purpose of creating humans and other life in the form it exists today."

90% of scientists preferred the "natural processes" option, and 8% preferred the "supreme being" option.

35% of the public preferred the "natural processes" option, and 24% preferred the "supreme being" option, indicating, perhaps, 59% of the 31% of the public believing in "evolved-over-time" agreed with free choice processes.

Three-quarters (75%) of college graduates believe that humans have evolved over time, compared with 56% of those who ended their formal education with a high school diploma or less. As a religious refugee from Texas decades ago, Guambat is inclined to believe that the number of Texans "educated" by the Texas Board of Education who believe humans evolved is statistically insignificant.

Don't take Guambat's word, though. You can read the summary of the report here.

The summary makes the observation that 79% of adults say that science has made life easier for most people, but only a majority is positive about science’s impact on the quality of health care, food and the environment. 61% say that government investment is essential for scientific progress, while 34% say private investment is enough to ensure scientific progress is made. 

Guambat reckons this 34% correlates somehow with the fact only a majority is positive about science's impact on the quality of life. But Guambat, being no scientist by any stretch of evolution, lacks the tools to test the hypothesis, and is terrified of tests anyway.

As an aside: Texas finally approves history textbooks amid religious and political concerns

Science (fiction?)

Novel Way Discovered to Decode and Read DNA: Scientists

According to a new report, scientists have discovered a new way to read and decode DNA. Scientists are suspecting this research could forever change the ways on how doctors uncover, diagnose and treat various diseases.

Researchers said the main aim of this research is to understand the process of storage of biological functions in the human genome.

The research, published in the journal Science, states how genomes use genetic code to write information about proteins and that too in two separate languages. Researchers believe that the second language lies below the first and instruct the cell to control the genes.

Dr. John Stamatoyannopoulosm, lead researcher, said: "For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made".

Researchers said this novel research has thrown light on the fact that the DNA is an incredibly powerful information storage device, which has been fully exploited by nature.

Don't Be Duped By 'Duon' DNA Hype

I can only hope that Stamatoyannopoulos didn’t really say that. The authors report that changes in a single DNA sequence can influence both the protein it encodes and the place where other proteins bind to initiate copying. So evolutionarily, a single change could influence two endpoints–copying the sequence and what gets made using the same sequence. That’s cool, but not actually new.

With today’s headlines hyping “Second Code Uncovered Inside the DNA,” you might think that scientists are running around in circles in their labs, tearing out their hair, and screaming. But the real reaction of scientists to these headlines is more along the lines of this Twitter conversation among several scientific experts and science writers. They have good reason to be snarky.

The hype began with the way hype often begins: an institutional news release offering us the holy grail/huge breakthrough/game-changing finding of the day. This kind of exaggeration is the big reason any science consumer should look well beyond the news release in considering new findings. A news release is a marketing tool. You’re reading an advertisement when you read a news release; it’s also scientifically garbled and open to all kinds of misinterpretation, as the comments at the link to the release make clear.

Scientists have not assumed that the genetic code “was used exclusively to write information about proteins,” or even ever assumed that it “writes information about proteins,” whatever that means. A quick primer: Proteins are molecules that do the work of an organism, and that includes the work of copying DNA for protein production and cell division. Even nonmajors biology textbooks cover the fact that the DNA sequence both contains code for proteins and serves a regulatory purpose, making it possible to copy that code into a form the cell can read, recipe-like, to build the proper protein.

(edited in article) I’d be stunned if UW scientists were genuinely “stunned” to discover this dual use of DNA sequences to “write” “two separate languages” because what they really describe is the use of a single language, the language of nucleotides, for two known purposes. They themselves noted that “the potential for some coding exons to accommodate transcriptional enhancers or splicing signals has long been recognized.”

The release also contains gems such as “The genetic code uses a 64-letter alphabet called codons.” This sentence makes me sad. Codons consist of three nucleotides–which we designate with the letters A, C, G, and T/U–and there are 64 of these triplets, 61 of which serve as molecular code words for 20 amino acids (here is a DNA nucleotide codon table, too; these are the codons the authors address). Some amino acids get more than one word to designate them. The cell “reads” these code words and uses the amino acids they designate to build proteins.

The other problem is the ubiquitous use of the phrase “second code” in so many of the headlines related to this story when the authors themselves state: “ Although nearly all codon biases parallel TF recognition preferences genome-wide…” with the arginine codon as an exception. That’s not a “second code,” even though the news release describes it that way. It’s a different (but already recognized) use of an existing code, now identified as occurring at a greater than previously recognized frequency in areas that use the same code for proteins.

So what was the real import of the study that warranted its publication in Science, a “glamor” science publication? The authors (whose paper I enjoyed) seem to have found that the genome contains more of these dual-use triplet DNA sequences than previously thought, which might make them more relevant when examining some aspects of evolution (see “Single change could influence two endpoints”). And, it seems, the authors wanted the opportunity to, um, codify their own term for these dual-use sequences: duons. I wonder if they realized that the name had already been taken?

Ah, science. Guambat wonders why Mrs Guambat spends so much time watching all the "Housewives of..." shows, when they hardly know the meaning of the term "bitchy". Academic "science" (so often commercial "innovation") could open a whole new realm of reality show in way it never imagined.

Darwin denyer sits on US House Science Committee

Congressman calls evolution lie from 'pit of hell'

He sits on the U.S. House Committee on Science, Space and Technology.

Georgia Rep. Paul Broun, M.D., said in videotaped remarks,

"All that stuff I was taught about evolution and embryology and Big Bang theory, all that is lies straight from the pit of hell. And it's lies to try to keep me and all the folks who are taught that from understanding that they need a savior."

Broun also said that he believes the Earth is about 9,000 years old and that it was made in six days.

The Republican lawmaker made those comments during a speech Sept. 27 at a sportsman's banquet at Liberty Baptist Church in Hartwell.

Broun, a medical doctor, is running for re-election in November unopposed by Democrats.

Read more: http://www.seattlepi.com/news/article/Congressman-calls-evolution-lie-from-pit-of-hell-3924955.php#ixzz28YITIW8J

Cancer?

Las Vegas 1972 - 2010 by NASA/LandSat

I think, therefor I am that I am

Analytical thinking may undermine belief: Study

The psychology report, published Thursday in the prestigious journal Science, reveals that religious belief drops after subjects perform analytical tasks or are exposed to Rodin's sculpture, The Thinker.

The research duo, UBC social psychologists Will Gervais and Ara Norenzayan, who have earned international reputations for their groundbreaking studies into religion in the past six years, maintain all humans use two valuable types of thinking - intuitive and analytical. How much you rely on one kind of thinking over another generally determines how religious you are.

People who are highly intuitive tend to be more religious. Intuitive thinking helps people recognize the difference between the body and the mind, imagine life after death and discern purposes in the universe.

In contrast, analytic thinking reduces intuitions of God, of an afterlife and of experiences of divine presence, say Gervais and Norenzayan, whose latest research surveyed 650 people, mostly from B.C.

Thinking can undermine religious faith, study finds

Scientists have revealed one of the reasons why some folks are less religious than others: They think more analytically, rather than going with their gut. And thinking analytically can cause religious belief to wane — for skeptics and true believers alike.

The cognitive origins of belief — and disbelief — traditionally haven't been explored with academic rigor, said lead author Will Gervais, a social psychologist at the University of British Columbia in Vancouver, Canada. "There's been a long-standing intellectual tradition of treating science as one thing and religion as separate, and never the twain shall meet," he said. But in recent years, he added, there has been a push "to understand religion and why our species has the capacity for religion."

Studies suggest that religious beliefs are rooted in this intuitive processing, Gervais said. So, he wondered, would thinking analytically undermine religious belief as it overrides intuitive thought?

To find out, his research team had college students perform three thinking tasks, each with an intuitive (incorrect) answer and an analytic (correct) answer. For example, students were asked this question: "A bat and a ball cost $1.10 in total. The bat costs $1.00 more than the ball. How much does the ball cost?" The intuitive answer — 10 cents — would be wrong. A little math on the fly reveals that the correct answer would be 5 cents.

After answering three of these questions, the students were asked to rate a series of statements on belief, including, "In my life I feel the presence of the Divine," and "I just don't understand religion." Students who answered the three questions correctly — and presumably did a better job of engaging their analytical skills — were more likely to score lower on the belief scales.

To tease out whether analytic thinking was actually causing belief to decrease, the researchers performed a series of additional experiments. First, students were randomly assigned to look at images of Auguste Rodin's sculpture "The Thinker," or of the ancient Greek statue of a discus thrower, "Discobolus." Those who viewed "The Thinker" were prompted to think more analytically and expressed less belief in God — they scored an average of 41.42 on a 100-point scale, compared with an average of 61.55 for the group that viewed the discus thrower, according to the study.

So does this mean that religious faith can be undermined with just a little extra mental effort? Not really, said Nicholas Epley, a social psychologist at the University of Chicago who was not involved in the study. But it does show that belief isn't set in stone, but can respond to a person's context.

I am that I am.

I yam that I yam

Suits me

Poppa Jack threw his out years ago.

MIT develops a suit that makes you feel like you're 75 years old

Braces on the suit mimic joint stiffness and make it hard to walk, leg straps limit how fast you can travel, and a helmet causes your head to be forced forward, mimicking the curved spine of an older adult. Yellow goggles and earplugs are the final touch on the outfit, making it difficult to read and hear some things.

Guambat is waiting for them to invent a Super Man suit.

Crowd computing

Going where no computer has gone before. May the formidable force be with them.

US gamers crack puzzle in AIDS research that stumped scientists for years

In just three weeks, online gamers deciphered the structure of a retrovirus protein that has stumped scientists for over a decade, and a study out Sunday says their breakthrough opens doors for a new AIDS drug design.

Looking for a solution, researchers at the University of Washington turned to Foldit -- a program created by the university a few years ago that transforms problems of science into competitive computer games -- and challenged players to use their three-dimensional problem-solving skills to build accurate models of the protein.

With days, the gamers generated models good enough for the researchers to refine into an accurate portrayal of the enzyme's structure. What's more, the scientists identified parts of the molecule that are likely targets for drugs to block the enzyme.

"We wanted to see if human intuition could succeed where automated methods had failed," said Firas Khatib, a lead author of the study, published in the journal Nature Structural & Molecular Biology.

"The ingenuity of game players is a formidable force that, if properly directed, can be used to solve a wide range of scientific problems," Khatib said.

Seth Cooper, a co-creator of Foldit, added, "People have spatial reasoning skills, something computers are not yet good at. Games provide a framework for bringing together the strengths of computers and humans. The results in this week's paper show that gaming, science and computation can be combined to make advances that were not possible before."

Might explain the turkeys

Considering the big Christmas feast, this item might explain why Guambat's little rats are such turkeys:

You are what your father ate

As they say, you are what you eat. And if you’re a mouse, you’re also what your father ate.

So say researchers from the University of Massachusetts Medical School and the University of Texas at Austin. In a study published this week in the journal Cell, they report that a father’s diet influences how metabolic genes function in his offspring.

The research team fed some male mice a normal diet, while other mice got a low-protein diet. All the males mated with females who ate the same healthy diet. Sure enough, the offspring of the protein-deprived fathers had hundreds of genetic changes that weren’t seen in the mouse pups whose fathers ate the normal amount of protein. The changes were observed even when the fathers never met their offspring.

Doomed: the "tree-book"

Guambat was reading yet another review of the ascendancy of "e-books", such as the Kindle, iPad, eReader, Nook, etc. The guffaw is over the technological "advance" it makes and how the treebook will soon be a thing of the past. It's doomed, they say.

Fascination with gadgetry is totally understandable to Guambat.

Many eons ago in Guambat's youth, he was enamored of a plastic submarine that was marketed on a box of cereal. He pestered his Mom until she gave in, but at a price. She said that it would be the one and only gadget she would ever get if Guambat tired of it quickly, which she bet would happen.

Oh NO, exclaimed the enthusiastic Guambat. It's like a real submarine and dives and surfaces and all that.

When it came at last in the (snail)mail, it was taped in a small package. It was put to shame by Crackerjack Box toys.

It was so small, even Guambat's little boy fingers could hardly deal with it. Dealing with it involved prying open a small capped hole in the base of the thing, stuffing a pinch of baking soda in it, capping it back up, and dropping it in a glass of water.

Wherein, it flopped over as the baking soda fizzed away, bobbed to the top of the glass and, at some great length of time (anything beyond a minute was a great length of time to an impatient young Guambat), settled to the bottom of the glass. Much like the feeling Guambat had when he realized that was the last thing he'd ever get from a cereal box, except cereal.

Guambat's great joy at getting the newest gadget has been tempered all these years by that sunken experience.

Gee, Thanks, Mom.

Anyway, back to the ebook vs treebook theme.

This opinion piece in the WSJ: From Gutenberg to Zoobert

In the hit 1998 film "You've Got Mail," Meg Ryan's independent bookstore couldn't compete with the big chain-store competitor.

The creative destruction in the book business has led even Andy Ross to have some sympathy for Barnes & Noble. Mr. Ross was the owner of Cody's Books, a well-known independent bookstore located near the Berkeley campus of the University of California. He owned Cody's Books for some 30 years before competition from the big stores closed it down in 2008.

[Before Mrs. Guambat became Mrs. Guambat, she would regularly take Guambat to Cody's as sort of a date, and they happily spent many hours transfixed in the isles and stacks, mesmerized by the cacophony of telepathy from thousands of authors living and dead: "read me, read me".]

"The only thing anyone is talking about in the book business is e-books," Mr. Ross told me last week. "I see it as being similar to the music industry. There is going to be a tipping point where e-books become the dominant medium, thus ending 500 years of the Gutenberg Age."

Just a couple of months ago, the WSJ ran this story, in the same "vain": 'Vanity' Press Goes Digital

Writer Karen McQuestion spent nearly a decade trying without success to persuade a New York publisher to print one of her books. In July, the 49-year-old mother of three decided to publish it herself, online.

Much as blogs have bitten into the news business and YouTube has challenged television, digital self-publishing is creating a powerful new niche in books that's threatening the traditional industry. Once derided as "vanity" titles by the publishing establishment, self-published books suddenly are able to thrive by circumventing the establishment.

The market is likely to shift into two tiers, "branded/high-quality" and "cheap/good enough," predicts author and lecturer Seth Godin. Mainstream publishing houses have long depended for much of their profit on selling backlist titles, books in print for more than a year. In coming years, there will be adequate substitutes for many of those works at a quarter of the price, he says.

And a couple of days ago, the WSJ noted this item: Mass Paperback Publisher Goes All Digital (reproduced, mostly, here)

As digital books continue to gain market share, one of the country's oldest mass paperback publishers is abandoning its traditional print books and making its titles available in digital format and print-on-demand only.

Dorchester Publishing Inc., a closely held book and magazine house, said it is making the switch after its book unit sales fell 25% last year, in part because of declining orders from some of its key retail accounts

All of which made Guambat recall this.

The Doomsday Book is a detailed survey of the land held by William the Conqueror and his people, the earliest surviving public record, and a hugely important historical resource.

According to this website:

The Domesday Book is closely linked with William the Conqueror's attempt to dominate Medieval England. Along with a string of castles throughout England, the Domesday Book was to give William huge authority in England.

To further extend his grip on England, William I ordered that a book be made containing information on who owned what throughout the country.

This book would also tell him who owed him what in tax and because the information was on record, nobody could dispute or argue against a tax demand. This is why the book brought doom and gloom to the people of England - hence "Domesday Book".

The decision of what someone owed was final - rather like Judgement Day when your soul was judged for Heaven or Hell.

William ordered the survey of England to take place about twenty years after the Battle of Hastings. The Saxon Chronicle states that it took place in 1085, while other sources state that it was done in 1086. The whole survey took less than a year to complete and the books can be found in the Public Records Office.

The Domesday Book forms a remarkable record of the state of England in the mid-1080's.

So remarkable is the history, and the shear mankindness, of this treebook, that the BBC decided to go it one better and assure its place for the ages, as the following article in 2002, written almost One Thousand years after the Doomsday Book, described.

Digital Domesday Book lasts 15 years not 1000

It was meant to be a showcase for Britain's electronic prowess - a computer-based, multimedia version of the Domesday Book. But 16 years after it was created, the £2.5 million BBC Domesday Project has achieved an unexpected and unwelcome status: it is now unreadable.

The special computers developed to play the 12in video discs of text, photographs, maps and archive footage of British life are - quite simply - obsolete.

As a result, no one can access the reams of project information - equivalent to several sets of encyclopaedias - that were assembled about the state of the nation in 1986. By contrast, the original Domesday Book - an inventory of eleventh-century England compiled in 1086 by Norman monks - is in fine condition in the Public Record Office, Kew, and can be accessed by anyone who can read and has the right credentials.

'It is ironic, but the 15-year-old version is unreadable, while the ancient one is still perfectly usable,' said computer expert Paul Wheatley. 'We're lucky Shakespeare didn't write on an old PC.'

Nor is the problem a new one. A crisis in digital preservation now afflicts all developed countries. Databases recorded in old computer formats can no longer be accessed on new generation machines, while magnetic storage tapes and discs have physically decayed, ruining precious databases.

For millennia, men and women have used paper to create everything from the Dead Sea Scrolls to Neville Chamberlain's 'piece of paper from Herr Hitler'. In the past few decades, computers, scanners, cassettes, videos, CDs, minidiscs and floppy disks have been used to replace the written word. Yet in just a few short years these digital versions have started to degrade.

The space agency Nasa has already lost digital records sent back by its early probes, and in 1995 the US government come close to losing a vast chunk of national census data, thanks to the obsolescence of its data retrieval technology.

Betamax video players, 8in and 5in computer disks, and eight-track music cartridges have all become redundant, making it impossible to access records stored on them. Data stored on the 3in disks used in the pioneering Amstrad word-processor is now equally inaccessible.

Our digital heritage - only a few decades old - is already endangered, as broadcaster Loyd Grossman pointed out last week. 'Last year marked the 30th anniversary of email, but it is salutary that we do not have the first email message and no knowledge of its contents,' he said at the launch of the Digital Preservation Coalition. Saving Domesday Project is viewed as one of the coalition's top priorities.

Guambat really, really hopes you have stuck with this post down to here, because this is where tragedy meets irony. The Doomsday Preservation Group website contains the following message (click to enlarge; right click to open enlargement in new tab):

http://www.domesday1986.com/domesday-preservation-adrian-pearce.html

See also this informative piece,

Lost in Cyberspace: The BBC Domesday Project and the Challenge of Digital Preservation (Released June 2003)

We're not talkin' Kiwis or sheep here, but ...

Neanderthals and humans interbred, fossils indicate

Humans and Neanderthals likely interbred 50,000 to 80,000 years ago in the Near East, concludes the international genetics team's pair of studies in the new issue of the journal Science.

It turns out, based on a new fossil analysis out Thursday, that people of European and Asian descent inherited a small amount, an average 1% to 4% of their genes, from the extinct species. The finding splits the difference in a long-running scholarly debate over whether people are solely African in origin, or spring from "multiregional" interbreeding of early human species.

Stocky, thick-browed and heavy-boned, the Neanderthals last shared a common ancestor with the African precursors to modern humans about 500,000 years ago. The Neanderthals populated the Near East and Europe until they vanished from the fossil record about 30,000 years ago. The gene maps produced by the DNA analysis of the bones found Neanderthal genes scattered randomly among non-Africans, Paabo says, indicating they don't account for any racial differences between modern-day Africans and anyone else. Also, the study finds no sign of human genes intruding into the Neanderthal lineage.

The studies also revealed a few dozen genes altered in humans since they genetically diverged from Neanderthals; some related to skull and brain development. But overall, "they were not very genetically distinct from us," Paabo says.