Sandwalk: The Central Dogma Dies Again! (not)

You expect IDiots to be idiots so it's not surprising that they consistently screw up their analyses of scientific papers. The latest is a post by David Taylor on the Central Dogma of Molecular Biology [Revisiting the Cental Dogma] [Revisiting the Central Dogma]. He has just noticed a paper published in 2011 where two scientists challenge the Central Dogma. Naturally, this is interpreted to mean that Intelligent Design Creationism is true.

It's frustrating to read yet another scientific paper announcing the demise of the Central Dogma of Molecular Biology. If you've been following the literature, you'll know that the Central Dogma is regularly killed off about ten times per year?a rate that's been fairly constant for thirty years. But to paraphrase Mark Twain, reports of the death of the Central Dogma are greatly exaggerated.

Let's look at the paper by Sarah Franklin and Thomas M. Vondriska from the David Geffen School of Medicine in Los Angeles California (USA) (Franklin and Vondriska 2011). This is a paper that specifically addresses the Central Dogma of Molecular Biology so you'd expect that the authors understand what they are attacking, right?

Here's the opening paragraphs ...

Arguably the greatest postmodern coup for reductionism in biology was the articulation of the central dogma.¹ Not since ?humors? were discarded from medical practice and logic and experiment instituted as the cornerstones of physiology (which they remain today) had such a revolutionary idea transformed biology and enabled scientific inquiry. Because of its simplicity, the central dogma has the tantalizing allure of deduction: If one accepts the premises (that DNA encodes mRNA, and mRNA, protein), it seems one cannot deny the conclusions (that genes are the blueprint for life). As a result, the central dogma has guided research into causes of disease and phenotype, as well as constituted the basis for the tools used in the laboratory to interrogate these causes for the past half century.

The past decade, however, has witnessed a rapid accumulation of evidence that challenges the linear logic of the central dogma. Four previously unassailable beliefs about the genome?that it is static throughout the life of the organism; that it is invariant between cell type and individual^2?4; that changes occurring in somatic cells cannot be inherited (also known as Lamarckian evolution⁵); and that necessary and sufficient information for cellular function is contained in the gene sequence?have all been called into question in the last few years. Revelations of similar scale have occurred in the transcriptome, with the discovery of the ubiquity (and variety) of mRNA splicing.⁶ So too with the proteome, which has undergone perhaps the most dramatic shift in understanding as a result of the aforementioned changes to the transcriptome and the genome, as well as by the explosion of technology development that has enabled both quantitative and qualitative analysis of large groups of proteins and their modifications in a single experiment. It is now clear that information flows multidirectionally between different tiers of biological information, of which genes, transcripts, and proteins constitute only the most obvious ³.

Reference 1?the reference to the meaning of the Central Dogma?is the Nature paper published by Francis Crick in 1970. That paper was intended to clarify the meaning of the Central Dogma after the discovery of reverses transcriptase. Crick was concerned about the fact that many scientists were confused about the meaning of the Central Dogma so he attempted to set them straight by clearly stating that the Central Dogma was NOT "DNA makes RNA makes protein" (the Sequence Hypothesis) but ....

... once (sequential) information has passed into protein it cannot get out again (F.H.C. Crick, 1958)

The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. (F.H.C. Crick, 1970)

I explained this in Basic Concepts: The Central Dogma of Molecular Biology.

Since Sarah Franklin and Thomas M. Vondriska reference the 1970 Crick paper, you'd expect them to have read it but they clearly haven't read it at all or they would know that their definition of the Central Dogma is wrong. I don't understand how this happens. How is it possible that two scientists could publish a paper criticizing the Central Dogma without even knowing what the Central Dogma actually says? How is it possible that the reviewers and editors of this journal could let such a paper be published?

For that matter, how is it possible to publish yet another paper announcing the death of the false version of the Central Dogma? How many times can you beat a dead horse even if it's a mythical horse?

Footnote: Let's look at the "Four previously unassailable beliefs about the genome."

1. (the genome) is static throughout the life of the organism. We've known that this is untrue since the 1970s when genome rearrangements in bacteria were discovered. We've known about immunoglobulin gene rearrangements for over twenty-five years. We've known about mating type in yeast for at least as long as that. We've known about drastic genome rearrangements in protozoa since the 1980s. I assume that what Franklin and Vondriska really mean to say is they have just discovered what they should have learned as undergraduates.
2. (the genome) is invariant between cell type and individual. See above. Read a textbook.
3. changes occurring in somatic cells cannot be inherited (also known as Lamarckian evolution. I'm not sure what this means. Do they mean that changes occurring in somatic cells can somehow be transferred to the germ line and inherited by offspring?
4. necessary and sufficient information for cellular function is contained in the gene sequence. A basic principle of biology is that you need a cell to make another cell. Most people learn this in high school.

---

Crick, F.H.C. (1958) On protein synthesis. Symp. Soc. Exp. Biol. XII:138-163.

Crick, F. (1970) Central Dogma of Molecular Biology. Nature 227, 561-563. [PDF file]

Franklin S. and Vondriska, T.M. (2011) Genomes, Proteomes, and the Central Dogma. Circulation: Cardiovascular Genetics 4:576 [doi: 10.1161/?CIRCGENETICS.110.957795]

Source: http://sandwalk.blogspot.com/2012/11/the-central-dogma-dies-again-not.html

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Obama to visit Myanmar, Cambodia, Thailand

WASHINGTON (AP) ? Less than two weeks after his re-election, President Barack Obama will become the first U.S. president to visit the once pariah nation of Myanmar, drawing attention to the country's shift to democracy and highlighting what his administration regards as a marquee foreign policy achievement.

Obama will also travel to Cambodia, a first for a U.S. president as well, and to Thailand during the Nov. 17-20 trip. In Cambodia, the president will attend the East Asia summit in Phnom Penh and meet with leaders of the Association of Southeast Asian Nations.

The symbolic highlight of the trip, no doubt, is Obama's stop in Myanmar, also known as Burma, a country emerging from five decades of ruinous military rule. While there, Obama will meet with President Thein Sein and also with Nobel laureate Aung San Suu Kyi, the White House said.

While the trip places new focus on Obama's foreign policy and to American attention to the Asia and Pacific region, it also comes at as Obama begins sensitive negotiations with congressional leaders about how to avoid looming tax increases and steep cuts in defense and domestic spending.

Obama ended the longstanding U.S. isolation of Myanmar's generals, which has played a part in coaxing them into political reforms that have unfolded with surprising speed in the past year. The U.S. has appointed a full ambassador and suspended sanctions to reward Myanmar for political prisoner releases and Suu Kyi's election to parliament.

In a statement, White House press secretary Jay Carney said Obama intended to "speak to civil society to encourage Burma's ongoing democratic transition."

A procession of senior diplomats and world leaders have traveled to the country, stopping both in the remote, opulent capital city Naypyitaw, built by the former ruling junta, and at Suu Kyi's dilapidated lakeside villa in the main city Yangon, where she spent 15 years under house arrest.

The East Asia Summit in Cambodia will also provide Obama with opportunities for possible sideline discussions with a number of fellow heads of state, including leaders such as outgoing Chinese Premier Wen Jiabao. Also expected to attend are Russian President Vladimir Putin and Japanese Prime Minister Yoshihiko Noda.

"The Myanmar trip is potentially historic, and for that reason has both tremendous opportunity and risk associated with," said Matthew Goodman, a former Obama international economics adviser.

But the East Asia Summit, he added, is also important "as an opportunity to reaffirm U.S. engagement as an Asia-Pacific power in regional affairs and for the newly re-elected president to touch base with all the relevant regional allies, partners and other countries."

"There's going to be great interest in understanding his aspirations for his second term, and on Obama's side for reassuring these other countries about continuity and desire for continued engagement," Goodman, now at the Center for Strategic and International Studies, said.

As for Myanmar, the most senior U.S. official to visit previously is Hillary Rodham Clinton who in December became the first U.S. secretary of state to travel to Myanmar in 56 years.

The Obama administration regards the political changes in Myanmar as one that could dilute the influence of China in a country that has a strategic location between South Asia and Southeast Asia, regions of growing economic importance.

But exiled Myanmar activists and human rights groups are likely to criticize an Obama visit as premature and one that rewards Thein Sein before his political and economic reforms have been consolidated. The military is still dominant and implicated in rights abuses. It has failed to prevent vicious outbreaks of communal violence in the west of the country that have left scores dead.

In a statement Friday, the government of Myanmar said it "warmly welcomes" Obama's upcoming visit and a spokesman for the country's president said the U.S. support would strengthen Myanmar's commitment to reform.

The spokesman, Maj. Zaw Htay, said the government hopes "bilateral relations and cooperation will significantly increase after this historic visit."

While no U.S. president has ever visited Cambodia or Myanmar, Thailand is one of the America's oldest allies in Asia and has been a stop for American commanders in chief since the mid-1960s, according to the State Department historian's office, which compiles records on presidential travel.

George W. Bush visited Thailand twice while president, in 2003 and 2008, Bill Clinton visited in 1996. During the war in neighboring Vietnam, Richard Nixon traveled there in 1969 and Lyndon Johnson in 1966 and 1967, the records show.

___

Associated Press writers Matthew Pennington and Matthew Lee contributed to this report.

Source: http://news.yahoo.com/obama-visit-myanmar-cambodia-thailand-190753640--politics.html

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Comet collisions every 6 seconds explain 17-year-old stellar mystery

Friday, November 9, 2012

Every six seconds, for millions of years, comets have been colliding with one another near a star in the constellation Cetus called 49 CETI, which is visible to the naked eye.

Over the past three decades, astronomers have discovered hundreds of dusty disks around stars, but only two ? 49 CETI is one ? have been found that also have large amounts of gas orbiting them.

Young stars, about a million years old, have a disk of both dust and gas orbiting them, but the gas tends to dissipate within a few million years and almost always within about 10 million years. Yet 49 CETI, which is thought to be considerably older, is still being orbited by a tremendous quantity of gas in the form of carbon monoxide molecules, long after that gas should have dissipated.

"We now believe that 49 CETI is 40 million years old, and the mystery is how in the world can there be this much gas around an otherwise ordinary star that is this old," said Benjamin Zuckerman, a UCLA professor of physics and astronomy and co-author of the research, which was recently published in the Astrophysical Journal. "This is the oldest star we know of with so much gas."

Zuckerman and his co-author Inseok Song, a University of Georgia assistant professor of physics and astronomy, propose that the mysterious gas comes from a very massive disk-shaped region around 49 CETI that is similar to the sun's Kuiper Belt, which lies beyond the orbit of Neptune.

The total mass of the various objects that make up the Kuiper Belt, including the dwarf planet Pluto, is about one-tenth the mass of the Earth. But back when the Earth was forming, astronomers say, the Kuiper Belt likely had a mass that was approximately 40 times larger than the Earth's; most of that initial mass has been lost in the last 4.5 billion years.

By contrast, the Kuiper Belt analogue that orbits around 49 CETI now has a mass of about 400 Earth masses ? 4,000 times the current mass of the Kuiper Belt.

"Hundreds of trillions of comets orbit around 49 CETI and one other star whose age is about 30 million years. Imagine so many trillions of comets, each the size of the UCLA campus ? approximately 1 mile in diameter ? orbiting around 49 CETI and bashing into one another," Zuckerman said. "These young comets likely contain more carbon monoxide than typical comets in our solar system. When they collide, the carbon monoxide escapes as a gas. The gas seen around these two stars is the result of the incredible number of collisions among these comets.

"We calculate that comets collide around these two stars about every six seconds," he said. "I was absolutely amazed when we calculated this rapid rate. I would not have dreamt it in a million years. We think these collisions have been occurring for 10 million years or so."

Using a radio telescope in the Sierra Nevada mountains of southern Spain in 1995, Zuckerman and two colleagues discovered the gas that orbits 49 CETI, but the origin of the gas had remained unexplained for 17 years, until now.

###

University of California - Los Angeles: http://www.newsroom.ucla.edu

Thanks to University of California - Los Angeles for this article.

This press release was posted to serve as a topic for discussion. Please comment below. We try our best to only post press releases that are associated with peer reviewed scientific literature. Critical discussions of the research are appreciated. If you need help finding a link to the original article, please contact us on twitter or via e-mail.

This press release has been viewed 38 time(s).

Source: http://www.labspaces.net/125196/Comet_collisions_every___seconds_explain____year_old_stellar_mystery_

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Obama to hold news conference on Wed.

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Multiple Sclerosis Research: Research: Some exercise is good for you

Epub: Garrett M et al. Exercise in the community for people with minimal gait impairment due to MS: an assessor-blind randomized controlled trial Mult Sclerosis [Epub Nov] doi: 10.1177/1352458512461966

Background: While there is an increasing body of evidence supporting the efficacy of exercise in people with multiple sclerosis (MS), additional information on the effectiveness of combining aerobic and resistance training, and yoga is required.

Objectives: This study evaluated the effectiveness of community exercise interventions for people with MS having minimal gait impairment.

Methods: A multi-centred, block-randomised, assessor-blinded, controlled trial was conducted. Participants were randomised in groups of eight to physiotherapist (PT)-led exercise (n = 80), yoga (n = 77), fitness instructor (FI)-led exercise (n = 86) and they took part in weekly community-based group exercise sessions. Those in the control group were asked not to change of their exercise habits (n = 71). The primary outcome was the Multiple Sclerosis Impact Scale (MSIS) 29v2 physical component, measured before and after the 10-week intervention. Secondary outcomes were the MSIS 29v2 psychological component, the Modified Fatigue Impact Scale (MFIS) and the 6-Minute Walk Test (6MWT).

Results: The group x time interaction approached significance for the MSIS-29v2 physical component (f = 2.48, p = 0.061) and MFIS total (f = 2.50, p = 0.06), and it was significant for the MFIS physical subscale (f = 4.23, p = 0.006). All three exercise interventions led to a statistically significant improvement on the MSIS-29 psychological component and both the MFIS total and physical subscales, which were greater than the control (p < 0.05). Only the PT-led and FI-led interventions significantly improved the MSIS-29 physical and 6MWT to levels greater than the control (p < 0.05).

Conclusions: This study provides evidence for the positive effect of exercise on the physical impact of MS and fatigue. The group nature of the classes may have contributed to the positive effects seen on the psychological impact of MS.

As we have said many times before exercise is good for health. Maybe join me on the Not so Great North Run.

Source: http://multiple-sclerosis-research.blogspot.com/2012/11/research-some-exercise-is-good-for-you.html

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The Air Car Rides Again?

The air-powered car: It?s one of those elusive but irresistible ideas. PM highlighted one attempt at a pneumatic car as early as 1945, yet none has managed to come close to the internal combustion engine in terms of range.

That hasn?t stopped modern companies from trying. Indian automaker Tata?s range of Air Cars, powered by 4350 psi of compressed air, were announced in 2007. But the technology, licensed from Luxembourg-based Motor Development International, never quite made it. When the company failed to deliver in 2009, onlookers, including PM, began to cast doubts. "We found that it wouldn?t be able to perform in normal driving conditions," says Andrew Papson, a senior associate at technology consulting firm ICF International. He co-authored the study that debunked the compressed-air car. "You wouldn?t get the range that would make a car feasible."

With so many years of air-car technology being five years away, you can understand the modern skepticism that this technology will ever come to fruition. But here comes a new and interesting idea to the fray.

Soft-spoken Peter Dearman has been quietly toiling away in a garage in the Midlands of Britain, developing his own take on the pneumatic engine. Instead of relying on compressed air?with an energy density that pales in comparison to that of gasoline or lithium-ion batteries?his Dearman Engine uses liquid air, which, according to his Dearman Engine Co., has a density similar to lithium-ion batteries?an important hurdle to overcome if air-powered cars are to travel any significant distance before refueling.

Rather than behaving like a volatile propellant such gasoline or hydrogen, liquid air acts more as a non-chemical battery, functioning as a medium for energy transfer. Industrial gas companies have long produced liquid gases using what?s called the Joule-Thomson effect. Essentially, it works by compressing the air, whisking away any heat produced by compression, and then expanding it back to ambient pressure, further cooling the gas. When cooled to minus 321 F, the air turns into a liquid?effectively storing the energy required to cool it.

While it doesn?t produce the liquid air onboard, Dearman?s engine injects the liquid from a vacuum-sealed tank into a cylinder at ambient temperature; the liquid sublimates, instantly transitioning to a gas and releasing a surge of energy through gas expansion that drives a piston. It?s the elementary mechanics of an engine, minus an ignition system and combustion cycle.

And so far it works, in practice. Dearman retrofitted his engine to a small hatchback and was able to hit speeds of up to 35 miles per hour, he told Sky News, with nothing but cold air coming out of the tailpipe.

According to Mika?l Toussaint, a spokesman for Dearman, the engine can output a maximum of 94 hp. Not too shabby for a car that runs on the very same air we breathe. Engineering firm Ricardo is refining a demonstration version of the Dearman engine for a late 2013 release?though we?ve heard that one before.

Is Dearman?s engine ready for the road? Papson says that the technology makes sense to him, but he?s skeptical of its efficiency. In terms of energy density?a crucial metric for determining a car?s range?liquid air and lithium-ion batteries are not equals, Papson says. He cites one study done in 1988, in which a team of Stanford researchers pinned the energy density of liquid air at 181 watt-hours per liter (w-hr/l). Although that?s much greater than compressed air?s 16.7 w-hr/l, it?s less than a quarter of what modern lithium-ion batteries can do.

Energy-density issues aside, there?s still the issue of efficiency. "The big question about this technology is not the fuel itself, but how it?s expanded and how it goes through the engine," Papson says. "Even if you have a liquid-air tank that has the same energy as automotive batteries, if it?s expanded poorly you could use half of that just in the thermodynamic process."

Indeed, Dearman?s numbers point toward this conclusion. Running at ambient temperature, the specific energy?a measure of how much power is in one kilogram?of the liquid air in Dearman?s engine peaks at 87 w-hr/l; less than half what the Stanford researchers reported possible. Even introducing low-grade waste heat to improve the efficiency of the reaction with a small-diesel-engine hybrid system bumps the energy availability up to only 104 w-hr/l. That?s a drastic improvement over compressed-air cars in terms of energy density. But compared to EVs?which tout roughly 80 percent efficiency?the Dearman Engine just doesn?t make sense in a transportation application, Papson says.

However, just because liquid-air-powered engines might not work in cars doesn?t mean they can?t work elsewhere.

Highview Power Storage, another UK-based company, took the idea of liquid air functioning as a battery, and adapted it to store energy generated by wind turbines and other sources of renewable energy. "Essentially, what we?ve done is married two industries," Highview COO Toby Peters says.

Like Dearman?s engine, Highview?s system uses liquid air as a nonchemical battery, using off-peak generated power to cool air into a liquid and storing energy in the process. When demand rises, the liquid air is boiled off, spinning a turbine and regenerating energy during peak hours. When used in tandem with the waste heat produced from an industrial plant, the system is up to 70 percent efficient, Peters says.

Storing power is not a major issue for thermal power plants that can increase generation to meet high demands. But it?s a huge concern for "wrong time" renewable energy. "The wind is blowing at three o?clock in the morning, but you need the power at seven o?clock in the morning," Peters says. "Electricity is essentially the only commodity that you can?t warehouse."

For a year, Highview?s pilot program has been storing energy generated from a wind farm in the southeast of England and supplying Britain?s National Grid with 2.5 megawatts per hour during high demand, Peters says. Aside from being relatively location-agnostic, Highview?s technology is built from components that already exist?what Peters calls mature components. "Compressors, turbines, heat exchangers?stuff that comes from a GE catalog," he says. The benefits from using existing components are twofold, he says. "First, you don?t need to invest in new manufacturing plants?which is quite important given the state of the economy. Second, you?ve got components that are well-known, robust, and proven in their performance and longevity."

In an industry that?s in dire need of an inexpensive, zero-emissions system for storing "wrong time" energy, Highview?s solution could be more feasible than any automotive applications for liquid air. "The primary restriction on the car is you have limited space to store fuel," Papson says. "In an industrial application or an energy application you have much more freedom to have large fuel tanks?whatever the fuel may be?then you don?t have to worry about these efficiency issues as much."

Source: http://www.popularmechanics.com/cars/news/auto-blog/the-air-car-rides-again-14543822?src=rss

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Family Movie Guide: Skyfall, Lincoln, and New DVDs

New column: each week we'll be bringing you the best bets for family viewing.

Welcome to the inaugural edition of RT's Family Movie Guide! Each week, we'll be bringing you the best bets for new movies in theater and on DVD and Blu-ray to help you make informed decisions about what films are appropriate for family viewing. This week, we've got Skyfall, the newest installment in the James Bond franchise, as well as Steven Speilberg's historical drama Lincoln and some brand new DVDs. Read on for more information!

In Theaters This Week:

New On DVD:

Source: http://www.rottentomatoes.com/m/1926217/news/1926217/

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Republican VP hopeful Ryan votes in Wisconsin (Reuters)

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