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LEAVING MY DEPARTMENT'S BEER HOURS

credit: Stephen

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My favorite quote:

  In order to move forward, a scientist must have the courage to take the risk of being wrong. You stick your neck out so that you can perhaps see a bit farther than the others.

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The architecture of RNA polymerase fidelity

The basis for transcriptional fidelity by RNA polymerase is not understood, but the ‘trigger loop’, a conserved structural element that is rearranged in the presence of correct substrate nucleotides, is thought to be critical. A recent study sheds new light on the ways in which the trigger loop may promote selection of correct nucleotide triphosphate substrates

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Restriction enzymes are commonly used by molecular biologist to be able to cut and paste genes into systems for expression or cloning.

.           Ribbon diagram of the restriction enzyme EcoRI

           Restriction enzymes are naturally occurring enzymes that cut DNA. Many restriction enzymes have been isolated from bacteria, providing a valuable tool for molecular biologists. Enzyme EcoR1 is an endonuclease enzyme isolated from strains of E. coli, and is part of the restriction modification system. It cuts one strand of the DNA double helix at one point and the second strand at a different, complementary point (between the G and the A base). The separated pieces have single stranded “sticky-ends,” which allow the complementary pieces to combine.

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Just a Reminder...

To everyone out there. Earlier today, we as a species sent an SUV sized rover nearly 570 million kilometers through outer space, to a spot ~22km in diameter on another planet. It made its way by falling through this planets atmosphere, deploying a parachute, hovering with rockets above the surface, then lowering itself to the ground via a crane system. All done autonomously. This plutonium powered rover carries with it miniaturized, state-of-the-art laboratory with a piece of equipment designed to detect groups of molecules present in any samples by obliterating them with its mounted laser. Go us.

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The Mars Curiosity Rover will be the largest man-made object ever to land on another planet, and it’s predicted to touch down on Sunday August 5 or Monday August 6, depending on where you are—just hours away.

Landing Time:

10:31 p.m. US Pacific Standard Time

1:31...

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WHEN MY STATS COME BACK INSIGNIFICANT

credit: Luke

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The physics of pitching a baseball

Recently, I stumbled on a story about New York Yankees pitcher Freddy García. In april of 2011, García was pitching against the Toronto Blue Jays. In the top of the 5th, Garcia threw this pitch to batter Juan Rivera. Now to the casual baseball observer, you might think this was just was an exception throw, which it was, but then move on to the rest of the game. However, to the folks who watch these events carefully, there was something unusual about this pitch. So unusual in fact, that there existed at the time no physical explanation for that observed movement of a baseball.

There are a number of forces acting on a pitch. The most basic ones we can initially think of are 1) the forward force given to the ball by the pitcher and 2) the force of gravity. The less force a pitches gives to the ball, the longer it will take the ball to arrive to the catcher and the more time gravity will have to accelerate the ball toward the ground.

Typically, to get movement on a baseball that deviates from this gravity dependant sinking, a pitcher will alter his grip to deliver the pitch with different kinds on spin it. This spin alters the way air flows around the ball as it heads toward the catcher. This 3rd force, caused by the the Magnus Effect, tells us that there will be a force on the ball perpendicular to the axis of rotation. If a pitcher throws a 4-seam fastball with enough backspin, the magnus force be greater then the force of gravity (at least over the 60 feet 6 inches between the pitchers mound and the catcher) and cause the ball to rises up on the batter. This is due to how air flows around a spinning ball. Much like how the wing of an airplane alters airflow, the spinning ball causes differences in air pressure around in, resulting in a new force component.

These three forces are all well and good for explaining most movement on a baseball, but they dont explain García's pitch. There is only a small amount of backspin on a relatively slowly thrown ball, which explains why gravity has time to pull it down. However, the ball cuts to the pitchers left, while the Magnus effect would predict rightward motion due to its spin. So what's going on??

Australian physicist (and apparent baseball and cricket enthusiast) Rod Cross discovered an explanation for this effect by testing polystyrene balls, which are lighter and show exaggerated movements. In his paper published in American Journal of Physics earlier this year, Rod demonstrated how the seam of a cricket ball, along with surface difference that accumulate during a game, affect the movement of the ball when bowled.

But a cricket ball has its seam straight down the middle, while a baseball has its seam in a figure eight pattern. So how are the two connected? If you watch the original video of García's pitch closely, you'll notice that the axis of rotation of the ball is such that the smooth face of the ball is always toward the axis of rotation (top left of ball). Most of the time this isn't the case, and the ball rotates in a way to average out its smoothed and seamed faces. Because of that, this effect is almost never observed.

Check out the man himself explaining it:

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Sciencesoup's Basass Scienctist of the Week: Lynn Margulis

Badass Scientist of the Week: Lynn Margulis

Lynn Margulis (1938–2011) was a world-renowned evolutionary biologist, a member of the US National Academy of Sciences, a recipient of the National Medal of Science, and one of the most creative challengers of mainstream Darwinian thinking. She was born in Chicago, and after just two years of high school, she began studying at the University of Chicago. It was here that, aged 16, she met the infamous Carl Sagan, whom she married two years later. After completing a Master’s degree in Genetics and Zoology and a PhD in Genetics, she and Sagan divorced, and Margulis moved to Boston to teach fulltime at Boston University, continue to research, and raise two children at the same time. It was at this time that she began to challenge what she called “ultra-Darwin orthodoxy”, downplaying the traditional natural selection idea of competition and instead suggesting that symbiosis is equally important feature—i.e., cooperation. Her idea was considered evolutionary heresy and her findings were rejected by 15 academic journals—as were her grant applications. One read: “Your research is crap. Don’t ever bother to apply again.” Margulis, however, continued to collect data and finally published her paper in 1967. Soon, data to support symbiosis accumulated and it became an orthodox theory, and Margulis came to be regarded as a respected researcher. Her expertise in microbes also led her to the British atmospheric chemist James Lovelock, with whom she developed the concept of “Gaia”, which proposes that the Earth is a self-regulating living ecosystem, all life locked in a symbiotic relationship. Margulis was committed to helping the public understand science, and she lectured, produced videos and reviews, and wrote a range of popular science books all throughout her life. She passed away at 73 following a stroke. Without creative, persistent rebels like her, science would never progress.

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Check out this NOVA clip explaining the importance of the new Mars mission and some details on how its all going down.

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Through the assembly of genetic components into “circuits” that perform logical operations in living cells, synthetic biologists aim to artificially empower cells to solve critical problems in medicine, energy and the environment. To succeed, however, they’ll need far more reliable genetic...

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WHEN I PRESENT GOOD RESULTS AT THE GROUP MEETING

credit: Annelyticalchemist

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WHEN SOMEONE ASKS ABOUT THE RELEVANCE OF MY RESULTS

credit: Kate

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The Conversion of a Climate-Change Skeptic

Richard Muller, a professor at University of California Berkeley and a MacArther Foundation fellow, was a strong global warming skeptic only three years ago. In his recent NY Times op-ed, Muller lays out the logic behind his seemingly abrupt change in thinking. Richard began gathering and analyzing data through a scientific project started up with his daughter. The group, Berkeley Earth Surface Temperature, was able to include in their temperature analysis data much earlier points in history than previous studies. In addition, the group was able to use data from significantly more weather stations by demonstrating that the numbers they reported, previously believed to be unreliable, were statistically valid. Those data were then fit to various models. Some of those models including warming affects due to solar changes, some to urban sprawl, and others to periodic shifts in global climate. However, the model which best fit the data was one in which elevations in the surface temperature of the earth (2.5F in the last 250 years, 1.5F in the last 50, source) was increasing atmospheric carbon dioxide.

Later in his op-ed, Richard goes on to say:

These facts don’t prove causality and they shouldn’t end skepticism, but they raise the bar: to be considered seriously, an alternative explanation must match the data at least as well as carbon dioxide does...Our result is based simply on the close agreement between the shape of the observed temperature rise and the known greenhouse gas increase.

One of the most poorly understood concepts held by the public about science is the scientific method. The workflow of any good scientist is to collect their data, create a model which fit all of their own and others data, then run new experiments which test theories their model predicts. Any new data that doesn't fit the model present an opportunity to learn and gain insight to some truth previously obscured.

In his work, and in his thinking as well, Richard demonstrates this eloquently.

Interviews with Richard can be found here and here.