It's Alive! Magnetic putty has all the right moves.

A special thanks to Joanne Manaster for sharing this video on Google+ earlier today. Phenomenal.

The putty looks like living skin growing around and engulfing those poor cubes and balls.

Is it weird that "lava-sphincter" is the thing that pops into my head as I watch this? 

Makes me wonder how those hydrated sacs of molecular machines we call cells move and grow.

Shattering Prince Rupert's Drop

Thank to Dustin from @SmarterYouTube aka "Smarter Every Day" for putting together this mind-shattering explanation of the mysterious Prince Rupert's Drop.

Breaking Data from South Pole

"How the structure in the universe grew over time...a conceptual version using the filament for structure pieces that take shape." ~Paul

News Flash:

McMurdo Station, Antarctica (TPG) -- The ten-meter-telescope at the South Pole has breaking data strongly indicating that our universe is a product of a 7-D printer. The big bang was simply the moment the printer was turned on. That's right! Some unknown entity has created and is operating a printer that can render in seven dimensions and has created our universe, matter, black holes, spiral nebulae, ferns, moons, galaxies and suns. And you.

In conjunction with the Neutrino detector, famously known as “ice cube” and the cosmic ray detector, scientists have strong evidence that everything we have observed to this date is the direct result of a giant machine that is printing the designs of its maker.

“To ascertain the intelligence of a being that would imagine and build a machine to print in seven dimensions is impossible” says Paul Sullivan, South Pole Science Manager.

No one has ever thought to put together data from three concurrent science experiments until last December when a graduate student toured the facilities at McMurdo Station on her way to South Pole.

“What I found was astounding” said Ashaika Jones. “The data from the Cosray detector in McMurdo corresponded almost exactly with the neutrino hits and the Cosmic Microwave Background Radiation (CMBR) numbers. And when you look at the current estimates for Dark Matter, then it really starts to make a compelling argument.

It all makes sense when we realize that Dark Matter is only the raw material for the printer, like plastic. CMBR is the exhaust of the machine. Neutrinos are the stray, wasted power particles and time is simply the fourth dimension. Can we have some Pink Floyd now, please...

To have the capability to print a black hole would require at least seven dimensions of accuracy and thus the current, conservative estimate from astronomers as to the size of the printer. “It could be that the printer has many more dimensions at its disposal” says someone important from NASA. “Why would we think that we are the only thing that has been printed by a such a wonderful contraption?”

This new information, while still under confirmation by peer-review, has already thrown the stock-markets into chaos, the Vatican into submission and the general public into silence. The three big questions are now irrelevant and no one is sure where to go next.

The "Intelligent Design" wing of the Tea Party is now claiming divine knowledge and is launching education reform and multiple candidates for state and national positions. Global Warming watchdogs have stopped selling carbon credits and Space Exploration has been put on hold indefinitely. Top scientists from all three experiments and collaborators from around the world have issued statements that confirm the findings but urge caution until all the data has been scrutinized.

In a way, we have discovered the Aliens, but creatures so remote and large that we would have little chance of communicating or interacting with them. It would be like a bacteria, trying to communicate with us. Not even bacteria, it would be as if a molecule we printed tried to make contact. We would not even think to look for it.

Aside from the obvious consequences of our entire known universe being a tchotchke on a shelf, a trivial plaything of some grandly larger universe, life may or may not go on as usual down here on Earth. 

Certainly we will all be humbled into a reality very different from the one we now know. Certainly, we will reconsider many things, from epitaphs to charitable contributions to fresh drinking water. We will, most likely, note the day that the mystery was stripped from our psyche and replaced with the certainty of inconsequence. Perhaps we will stop funding science altogether, knowing that we really don't want to know the answers to our questions.

So thank you, Ashaika Jones, for your great discovery. I hope you know that your Nobel Prize will be printed on the 7-D printer along with the rest of it and I hope it makes you very, very happy.

This is a TPG Guest-Post from the mind of Terra Sinclair ;)

Super Slo-mo Slinky in HD Glory

Nightfall: minute physics explains

Richard Feynman lectures at Cornell 1964

Big thanks to fellow blogger Jennifer Ouellette for sharing this wonderful lecture on gravity by Richard Feynman at Cornell University recorded in 1964. The preservation of the spirit of great teaching displayed by Feynman is, in my opinion, a testament to the archival value of YouTube.

Tesla Museum!

Nikola Tesla is one of the most unsung heroes in history. But this week Tesla is finally getting the vindication he deserves through an outpouring of public support. An internet Über-site called The Oatmeal run by a young man named Matthew Inman has raised over $1 million to buy the land where the Tesla's old laboratory once stood. Inman partnered with the non-profit organization Indiegogo, and the State of New York to raise the funds to buy the land in just nine days. The plan is to build a kick-ass museum on the site commemorating Tesla's contributions to science and technology.

But who is Nikola Tesla you may ask? 

Born a subject of the Austrian Empire in 1856 Tesla came to the United States from present-day Croatia in 1884 to work for Thomas Edison. A slender man with a well-kept mustache Tesla brought with him his wild eyes and sharp mind filled with ideas that would change the world. Michael Faraday had only recently formalized the concepts of electromagnetism while Tesla used these ideas to build motors that could generate alternating electric current from any kind of turbine. 

Though it was his early investigations into wireless energy transfer that began his career-long mission to bring free electricity to every household on the planet. 

Tesla tried to usher in the age of alternating current, radio, and television with fanfare. However his showmanship as a scientist often made skeptics of his colleagues. When presenting his new concepts he insisted one of his coils be spouting off the visual manifestations of electricity, popping and fizzling so loudly as to make his words inaudible. If his contemporaries could have heard his voice they would see he had an infectious obsession with progress and the idea that the hidden powers of electricity and magnetism could be unlocked to allow humanity to live more easily. 

 

His efforts to realize this vision were thwarted by J. P. Morgan and other financial backers who caught wind of Tesla's scheme to deliver free electricity wirelessly to the public through Tesla's giant telecommunications tower at Wardenclyffe. There was no profit to be made by giving people what the needed freely.

Tesla spent the last years of his life spiraling into madness and obscurity. He did not marry or have any long-term companionship save for the pigeons he fed from his hotel window. He became so obsessed with the number three that all aspects of his life somehow revolved around that number including his chosen place of residence.

Between January 5th and January 8th 1943 Nikola Tesla, like an electron popping out of an uncertain orbital, passed out of earthly existence in room 3327 on the 33rd floor in the Hotel New Yorker.  

The story of this man's life is more magical because of its truth than the most fantastic fiction ever written. I imagine his life as a heavenly existence spent in reality passing time with some of history's brightest stars - Mark Twain, John Muir, Teddy Roosevelt, and Thomas Edison. His vision for free and equitable POWER (in all philosophical and practical definitions of the word) for every man woman and child on earth has still not been fully realized. But as the internet gains depth and gravity this vision is pieced together slowly and perhaps one day will be complete.

I would like to thanks Matthew Inman for his efforts in raising funds for the Tesla Museum. I hope to bring my grandchildren there one day and I will think back to this particular entry on Tom Paine's Ghost.

Yo-Yos in Space!

NASA astronaut Don Pettit gets excited about yo-yos and physics!

Lawrence Krauss at Chautauqua

Lawrence Krauss sat down to record On Being with Krista Tippett at Chautauqua Institution in July 2012. I wrote this post after attending. I am glad to have found the entire interview and Q&A session available to watch on you tube. I'm curious to hear your thoughts. I realize the video is long but it is certainly worth the time.

 

Why Higgs matters? Lawrence Krauss explains

Image courtesy of CERN.

By Lawrence Krauss - Slate

Who would have believed it? Every now and then theoretical speculation anticipates experimental observation in physics. It doesn’t happen often, in spite of the romantic notion of theorists sitting in their rooms alone at night thinking great thoughts. Nature usually surprises us. But today, two separate experiments at the Large Hadron Collider of the European Center for Nuclear Research (CERN) in Geneva reported convincing evidence for the long sought-after “Higgs” particle, first proposed to exist almost 50 years ago and at the heart of the “standard model” of elementary particle physics—the theoretical formalism that describes three of the four known forces in nature, and which to date agrees with every experimental observation done to date.

The LHC is the most complex (and largest) machine that humans have ever built, requiring thousands of physicists from dozens of countries, working full time for a decade to build and operate. And even with 26 kilometers of tunnel, accelerating two streams of protons in opposite directions at more than 99.9999 percent the speed of light and smashing them together in spectacular collisions billions of times each second, producing hundreds of particles in each collision; two detectors the size of office buildings to measure the particles; and a bank of more than 3,000 computers analyzing the events in real time in order to search for something interesting, the Higgs particle itself never directly appears.

Continue reading at Slate.com.

John Robinson - Tiny Ghosts

Brian Greene asks - what is space?

Watch The Fabric of the Cosmos: What Is Space? on PBS. See more from NOVA.

Before Sagan came Bronowski

During my second year of graduate school I became obsessed with Carl Sagan. I read many of his books - Dragons of Eden being my favorite. I incessantly watched episodes of the Cosmos series. The more episodes I watched the more I fell in love with the history of science. It became clear to me that, contrary to popular belief, science is an extremely HUMAN endeavor. The series clearly demonstrated how concepts build on each other over time. Understanding how this process of accumulating concepts works is essential to understanding any one branch of science, no matter how tiny and frail that branch may be.

When I found out that Sagan had based his Cosmos on the earlier work of another I was immediately primed to go deeper into this rabbit hole. His name was Jacob Bronowski and he produced a 13 part series called the Ascent of Man. This series made its debut on the BBC in 1973. Tragically, Bronowski died a year later. Though the title might be a bit misogynistic for this age the messages within are timeless. 

Recently in the middle of dinner at a sushi restaurant here in southern Oregon I had an encounter with a creationist in his early 30s. I saw this as an opportunity to try and teach him the evidence for evolution and the geologic age of the earth in the most direct way possible. One question that many creationists ask is how could a person just come into existence randomly? How could all the atoms of a human being just pop into existence? 

Back at Umi-Sushi this very question was asked. I tried my best to explain that this is not what evolution suggests and that physical beings are the product of millions of years of accumulated chance. I tried my best to explain this and I hope my partner in conversation stayed with me. The fact that he continued to ask questions told me he was indeed open-minded. I caught him at a good time in his life as he was not totally entrenched in his beliefs as I suspect some people can be. Questions were sparked in his head and that was the first step. I wish I had memorized the unscripted monologue Jacob Brosowski launches into in the video below. Beginning at 30:30 in he explains a concept echoed by Carl Sagan - in essence we are made of star-stuff. As I have talked to people over the years who have had their own scientific epiphanies, the epiphany, in many cases begins with this beautiful notion that every human being began to exist in the center of a star somewhere out there. 

Message (Crammed) in a Bottle

To sell a bottle of Champagne as "bubbly" a vendor must ensure the wine has absorbed between five and six atmospheres of carbon dioxide. To anyone who has ever popped the cork on champagne you know there is enough force there to do some serious damage to an innocent bystander in the event of poor aim.

Viruses spend part of their existence as a kind of bottle (capsid) with a message inside (DNA or RNA). The message inside carries the code or blueprint to make more viruses, more messages, more bottles. This message isn't short. If it were written out as As Ts Gs an Cs on regular 8 X 11" printer paper it would take up between 100-200 pages, depending on the specific virus we're talking about. Imagine trying to jam 100 leaves of paper into a wine bottle! The analogy isn't prefect as the viral message looks more like a rope than sheets of paper. Regardless, the message has to be crammed into an extremely tight space. The bottle's volume in this case being 0.065 cubic millimicrons. When the packing is done the DNA or RNA has been condensed from a free floating strand 6,ooo times like a tightly coiled garden hose at immense density. The pressure inside that tiny bottle reaches nearly 60 atmospheres. 10 times the pressure in the champagne bottle!

This raises many questions. How does a virus manage to pull or suck that long piece of rope inside its shell? Especially at the end when the pressure is at its peak? <--- The illustrated capsid cutaway shows the immense density with which the rope is crammed. How does such a tiny bottle not break under such intense pressure? Where's the cork and how does it stay put? And who or what pops the cork?

Dr. Carlos Bustamante of the University of California, Berkeley is answering these questions in incredible detail using single-molecule biophysical techniques. His lab is able to "grab the cat by the tail" and measure individual molecules directly. They specialize in DNA translocases. These are molecular machines or machine-like entities as he calls them.  Tiny "motors" that convert chemical energy into physical energy. When your eyes move to read these words the muscles are using the same chemical reaction's to pull your eyeballs from side to side as a virsus uses to pull that rope inside the bottle. This reaction is the hydrolysis of Adenosine triphosphate, the famed ATP, the energy "currency" of the cell. 

From Morais, M.C., Koti, J.S., Bowman, V.D., Reyes-Aldrete, E., Anderson, D.L., and Rossmann, M.G. 2008. Structure 16:1267–1274. © 2008, from Elsevier.

The viral machine is displayed in panel B. The capsid is pictured in gray while the motor sits at the "gate" and pulls the DNA inside. 

The motor is made of a five piece ring of small RNA molecules (pink) and five ATPases (lavender). In this particular single molecule study they are using two polystyrene beads to tether two ends of a long piece of DNA (the set up is pictured in panel A below). The strand is held in what is called an optical trap - those red sideways vase looking things. I blogged about how optical tweezers work before here's the link if you want to read about how this works. The goal in this study was to capture the capsid on one bead (coated with capsid protein antibodies) and the other end of the DNA  strand is bound to the other bead by a biotin-strepdavidin bridge. Not only did the researchers accomplish this feat but they were able to tug on either side of the system to measure how much force the motor was exerting on the DNA strand as it was sucking it into the capsid.

From Moffitt, J.R., Chemla, Y.R., Aathavan, K., Grimes, S., Jardine, P.J., Anderson, D., and Bustamante, C. 2009. Nature 457:446–1450. © 2009 Nature Publishing Group, a division of Macmillan Publishers Limited.

They discovered that with zero tension the capsid is packed with DNA at the rate of 100-120 base pairs per second. These studies also build a model for how they think the motor is working.  As said before, the motor requires a chemical reaction (hydrolysis of ATP) to work.  In this controlled environment the researches can set the concentration of ATP. When and only when all five site on the motor are loaded with their ATP molecules can the motor pull the strand.  Like a revolver laying with the cylinder open and someone pouring bullets on top of it, the "gun" can only fire after it is fully loaded by the random addition of bullets. When the concentration of ATP is low the rate of firing is less frequent, higher  - more frequent.

The simplicity of this model as understood by observing single molecules, for me, made years of Michaelis-Menten kinetics (the dry math that drives people away from studying biochemistry) come to life in a visual context.  I could see in my mind's eye exactly how concentration affects the rate of a reaction.

Not only were they able to define this requirement but they also show that only 4 of the five ATPs are used per "firing" and that each single ATP molecule hydrolyzing (thus power stroking the motor) corresponds to a pull of 2.5 base pairs.  And, that the motor moves the DNA inside the capsid at 10 base pair intervals (2.5 base pairs x 4 ATPs = 10 base pairs).

This basically means that a lot of energy is required from the surroundings for a virus to be able to package itself.

But when it's finished how does the capsid not explode from all that pressure? This has to do with the structure of the bottle.  The capsid is made of self-assembling capsid proteins that arrange themselves by interlocking joints. Like the ancient cultures of Bolivia who constructed their temples with interlocking rocks to withstand centuries of earthquakes these puzzle-boxes withstand 60 atmospheres of pressure by doing the same. 

The refinement of these models displays the best in what scientific inquiry has to offer in the twenty first century while still reminding us how new evidence can overturn old assumptions. As the trend toward studying single bio-molecules as they do the voodoo they do so well continues, our understanding of nature is refined to unprecedented clarity. 

These results were presented by Dr. Bustamante at the Inaugural Robert W. and A-Young M. Woody Lecture at Colorado State University last Thursday.  When a single lecture can breath new life into a graduate student in the throes of dissertating it says something about the power of good science and good scientific communication. 

Yu, J., Moffitt, J., Hetherington, C., Bustamante, C., & Oster, G. (2010). Mechanochemistry of a Viral DNA Packaging Motor Journal of Molecular Biology, 400 (2), 186-203 DOI: 10.1016/j.jmb.2010.05.002

Moffitt, J., Chemla, Y., Aathavan, K., Grimes, S., Jardine, P., Anderson, D., & Bustamante, C. (2009). Intersubunit coordination in a homomeric ring ATPase Nature, 457 (7228), 446-450 DOI: 10.1038/nature07637

Desktop Diary

This video from Sciencefriday.com displays the habitat of Dr. Brian Greene, author of The Hidden Reality. He is a new hero of mine.

The concept of infinity has always frightened me a little. The thought of numbers so big they are impossible to ever count has caused me to look at my limitations as a human on numerous occasions. One time after I had my appendix removed, I remember lying in the hospital bed crying for my mother because I had had a bad morphine dream. The dream was of the upper half of my body being smothered by a planet that was growing infinitely out of control. My legs were sticking out the bottom with an orb of infinite size squeezing the life from my upper half. It was horrifying.

Anyway. Brian Greene does a wonderful job in his book of laying out the concept of an infinite universe. He almost makes infinity seem comforting in a way. If the universe is indeed infinite, then there should be an infinite number of configurations of particles and that said, there is another person on another earth in another solar system out there who is exactly like me, who is dropping his first post on John Paine's Ghost. That makes the universe seem less lonely.

With a strong recommendation snag a copy.

Brian Jones presents a huge TESLA COIL

I am Iron Man. Thanks for the heads up on this one Jared!

Single Molecule Chromatin Studies

Michelle Wang of Cornell University spoke during the morning session of the Keystone Symposium on chromatin regulation in Taos, New Mexico today. She described her research focused on understanding how nucleosomes behave when they are pulled apart upstream the moving transcription machinery. This is like investigating how a train moves along a track when the track is tied up in knots. The train is the polymerase (transcription machinery) and the track is the DNA. She does this work by using amazingly delicate single molecule studies. By trapping either end of a stand of DNA with nucleosomes assembled and then physically pulling on one side she can observe the corresponding force curve which gives a readout of how strong or weak the histone/DNA interactions are during the pulling event.

I have described the optical tweezing technique for studying single DNA stands on this blog before.

There is also a great summary of her lab's research here.


Hall MA, Shundrovsky A, Bai L, Fulbright RM, Lis JT, & Wang MD (2009). High-resolution dynamic mapping of histone-DNA interactions in a nucleosome. Nature structural & molecular biology, 16 (2), 124-9 PMID: 19136959