Scooped by a Ghost

Usually when you discover something new you wan’t your name on it. Especially if you beat someone to it. I win. Give me my recognition.

But Bruce Spiegelman, a cell biologist at Harvard Medical School’s Dana-Farber Cancer Institute in Boston, Massachusetts, did just get scooped. He was scooped by a mystery man. A publication appeared in Biochemical and Biophysical Research Communications that was an exact mimic of his current—and what he thought was unique—research. He was pissed. You could call him a mad scientist.

http://commons.wikimedia.org/wiki/File:MADMAN.jpg

How I imagine Spiegelman looked when he first saw the paper.

But it turns out the names on the paper are made up. The attributed school, the University of Thessaly, has no idea who these authors are. The email address of the corresponding author is from a domain called mail.com. That should have tipped the editor and reviewers off, but apparently no one bothered to check that these were real people.

Spiegelman insists that the information in the paper was taken from his own work, which he’s presented at 6 academic meetings. (Why he hasn’t gotten around to writing the paper yet, I don’t know.) Although the journal was withdrawn the paper, Spiegelman wants legal action. He wants to find out who wrote the paper and press charges.

What’s strange to me is that someone went to all this trouble to mess with him. The journal article is written well, obviously by a scientists, and argues valid points. After all, the results are real. They just belong to Spiegelman.

Was this a bitter competitor wanting to piss Spiegelman off? Was it an annoyed grad student who wanted to publish but Spiegelman was holding back for whatever reason? Whatever it was, they went to quite a bit of trouble. Passive aggressive science at its best.

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Age of Anthropocene: Let the Sunshine In

I learned today that there’s a chronological term (like Jurassic and Cretaceous) to mark when human activities negatively impacted (I’m a little hasty with the past tense here) the Earth’s ecosystems. The Anthropocene, to my surprise, started 8,000 years ago when humans first started clearing forests and fields to cultivate crops. Our effects were pretty stagnant until about 2,000 years ago when Romans and Chinese were running around building their empires and dynasties. But our destruction really gained speed during the Industrial Revolution when we started spitting plumes greenhouse gases, soot, and metals into the air.

We’ve messed up a lot of things. We know that. Or, at least, most of us know that.

To further prove that our actions really do have consequences, a recent publication in Nature Communications studied the effect of human influence on global tree cover. I had hoped they used Google Earth to map the tree cover, but they were more advanced than my armchair science. To get topography information they used data from Shuttle Radar Topography Mission and something called MODIS, which makes me think of TARDIS but is actually nothing like that (I’ve been watching a little too much Doctor Who lately). Both are NASA projects using satellites to map various aspects of Earth.

They found slopes “act as a refugee for trees.” The more humans came the more trees fled to the slopes, like frightened cats running up the stairs every time the front door opens and someone new struts in. With enough people around, our activities start to dictate where the trees go. Areas with low fertility rates and low projected population growth (they mentioned Switzerland by name) managed to increase tree density on slopes. Which is nice, we’re learning to cohabitate with plants… as long as they stay on the bumpy parts.

Taken from Figure 3.

Relationship between slope and tree cover, which is “strongly skewed” towards positive values.

Another interesting aspect is that they found political and economic models could predict changes in tree coverage. And they made a decent model of just how much our (not so) little human dealings affect the environment. Surprisingly they found tree coverage actually increased between 2000 and 2005 (why they studied tree coverage almost a decade ago is beyond me).

Hopeful researchers predict a transition into the Sustainoscene through renewable energy (the paper I linked was very excited about solar cells) and more environmentally friendly industrial practices. Maybe one day we’ll learn to live on this world without ripping it up. That or discover FTL space travel and a suitable world so we can keep ripping shit up.

Records without the record

I had an idea the other night. My boyfriend has recently gotten into records—yes, they still make records for new music. In the past six months he’s probably bought a hundred records. They’re taking up a lot of room in the living room.

His argument is that the sound quality is better. I didn’t believe him at first, mainly because I didn’t know or care anything about sound quality. Then he put on a band I knew, songs I’ve heard a millions times. I thought I was familiar with every squeak of a finger slide, every sucked in breath—basically all the side noises that come with making music. Then I listened to the record. There was so much going on. Background loops I’ve never heard. Music under the music. He was right, there is no comparison to record quality.

They just take up so much room. They scratch easily. They sell out quickly, and then they get expensive. Hundreds of dollars expensive. I thought of a better way to get record quality without, well, the records.

Imagine you have stimuli-responsive polymer, which is exactly what it sounds like. Now let the stimulus be an electrical pulse and the response be a volume change (it bulks up when you zap it with electricity). This is commonly called a piezoelectric material. Now line the grooves of a traditional record with small squares of electrodes and coat it in the polymer. That’s our new and improved record. You only need one.

Now to get music out of it. Records work by a needle running over little bumps and divots in the spiral grooves, kind of like this road in Lancaster, CA, except in that case the car is the needle. In our system, when you apply an electrical signal to a specific electrode on the imagined record, it would zap the polymer around it and puff up. There’s the bump the needle needs to read music.

All over our record we have electrodes controlled by a computer sending in information on where and how much to electricity to apply (so the position and size of the bump can be controlled). The music file would be stored on a computer in coordinates and electrical strengths (where and how much). The files would be small. Small enough to store all that extra information digital coding cuts out. Small enough for record quality.

In essence, the digital files would be converted to analog. You wouldn’t need a collection of physical records. And they wouldn’t be junking up my living room, Tim.

Simplify the Universe

Particle interactions calculated with a single term all done by hand?! That’s crazy. In case you have nothing to base calculating particle interactions in quantum field theory on, just imagine having thousands of puzzle pieces scattered everywhere to suddenly, without all the pesky pieces, having a single, unified picture. All it takes is some new thinking and a little geometry.

In this new model, physicists describe the universe by an amplituhedron, an infinite-dimensional geometric object. The volume of this object is equal to the scattering amplitude—the holy grail of particle physics—which physicists at the Large Hadron Collider use to describe particle interactions. In some amplituhedrons the amplitudes can be calculated directly. In others diagrams called “twistors” are needed.

What’s more, they’ve found the solution to everything. The volume of an infinite-sided “master amplituhedron” represents the amplitudes of all physical processes. The italics are supposed to impress you. Interactions between a finite number of processes, what us humans normally consider, are contained on various faces. Interesting to me, but probably not to anyone else, is that the master amplituhedron simplifies to a circle in 2D.

Amplituhedron

Amplituhedron representing an 8-gluon particle interaction, which normally needs ~500 pages of algebra.

The amplituhedron removes locality and unitarity. Particles that aren’t near either other in space or time can interact (what?) and the sum of the probabilities for all possible particle positions doesn’t have to be 1 (what?!). That works out for gravity though, which explodes—yes, explodes—in equations with locality and unitarity. Connecting gravity to particle physics is a big deal—no one’s been able to do it yet. Jacob Bourjaily, one of the researchers, described this method as “a starting point to ultimately describing a quantum theory of gravity.”

Nima Arkani-Hamed, the lead author (the main man, the head honcho), gave a talk about amplituhedrons at the SUSY 2013 conference, which is posted online. Warning: the talk is very technical, but interesting nonetheless (if only to watch a man in shorts and a shirt two sizes too large give a spitfire professional talk). Although, in the talk he says amplituhedrons can be “explained to a smart junior high school student,” which left me feeling like a stupid graduate student.

Shut up and calculate!

Quantum mechanics is confusing. Little by little you wrap your head around the math, just going with the assumption that objects are simultaneously particles and waves, until you feel like maybe there’s something to all those wavefunctions and probabilities. Then you ask what it all means. The confusion rushes back as your professor shrugs.

In the 1920s, the founders of quantum mechanics gathered together in Copenhagen, Denmark to discuss what their math said about the physical universe. In the end, they decided there are fundamental limits to what we can know. They came up with the Copenhagen Interpretation, which according to physicist David Mermin of Cornell University means “shut up and calculate!”

Everyone accepted the Copenhagen Interpretation—if the inventors of the theory aren’t quite sure what it means, how are you supposed to know?! But a small group of scientists aren’t content with the ambiguity of quantum mechanics. With the right perspective, they argue, the meaning will become clear.

The Perimeter Institute for Theoretical Physics is hoping to find clarity. As Christopher Fuchs, one of the Institute’s researchers, says the right perspective will “write a story—literally a story, all in plain words—so compelling and so masterful in its imagery that the mathematics of quantum mechanics in all its exact technical detail will fall out as a matter of course.”

Fuchs is proposing the probabilities inherent in quantum mechanics come from the viewer, not from the object itself. He’s designed a new approach called QBism that, using a type of statistics called Bayesian inference, gets rid of the wavefunctions, amplitudes, and Hilbert-space operators—all necessary in quantum mechanics—and replaces them with simple probabilities.

All in all it’s pretty exciting. I’ve been interested in quantum mechanics and what it really means since I was old enough to realize that we, as scientists, don’t really know everything about the universe. It will be a good day when we can explain the meaning of quantum mechanics to elementary school students in an interesting and understandable story. Maybe QBism will give us that story.

My thoughts on GMOs—so much lost potential

Everyone arguing for and against GMOs has it wrong. Genetically modified organisms in and of themselves aren’t the problem. As a species we’ve been cultivating and cross-breeding plants for centuries. Genetic modification speeds the process up. No additional chemicals are added; building blocks are just re-arranged.

The problem isn’t genetically modified organisms. It’s who is doing the modifying. Monsanto is the biggest company right now for GMOed seeds. Almost everything we, and our meat, eat comes from Monsanto crop. They’re big proponents of modifying stronger, more robust crops. (I’m not going to go into their business practices. That’s a whole other post.)

They also edit their product for consumer taste, which sounds great—finally, vegetables I like to eat!—but really isn’t. In general, people don’t like the taste of healthy things. We like cookies and donuts and ice cream cake. We don’t like mealy food, food that you really have to chew at, food that feels a little like a mouth full of chalk. Monsanto, and the other GMO companies, know this. So they take corn and turn it into little pellets of sugar. They take apples and make them more flavorful (which means more sugar). Americans want their food big. They want it cheap. And they want it now. Berries are modified to be twice their size with half the flavor. Tomatoes are almost tasteless. But, boy, look at the size.

We could be using GMOs for good, adding in nutrients and vitamins to our crops, but the process is being abused by consumerism. The point of genetic modification isn’t to “feed the people.” The point is to make money. Stronger crops make more food, are more resistant to disease, and last longer. But they aren’t better for us. The sad part is they could be, if only the modification wasn’t done solely for a profit.