This is Your Brain On Awesome Thoughts on the world from a student of the mind


Technology reveals what the naked eye cannot admire

** Here's another crosspost from the BSR! **

One of the reasons that fields such as biology and chemistry can be difficult for non-scientists to understand is that the objects and processes they study are far too small to be seen with the naked eye.  Envisioning what something like endocytosis might look like is as much an exercise in creativity as reality. However, technology is beginning to bridge this gap, and the result is every bit as fascinating as we could have imagined.

At the University of Cambridge, the "Under the Microscope" project aims to detail the beauty and complexity of biology at its tiniest.  Take, for example, this image of a "Killer T-cell" attacking a cancerous cell in the body:

In this video, we see the Killer T-cell (in green) identify and attack a cancerous cell beneath it (in blue).  While watching it, two things immediately came to my mind.  One was the accuracy of the T-cell in carrying out its duty of destroying the cancerous cell.  The environment was filled with all kinds of tiny cellular neighbors, and yet our hero knew what to aim for and how to get there.

The second thing that intrigued me was just how "living" that Killer T-Cell looked.  It pulsated and gyrated, moving back and forth as though uncertain what direction to take next.  Perhaps it should come as no surprise, but it's amazing to see something so tiny look so alive.

Now for something a little closer to my own field of study:

This is an image of a fly's brain, with a particular network of cells labeled in green. The construction of this image required a detailed understanding of what parts of the genome are responsible for creating he insulin cells imaged in the video.  Scientists altered the sequence of these parts of the genome so that the cells fluoresce in response to certain wavelengths of light.  The result is that we can turn the network of cells on like a lightbulb, revealing the intricate pathways the snake throughout the fly's body.

And for good measure, here's an example of what the non-biological world looks like up close:

What you see above is the growth of a batch of silicon nanowires.  While biology has been operating in the microscopic regime for millenia now, electrical engineering is just beginning to scratch the surface of what we can do with ultra tiny circuits.  From an engineering perspective, scaling components down to the level of nanometers introduces a host of problems (quantum tunneling, anyone?) that will keep researcher's hands full for many decades.

The microscopic world is beautiful because of just how different it is from what we're used to seeing. And yet, these tiny machines have been functioning since the beginning of life itself. What a wonder, then, that after so many years, we finally get to meet them face to face.

Note: If you're interested in University of Cambridge video series, the whole playlist can be found here.


Piecing together the past with IceCube

So it's been a long while since I've posted anything - it turns out that your first year of graduate school is a lot more work than one would think.  However, in a pledge to get back on the ball and write about some more science, here's a cross-post from the Berkeley Science Review.


I'd like all of you to try something before reading this article: go outside (or, if you live in the Bay Area, you may have to settle for your fridge), and take a look a a piece of ice. Doesn't seem to be much going on there, huh? Well, what if I told you that you could measure energy that originated from the creation of the universe using that piece of ice? Setting aside my possible insanity as an answer, you'd probably want a good explanation. Well, without further ado, allow me to explain...

how to see the history of the universe with a piece of ice:

Step 1: raise $271 million in venture capital.
Step 2: built a giant lepton detector in the south pole.
Step 3: record the energy released by sub-atomic collisions originating from the creation of the universe

See how easy that was?

Even if you're unable to carry out this little experiment by yourself, it turns out you're in luck because someone else is already trying it. I'm referring to the IceCube Neutrino Observatory, located in Antarctica.  It's run by researchers at the University of Wisconsin - Madison and aims to tell us something about the distant (and I mean distant) past by measuring the energy emitted in ice deep within the south pole.

The whole process relies on a property of sub-atomic particles called Cherenkov radiation.  Technically, this energy that is emitted when a particle travels faster than the speed of light in a medium.  Now you might not think that's possible, since theoretically nothing can travel faster than the speed of light, but that's where the "medium" part is important.

While light is faster than anything else in a vacuum, it often slows down significantly in some other medium (for instance, it travels about 75% as fast in water).   In such media, it is possible for particles to be accelerated faster than the surrounding light (for those of you with a particle accelerator laying around, give it a try!).

When this happens, a phenomenon occurs that can be likened to a boat traveling through water.  As the particle moves through the medium, it causes nearby atoms to emit light waves that "bunch up" in front of the particle.  The compacted light is then projected diagonally outwards as the particle continues moving, just like the wake of a speedboat.

This phenomenon is called "Cherenkov radiation", and you can see it almost any time a subatomic collision causes particles to burst apart at speeds faster than the speed of light. For example, these collisions occur frequently in nuclear reactors, causing them to emit a beautiful blue glow.

Another common source of faster-than-light particles is cosmic neutrinos that smash into water molecules embedded in ice when the reach the Earth.  This is where IceCube comes in.  Using a "neutrino telescope" -- an array of spherical optical sensors -- scientists located on the Antarctic ice cap are able to record information about Cherenkov radiation emitted during these collisions.

Here's how the process works:  some cosmic event causes a neutrino to go hurtling through space (they are extremely tiny and relatively inert, so they can go a looong ways before hitting anything).  This neutrino makes its way to Earth, where it happens to collide with a frozen water molecule deep within the ice at the south pole.  This collision causes an explosion of high-energy particles, which move so fast through the ice that they emit Cherenkov radiation.  The radiation is recorded by IceCube's detectors, and then analyzed to answer questions about the neutrino's source.

The process is far from perfect. As you might imagine, documenting the travels of a particle that literally crosses the universe to get here is an extremely delicate process.  Moreover, Cherenkov radiation can be generated by many other cosmic processes that don't have anything to do with neutrinos (for instance, from solar storms).  However, the pristine, untouched ice of the south pole gives us the best possible environment to record this activity.

Recording this information is useful for many purposes, but perhaps most interesting of all is that it might tell us something about what kind of event spawned the galaxy that we live in.  Millions of millions of years ago, the cataclysmic events of the early universe sent neutrinos hurtling across the galaxy.  Using information extracted from the neutrinos captured at IceCube, we may be able to infer exactly when and where these massive cosmic events occurred.

So the next time you go outside and complain about how icy it is, think about how many glimpses into the nature of life it might hold...if only you had a neutrino telescope.




Emotions, inspiration, and what it means to be human: an interview with Brian Christian

Brian Christian, bestselling author of The Most Human Human

This is a copy of my article for the Berkeley Science Review.  Check out their website for other sciencey articles and stories!

I'm going to do something amazing today.  I'm going to tell you what it means to be human. Well, actually, Brian Christian, author of the bestselling book The Most Human Human, is going to tell you what it means to be human.

Christian recently passed through Berkeley as part of his nationwide book tour. In between answering his fans' questions about consciousness, creativity, and robotic dating, he took a few minutes to sit down with me and explain why he's so interested in studying the distinguishing characteristics of humans and machines.

Christian's book, in part, describes his experience as a participant in last year's Turing Test, an annual competition in which man and machine vie for the title of "The Most Human". In the competition, a panel of (human) judges engage in short electronic conversations with a hidden responder, either a fellow human or a computer "chatbot". At the end of the conversation, the judges are asked to decide whether the person they were talking to was a human or a chatbot, and the winner is the responder who earns the most "human" votes.

Now you might be thinking "what a silly contest - of course human beings are the most human."  If this thought crossed your mind ten years ago, you'd be absolutely right. However, this intuitive reaction may not ring true for much longer. Chatbots have become increasingly adept at fooling human judges, and in 2009, one program fell just shy of winning the competition.

That brings us to Christian's desire to participate in the Turing test. Being the champion of human nature that he is, Christian heard of the close call and decided to take action by entering himself into the competition. In his words: "I wanted to know how I could get involved on behalf of humanity."

Christian's academic background made him a uniquely qualified competitor in the Turing Test. He holds degrees in Philosophy and Computer Science and at one point worked in a computational psychology laboratory. While these fields might appear to share little in common, Christian finds them "relevant in ways that don’t seem expected. Computer science and philosophy are... both about cognition, but they’re both about rigor.  Breaking things down to an atomic level."

His experience with both computer programming and human psychology has led him to notice the many similarities that exist between the two fields. "It is not a question of silicon vs. cells, it’s a question of the type of thinking." In his book, he provides evidence for this claim by describing an experiment in which computer programs were set up to remotely interact with unwitting human users over the Internet. The results included a teenage girl that would talk for hours with a chatbot, as well as a man that fell in love with an AI woman.

Christian points out that the roles can be reversed, too.  "Think of call operators – if you have to follow this very rigid set of rules, then you are essentially taking a fluid human intelligence and cramming it into the framework of a chatbot."

Nao, a humanoid robot, takes a break after a RoboCup soccer match

According to Christian, the growing similarities between humans and computers have led some people to revisit the definition of what makes us human. "Emotion is a little bit nearer and dearer to us in terms of how we perceive ourselves than it used to be," says Christian, drawing a contrast with the earlier perception that humans were the pinnacle of logical ability.  "It’s funny that we interact with computers so much that we’re [now] more inclined to celebrate those animal-like qualities."

Christian has noticed his own changing views on the subject, saying "as a kid I strove to be hyper rational, and I don’t necessarily do that right now."

Although some emotions may be replicated by machines in the future, Christian does believe in a few human qualities that will remain safe in the long run. "When I think of uniquely human emotions, one of them is curiosity" he says. "It seems like [curiosity is] right on this line where desire and will meet knowledge. I think wonder and awe are also situated in that middle space."

Above all, Christian says, "the most human act is contemplation. For me, the most important thing is to investigate the stuff that interests you and to articulate those thoughts."


For more of Christian's work, check out his article in the Atlantic and his recent appearance on RadioLab.  You should also buy his book.  It's excellent!


How to argue with a fence post

Here's a recent post that I wrote for the Berkeley Science Review.  Looks like I'm finally going to have time to start writing again!

I don't often go off on rants about the importance of science communication (well, not in blog form anyway), but a recent article in Mother Jones magazine got me thinking about how important it is for the scientific community to know how to speak to the public.

The article by Chris Mooney isn't about communicating science per se; it is about making arguments in general. You might think that convincing someone you're right in an argument is dramatically different from telling someone about the awesomeness of the natural world, but (sadly) many public voices in science are faced with just such an antagonistic situation. People don't just believe facts; they believe a selective group of facts that coincide with their particular worldview or belief system. Mooney describes a number of belief "experiments" that shed some insight into the ways that people incorporate information into their beliefs. Perhaps most interesting is the extent to which vastly different groups are guilty of the same practices.

Take for example the Seekers, a small cult based in Chicago in the 1950s. They were thoroughly convinced of their ability to communicate with ethereal aliens, one of whom was believed to be some sort of cosmological version of Jesus Christ (adding weight to my own theory that old JC was, in fact, a Time Lord). Like so many cults before (and after) them, the Seekers saw their day of reckoning come and go with nary a revelation nor apocalypse. Reason might suggest that these misled folks would end it there, that they'd pack up their bags, return to their lives (what was remaining of them, since many had sold their possessions and quit their jobs in anticipation of the big day), and agree not to speak of their monumental goof ever again.

But you probably know that's not what they did. Instead, they began to rationalize for what had occurred, suggesting that they had actually diverted an apocalypse from happening. An announcement was made to the world, lauding the Seekers for their devotion and suggesting that "the little group, sitting all night long, had spread so much light that God had saved the world from destruction." Sounds familiar, no?

These guys believed something that was obviously, painfully false. They were cult members... inherently irrational, right? Unfortunately, Mooney also points to a number of studies addressing how unwilling most people are to change their minds in the face of evidence that runs counter to their beliefs. In one study, liberals and conservatives were presented with an article about the 9/11 commission's findings on the lack of WMDs in Iraq. Many of the conservative participants were more likely to believe that WMDs had been hidden than before they read the article.  (Liberals shouldn't feel too high-and-mighty either. Similar effects have been found on both sides of the political spectrum.)

So why is this important in the world of science? An unfortunate thing about reality is that it often presents itself to us in unintuitive or confusing ways.  As scientists, our job is to wade through all that ambiguity and make sense of the tiny bits of truth that can be found in any set of data. Thus, we are often faced with the difficult challenge of making a case for a concept or theory that runs counter to what most people already believe. Ideally, the facts we have gleaned from our research would be enough to convince the public. In reality, we know that rarely happens.

This (finally) brings me to the topic of science communication. In a world full of individuals and organizations who would spread information designed to further their own interests, scientists have the daunting task of speaking for reality itself, for the world that exists apart from any subjective opinion or personal interest. Obviously, we're not perfect at this task. Selfishness and deceit are not unknown to the scientific community—all the more reason to think very carefully about how we communicate our findings.

Scientists have the ability to mine the universe of its secrets, to discover wonderful things about the world that can both advance and enrich society. For too many years discovery has been our only goal. The most fantastic discoveries in the world mean nothing if those ideas aren't shared within the scientific community and the world at large. Scientific findings have no voice; data makes no impassioned argument.  It is up to us, as scientists and discoverers, to speak for them.


An interview with Mary Roach

Here is my article just posted to the BSR Blog - check out the original version here.

Science is fascinating. At least, I think so. But maybe I'm not the best person to ask, given my position as a PhD student and academic minion researcher. While the idea of spending an afternoon coding an artificial neural network sounds fantastic to me, I am ready to accept that the large majority of people out there would think otherwise. Perhaps a better person to ask would be Mary Roach, a writer who manages to take complicated scientific ideas and paint a picture that is both understandable and amazing (often hilarious too). She has covered topics ranging from investigation of the supernatural to the history of sex research, and she has built an impressive body of commentary on the scientific process.

We at the Berkeley Science Review are always looking for ways to learn about science communication, so we invited Mary to come and tell us about her experiences. After the seminar, I had a chance to speak with her one-on-one about her feelings on science writing. For the record, Mary doesn't call herself a science writer (though the rest of the world probably would). "I’m actually a little uncomfortable with the label because I so revere the work of people like Carl Zimmer or Stephen Jay Gould," she admits. "These are people who are really smart, and they're writing at a much higher level for people with a science background." Mary holds a degree in Psychology from Wesleyan University, but is decidedly not a science geek by nature. "Compared to the people I’m interviewing, I know nothing."

If not a science writer, then what is she? A look into her methods might shed some light on the situation. Perhaps unsurprisingly, she turns to the same information resource that we all do. "If there’s something I want to pitch, I’ll do a lot of poking around on the internet seeing what’s out there," she explains, giving me yet another data point supporting my theory that Wikipedia can make us all geniuses. As for inspiration, Mary suggests that our day-to-day lives have enough gems embedded in them to come up with all kinds of interesting stories. To drive home this point, she told us how she got an idea for a story on meditation: "I saw an article about the war in Mozambique, and they mentioned that the president of Mozambique is deep into transcendental meditation. I thought 'this is perfect, because this is a guy who is really stressed out.''

The topic of her writing is only one part of the puzzle. Mary also emphasized the importance of focusing on the personality and character of all the researchers in her books. "I think it’s really important to try and find somebody interesting that can help the article move like a story." While a scientist's quirkiness and natural humor can certainly make her job easier, she reveals, "What usually makes them compelling is their passion for what they do." This, I think, is one of the most important points that any science writer can get across in their writing: that we pursue science because we love it. In Mary's travels throughout the scientific community, she manages to tap into the wealth of curiosity and interest that researchers have, and these emotions strike a chord in the minds of her readers.

Why do such ideas resonate? Mary suggests that it's these feelings of astonishment, amazement, wonder, awe, that are common to all of us, regardless of how many academic degrees we've got. "Curiosity and wonder seem like they should be part of normal human nature." And it is these qualities that allow Mary to learn so much from scientists. When asked about how her status as a non-scientist changed the way she interacts with her interviewees, she replies, "I think it’s relaxing in that they don’t feel competitive. I'm just somebody who’s interested in what they do."

At the end of the day, Mary loves what she does; she loves learning about new ideas, interviewing new people, and carving her own adventure into the world of science. As she puts it, "I have an excuse to step into all these worlds that I otherwise wouldn’t know anything about. I actually make a living doing this! It’s really fun!"