I've been amazed at the small explosion over Tommaso Dorigo's post concerning Lisa Randall's talk at a recent conference at CERN. He described her physically as well as the feel of the room when she began to present, and then proceeded to give a detailed account of the physics.
Asymptotia denounces him, Arcadian Functor defends him. Lots of debate about the objectification of women, the PC police, "sexophobia," and Italian culture in the comments on those three blogs lately. The angriest arguments have been concerned with what women face in this male-dominated field, most of them centered around women as eye-candy.
I get the impression that Dorigo was surprised by the sudden storm, and his main defense has been (as a clever but unknown 18-year-old pointed it out), that the subtitle of his blog is "private thoughts of a physicist and chessplayer." that Lisa Randall is a public figure and, like other celebrities, is open to such comments. [edited 2:14pm 8/31/07]
Andrea Giammanco, commenting on the now moderately-infamous Randall post (25) wrote I remember a conversation with some colleagues at the cafeteria, about two other colleagues that I knew and they didn’t. When talking about the male one, I was asked “is he smart?”, and when talking about the female one, the question was “is she pretty?”
I am ashamed to say that it took me a couple of seconds before saying “ehy, this is a textbook example of sexism on the workplace!”
But I've heard this conversation go the other way many times, talking about a lab partner or coworker. Often, women ask, "Is he cute?" before "Is he smart?" Political correctness will not stop people from noticing when a colleague is attractive, though it may keep people from talking about it.
So what if Dorigo noticed Randall's body? He noticed her discussion of the capacities and limitations of the LHC in far greater detail. Eye-candy is pretty and useless. In Dorigo's estimation, Randall is clearly beautiful and brilliant. And as long as he isn't discussing her looks in a professional setting or engaging in unwanted flirtation, I can't see a reason to condemn him. While many people consider blogs a professional space, Dorigo makes it clear in his subtitle that his is a personal record. Public, but not professional.
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Thursday, August 30, 2007
Eye-candy
Wednesday, August 29, 2007
Physics Inspired Fiction: The Dark Net
Back in 2001, I was fascinated by a study that found that 5% of the Internet is completely unreachable. The researchers who conducted the study called the hidden regions of the net the "Darknet." They said that some of the hidden regions belong to private companies, others are governmental or military, and some are the domains of hackers and online criminals.
In the years since the first study, lots of physicists have analyzed the structure of Darknet and written formal papers about their conclusions for APS journals. The research led me to wonder what sort of things go on in the Darknet, and inspired me to write a novel about it.
Check out my book The Dark Net to see what I came up with.
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Space Program Hits New Low
I realize that public support for NASA hinges in part on publicity, but this is just embarrassing. NASA is sending Luke Skywalker's original light saber prop into space. Check out the circus surrounding the announcement.
Do we need a clearer sign that sending humans into space is a waste of time and money?
I say ditch the manned space flight and stick with robotic missions that are cheaper, safer, and focus on real science, not hack publicity stunts.
-Buzz
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Tuesday, August 28, 2007
Making Neurons Remember
Recorded activity from the defendant’s brain is fed into a cybrid system. She has pleaded insanity, but the court requires hard evidence. Inside the cybrid, a living network of neurons communicates with a programmable chip and a computer. The system has been trained to recognized ordered and disordered brain activity. While a human psychiatrist might be fooled by an exceptional act, the difference between a calculated dissimilation and mental illness is obvious to the computer. Its assessment appears on the screen; she’s perfectly lucid.
This is just one of the applications that Eshel Ben-Jacob foresees for integrated systems. People often mentioned cyborgs on the world wide web, he said of the buzz that followed the first press releases of his work. “The vision that I have is to interface the neural network and the computer in a different way. And to do it with something which is called evolvable hardware.”
Cyborgs are human beings with added technological components. A cybrid is sort of the reverse, starting with a computer and adding living elements. Some technology for such a system has yet t
Eshel Ben-Jacob is one of two physicists at Tel Aviv University whose recent research is paving the way for neuro-memory chips. He and his doctoral student Itay Baruchi imprinted rudimentary memories onto a network of neurons interfaced with a computer. Despite the constraints of a tight budget, they are first to accomplish this feat. And they aren’t even formally neurobiologists.
Neural networks lend themselves to cross-over scientists. Electricity, traditionally the domain of physicists, is the signaling method used by neurons. Although he knew as early as junior high that he was interested in questions of consciousness and intelligence, Ben-Jacob chose to study physics and math to learn a clearer-cut set of rules that govern the universe before moving into the more labyrinthine realm of biology. Baruchi, also approaching the field through physics, encountered Ben-Jacob in his undergraduate years and has worked with him through most of his studies.
The physicist’s approach employed by Ben-Jacob offers a simplified model of neural networks and seeks to decipher the hidden principles that govern their behavior. He views neural networks as electrical circuits. While still complex, electrical circuits are more predictable than live neurons. Even the neural networks are just a basic component of Ben-Jacob’s real target: the brain. Physicists, as Ben-Jacob pointed out, like to start with the simplest, most fundamental version of a problem.
The problem is memory. How are memories recorded on neural networks? Their original motivation was pure curiosity about how a brain learns and remembers. After they had actually imprinted a memory onto a network, they realized that the experiment had taken a step toward living memory chips.
Inhibiting the Inhibitors
Before researchers can imprint new memories onto a neural network, they must first create a network of neurons interfaced with a computer. Inna Brainis, research assistant in the laboratory of Baruchi and Ben-Jacob, grew theirs on an array of electrodes, following a method that was developed in the last two decades.
Brainis began with cortical material from the brains of day-old rats which contains both neurons and glia cells. The glia cells are responsible for feeding, protecting, repairing, and cleaning up after the neurons. Research in the last decade has demonstrated that the glia does more than just support the neurons, serving regulatory purposes in neural communication through chemical transmitters.
Neurons have two ends: axons and dendrites. Axons send out signals, and dendrites receive them.
Across the cell membrane of a neuron, charges separate. The difference in charge between the inside of the neuron and outside becomes large, storing energy. Using the same principles, energy is stored by charge separation in a capacitor, a common element in electrical circuits. Voltage, or energy stored by the difference in charge, builds up between two plates that conduct electricity.
When a capacitor discharges, it quickly releases the energy stored by the charge difference. This is analogous to the firing of a neuron. The voltage across the neuron membrane builds until a threshold difference between inside and outside the neuron is achieved. Then, the neuron fires an action potential.
An action potential is a voltage pulse. The voltage runs along the axons and into the dendrites of connected cells, perhaps as many as 10,000 other neurons. As neurons receive pulses, voltage builds across their membranes. Once they reach the threshold, they also begin to fire, sending the signal on.
The places where axons meet dendrites, the junctions where signals are transmitted between cells, are called synapses. If a network of capacitors is connected by wires, the current can flow in either direction. Astrocytes, glia cells that engulf synapses, can serve as gatekeepers and regulate whether current is allowed to pass. This makes the cell junctions like transistors, another element in electrical circuits.
Although neural networks are far more complex than electrical circuits, it can be useful, in the mind of a physicist, to simplify the system into a circuit of capacitors and transistors.
To create a neural network, Brainis mixed cortical cells in a fluid and poured them over the multi-electrode surface, allowing them to settle into an even layer. They had ten minutes to attach themselves to the plate or else they were rinsed away. Over the next ten days, the neurons that had survived the rinsing sent out axons and dendrites, connecting themselves into a network that exhibits rich spontaneous activity.
Ben-Jacob finds the activity resulting from their interconnection surprising. “If you spread the neurons homogeneously, you don’t expect that they would show something that has some order to it. You’d think that it’s a big mess and there would be no sense in the mess.”
However, the connecting neurons adopted a particular firing pattern. In essence, they created their own simple memory. Such firing patterns have been dubbed synchronized bursting events.
“You can think about it like a Christmas tree,” Ben-Jacob suggested. Each flickering light is a neuron. “It’s quiet, quiet, quiet, and then all of a sudden it goes bzzzzz!” The lights flicker in a pattern – red, green, blue, red, yellow and so on. “The neurons fire quite rapidly for, altogether, 200 milliseconds or so, and then it’s quiet again.” A few seconds later, the lights flicker in the same order and with the same timing. The pattern continues at irregular intervals.
Inspiring firing patterns
Because synchronized bursting events repeat the same firing pattern, they are a form of stored information. Recently, scientists have interpreted them as rudimentary memories, and many researchers have conducted experiments seeking to imprint new memories onto the networks.
Neurons signal among themselves by voltage pulses, so electrical stimulation seemed a natural choice. While electrical pulses successfully changed the course of existing firing patterns, these patterns returned to normal after the stimulation session ended. Researchers turned to chemical stimulants.
Within neural networks, there are two kinds of neurons: excitatory and inhibitory. Stimulating excitatory neurons will increase network activity while stimulating inhibitory neurons reduces it.
A New Way to Teach
Researchers attempted to teach neural networks by reward, increasing network activity, through the stimulation of excitatory neurons. They also attempted to teach by punishment, reducing network activity, through the stimulation of inhibitory neurons or the inhibition of the excitatory neurons. None of these approaches successfully imprinted a new memory.
Baruchi and Ben-Jacob employed a third training method, “teaching by liberation,” as they describe it. Instead of exciting either type of neuron, Baruchi chose to inhibit the effects of the inhibitory neurons. If inhibitory signals are restrained, then the excitatory neurons are essentially free to do as they please. With their creativity unleashed, the neurons form a new synchronized bursting pattern.
Note that inhibitory neurons are not repressed directly. Rather, the inhibitory synapses are dampened, reducing the signals originating from inhibitory neurons. As a result, the inhibitory neuron may still send the command, “Stop that!” but it comes out so muffled that the other neurons don’t obey.
Stimulated Activity
Further setting their work apart from previous studies, Baruchi and Ben-Jacob placed the stimulant at a specially selected location rather than distributing it across the network. The injections were so small and the concentration dropped so quickly that the stimulant was localized to a minute region around a single electrode. Baruchi injected a tiny droplet every twenty seconds for a total dose of twenty droplets.
The neurons near this electrode became the starting point for a new synchronized bursting pattern. The firing pattern imprinted through exposure to the chemical stimulant coexisted with the original firing pattern. Now, the network stored two memories.
Twenty-four hours after the first round of stimulant, Baruchi and Ben-Jacob applied a second dose. The second round of stimulant was introduced at a location where neither of the two existing firing patterns began. Because the third firing pattern would begin wherever they placed the stimulant, they would risk overwriting one of the previous firing patterns if they tried to start two near the same point.
Twenty little droplets of stimulant later, a third firing pattern periodically expressed itself in the neural network. The three patterns coexisted in the network for more than forty hours. They mark the first example of persisting memories in a neural network that have been imprinted by scientists.
Limited resources, boundless resourcefulness
The method used to deliver these miniscule amounts of stimulant to such a specific location deserves some attention. The electrodes have a diameter slightly smaller than the width of an average person’s hair. Our clumsy human hands cannot manipulate objects on this level, so positioning a syringe over a particular electrode required some cunning.
A micrometer is a device ordinarily used to measure lengths at accuracies around 1000 times smaller than a millimeter. By rotating a knob, researchers can move an arm forward and backward on this tiny scale. Baruchi attached the syringe to this arm, allowing researchers to place the stimulant over a single electrode that had been selected according to network activity.
The syringe itself requires a bit of cleverness. How does one make a needle that small? It’s not actually that tough; simply heat a small glass tube until it is soft in the middle and then stretch it thin. Such a tube was mounted on a syringe. The researchers controlled the injections of stimulant very precisely by connecting a second micrometer to the piston of the syringe.
Beyond the ingenuity of the setup, it is highly cost-effective. Most of it is made from standard laboratory materials plus around thirty US dollars in additional supplies.
“When you do pioneering and conceptually daring research, you a have hard time getting financed since referees question the likelihood of success,” Ben-Jacob explained. “Most of the research was not supported by a grant. It’s lucky that I have students like Itay who are highly motivated, who have the intellectual courage and self-confidence to try something that has never been done. They research for the sake of doing the research.”
After seven years working together, he feels that Baruchi is more of a collaborator and a colleague. This experiment is among Baruchi’s last projects as a student. His thesis is currently under review for his Ph.D.
Student Baruchi has earned the profound respect of Professor Ben-Jacob for his diligence and scientific curiosity. Baruchi was employed part-time at hi-tech companies, doing work in algorithms and optics as he completed masters and doctorate degrees. “In some sense he funded the research,” said Ben-Jacob. “That’s something that’s very special. It’s very rare.”
While it is important that Baruchi and Ben-Jacob could manipulate the syringe on a microscopic level, they also needed to see what they were doing. Baruchi improved a special chamber that was originally built by Ronen Segev, a former student of Ben-Jacob. The chamber supports the neural network, records the data from the electrodes, and incorporates a microscope so that researchers can position the syringe.
The chamber is like an incubator, the environment in which neural networks are usually maintained. The temperature was held at 37˚C, or 98.6˚F. Likewise, the humidity and carbon dioxide levels were controlled to keep the environment suitable for growing neural networks, mimicking the conditions inside a mammal’s cranium. The neural network can live inside it for days or weeks during an experiment.
Building this chamber, Baruchi incorporated materials available at the laboratory, such as aquarium pumps, in addition to some relatively inexpensive parts that had to be purchased. “It might look like we’re really really poor,” Baruchi said with a laugh. “We’re okay. It’s not that we don’t have money to eat.”
Neuro-memory Chips and Beyond
Right now, Baruchi and Ben-Jacob can only control the starting point of the neuron firing patterns. Ben-Jacob believes that with strategically placed electrical stimulation, as well as the use of other chemicals, scientists may be able to control the order of the firing pattern as well.
Finding a way to structure the neurons will mark another step toward a neuro-memory chip. For this experiment, the neurons were spread homogeneously on the plate. The firing pattern of the neurons depends on their connections, so researchers will need to control their structure before they can make the behavior of the neural networks reproducible.
Perhaps Baruchi will return to the field later in life, but for now, he is starting a company in the field of renewable resources. Teaming up with Yael Hanein from the Faculty of Engineering at Tel Aviv University, Ben-Jacob is already working on controlling the geometry of the neural network using nano-technology. More specifically, they developed special electrodes made from islands of carbon nanotubes.
These biocompatible electrodes are employed to control the arrangement of the network since the neurons and glia cells prefer to attach to the electrodes. At the same time, thanks to their conductance properties, those electrodes record neural activity and apply electrical stimulations.
In the next stage, they will mount the carbon nanotube electrodes on microfluid chips. These chips contain tiny channels and gates that could be controlled by a computer, removing the need for the labor-intensive delivery of chemical stimulants via the micromanipulator device.
A computer connected to this integrated system would record and analyze network activity. It could operate the microfluid chip, delivering stimulant to the neural network and changing its activity. This cybrid, a hybrid of biological material and silicon, could be tuned to accomplish a specific task.
Ben-Jacob sees neuro-memory chips opening the way for evolvable systems. A neural network would be connected to a computer through a programmable chip that uses genetic algorithms.
A programmable chip running a genetic algorithm can change its connections at random, as biological organisms mutate. Then, the chip is tested for fitness. When given a particular input, does it return an appropriate response? If not, the chip mutates until it does.
This evolvable system constitutes a “toddler” computer, capable of learning. The neural networks are made from the cortical neurons of day-old rats, “infant networks,” as Ben-Jacob calls them. “If you give them a task, both the network and the evolvable, programmable chip will grow up and develop together during the few days that the network becomes mature.”
For example, neural networks may be used to detect toxins, quite similar to canaries used in mines of old. The desired system would report a “one” if there was toxin present and a “zero” if the area was toxin-free.
In order to get such a result, scientists would teach the system. A neural network would be exposed to a toxin. It would communicate with the programmable chip, which would change its connections until it reported a one, signifying toxin. In the absence of toxin, the programmable chip would be trained to interpret the neural network’s activity and report zero. A more sophisticated system could even differentiate among different toxins.
As in the courtroom scenario, an integrated system could be trained to recognize ordered and disordered minds. Researchers could give it examples of neural activity from healthy and mentally ill brains until the network could tell them apart. Again, a more sophisticated system might identify specific mental illnesses.
In current computer systems, human specialists know exactly how each program runs. Someone had to make each piece of hardware and software, someone designed every magnet, circuit board, and string of code. Evolvable hardware, capable of learning by example, would have unknown methods of deciding whether or not brain function is ordered or toxins are present. The next generation of computer technology may almost be able to think for itself.
Credits
Baruchi and Ben-Jacob's research: Physical Review E 75, 050901(R) (2007)
Images
All images from Ben-Jacob's group except
4. Network -- Pablo Blinder and Danny Baranes
5. Neurons and glia -- Pablo Blinder and Danny Baranes
7. Delivering stimulant -- Ben-Jacob's group in collaboration with Yael Hanein
10. Carbon nanotube electrode -- Ben-Jacob's group in collaboration with Yael Hanein
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Monday, August 27, 2007
N3UROCH!P Video
Buzz Skyline is embarrassed to be my boss.
Lyrics:
Eshel Ben-Jacob and Itay Baruchi
Were working in a laboratory out in Tel Aviv
They were trying to accomplish what no one else could do
And that is teach a neural network something new.
A neural network is some brain cells, attached to a plate
The neurons all connect ‘cause that’s their natural state
They fire in a pattern, electrically
It’s almost like there’s neural choreography.
The neurons have their first memory, a very simple one
Could we record another? It had never been done
Eshel and Itay thought the challenge might be fun
And so this experiment begun.
There are two kinds of neurons inside of every brain
If they didn’t work together, well, you’d probably be insane
The excitatory neurons, they always want to act
The inhibitory neurons say, “hey man, stop that.”
Two methods of training that work for sure
Is to reward a good deed and punish bad behavior
Experimenters had tried both methods and failed
The common wisdom was to no avail.
Neurons make up their own memory, if you just let them be
They’ll fire in a new pattern and this quality is key
A new memory can arise from network creativity
So if you want to teach the neurons set them free.
Itay added stimulant to a point in the network
And if something’s stimulated, you’d think it goes berserk
But to inhibitory neurons, the stuff was like a gag
Now they’re silent, so they aren’t such a drag.
The excitatory neurons, they started to jam
From that point, a new firing pattern began
And even when the stimulant diffused away
The new and old memories stayed.
The network has two memories, they go for three
A second round of stimulant sets neurons free
Another firing pattern busts onto the scene
Without disrupting the others, the method is clean.
Three different memories, existing in a tray
They fire all night and they fire all day
For forty hours those three firing patterns replay
And never do they fall to disarray
So from this experiment, our brains it seems
Form new memories by chemical means
And as an application, wouldn’t it be hip
If your computer used a living chip?
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Tuesday, August 21, 2007
Yikes! It Must Be for Real
Now, I don't want to alarm anybody, but there's an energy crisis out there! Sure, I'd seen the Al Gore movie, I'd replaced my light bulbs with those CFL ones that don't turn on right away, and I'd eased up on the gas pedal a bit, but I figured since everyone's still driving those big, massive vehicles, how bad could it be, right? But, this latest development has me shaking in my boots (or ballet flats, whichever you prefer). Are you ready for it? 
The journal Nature is offering a collection of articles on this whole energy issue....FREE OF CHARGE! For those of you who don't follow the cut-throat world of scientific journal pricing (what? You don't know any librarians?) Nature doesn't give away anything for free. In fact, just for typing the word "Nature" I'm sure they are sending us a bill right now (eh, I just went through the budget... we can afford another one...Nature). Oh wait, the free access to the collection is being supported by the U.S. Government's Department of Energy. That makes me feel a little bit calmer. In all seriousness, I haven't read every article but it looks like a pretty thorough collection.
The most pressing technological problem facing the world is uncoupling the provision of energy from the net production of carbon dioxide. This collection outlines the promises and pitfalls of new energy technologies. It looks at the potential of biofuels and nuclear power, explores new ways to lock away CO2, and considers renewables such as solar and wind power.Wait a minute! The U.S. government wants us to have free access to information on the energy crisis?! I'll be hiding under my desk if you need me.
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Friday, August 17, 2007
Bang! Queen's guitarist turns in his thesis
Sorry for the lack of posts recently! alpinekat, Buzz Skyline, and I have all been out of the office for extended amounts of time over the last couple of weeks. 
Call it what you will (a "star thesis", an "out of this world" thesis, or a "stellar thesis" from the Telegraph, ABC news, and Antara News respectively), Queen's guitarist Brian May just handed in his astrophysics doctoral thesis - 30 years in the making.
Now let me point out that his thesis hasn't been approved yet - if he is like most of my friends it probably won't pass the margin lady's inspection the first time and he still has the oral exam (scheduled for August 23). But cool is cool.
May's thesis, titled Radial Velocities in the Zodiacal Dust Cloud, shows that dust clouds in the solar system are moving in the same direction as the planets. Did we know this? Beats me. But it's interesting to note that he was able to pick up where he left off 30 years ago when his music career got in the way...
But hey, his colleague Dr Garik Israelin told the press, "I have no doubt that Brian May would have had a brilliant career in science had he completed his PhD in 1971."
Then he added, "Nevertheless, as a fan of Queen, I am glad that he left Science temporarily!"
In addition to resuming work on his thesis, May recently joined forces with Sir Patrick Moore and Dr. Chris Lintott to produce Bang! The Complete History of the Universe. 
"BANG! Space, time, matter … the Universe was born 13.7 billion years ago. Infinitely small at first, it expanded more rapidly than anyone can contemplate. Brian May, Patrick Moore and Chris Lintott explain how all this came about, from that moment when time and space came into existence, to the formation of the first stars, galaxies and planets, and to the evolution of human beings able to contemplate our own origins and ultimate destiny. Then on towards that destiny in the infinite future, long after the Earth has been consumed by the Red Giant Sun. The story is told in clear, straight forward terms, in the strict order in which the events happened, and uses no mathematics."
The book is available from the Official International Queen Fan Club ($30).
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Friday, August 03, 2007
Shedding the lab coat
Whew, I'm exhausted. I spent Saturday through Tuesday at the American Association of Physics Teacher's Summer Meeting in Greensboro, North Carolina. Besides trying some of the local BBQ (not such a big fan), I spent lots of time in the exhibit hall letting teachers know about Adopt-a-Physicist and the other resources APS has to offer them.
Located not too far from the APS booth were our good friends, Educational Innovations. Not only do they produce our PhysicsQuest kits, they also have an endless supply of science toys. They like to use our booth as Rocket Balloon target practice.
I attended an interesting session on using blogs, wikis, and forums in teaching physics and heard a great talk by a teacher who takes his junior and senior high school physics students to an indoor racing track each winter where they apply what they've been learning to driving. It's sort of like amusement park physics although, as the presenter pointed out, you can take students racing in the winter in Chicago.
News & Records, a Greensboro paper, had a great article about the conference - Physicists shedding stodgy lab coats, by Karin Dryhurst 7/31/07. You have to pay to view the article, so I'll just copy my favorite passage below.
[Brian] Jones and [Stanley] Micklavzina said they fit the Einstein stereotype.
"You're older, with crazy white hair. You're a physicist," Jones said.
But Jones, wearing a tie-dyed T-shirt and sneakers, said people have started to notice a change with more women and minorities joining the ranks.
Micklavzina said physics can be fashionable.
"You don't have to wear bad clothes," he said. But, the pair agreed, "it's too late for us."
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Wednesday, August 01, 2007
US Physics Olympiad Team Returns Victorious!
Okay, so the US isn't quite the top country (4th in my estimation), but out of 76, I think it's safe to say that the American students made an excellent showing. And look how happy they are!
The results, taken from coach Paul Stanley's reports, are:
China: four gold, one silver (total score 226.7)
Russia: Three gold, one silver, one honorable mention (216.1)
Korea: Two gold, three silver (217.2)
USA: Two gold, three silver (204.2)
Japan: Two gold, two silver, one bronze (206.9)
Iran: Two gold, two silver, one bronze (202.4)
Some say that the performance of a country has a lot to do with its size, and I think it's rather telling that three of the largest nations landed in the top four slots. Anyway, congrats to all the students who competed. And to the all-medaling US team, Physics Buzz salutes you.
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