Sleeping on the Wing

There is an old Monty Python skit where John Cleese and Graham Chapman play airplane pilots. Presumably on a long, tedious flight, they are clearly bored and keen on amusing themselves at the expense of their passengers.

They find entertainment through relaying worrisome, nonsensical messages. Cleese begins their prank with the truism, “Hello, this is your captain speaking. There is absolutely no cause for alarm.” And after some internal discussion about what there should be no cause for alarm about, they add: “The wings are not on fire.” The messages get more ridiculous, and hilarity (at least for the pilots) ensues.

Activity Recall in a Visual Cortical Ensemble

Associational memory, as its name implies, is a type of memory that allows one to fuse multiple events in memory. If your boss constantly yells at you in his office, you might begin to form some bad memories of being in that office. While the phenomenon of associative memory is a familiar experience, the neural basis for it isn’t well understood. A prominent theory, which was formed in the mid-20th century but only tested recently is that neurons encode associations by wiring together. In the boss’s office example, the sight of the boss’s office might activate one subset of neurons, and those neurons would then “fill in” activation of neurons that code for fear or memories of yelling (obviously this is a gross oversimplification - I’m only using it to demonstrate the principle).

Bat and Bird Songs for Systems Neuroscience

This week’s Science features an article about the songs of bats - not the ultrasonic echolocating calls most often associated with these wonderful creatures but complex vocalizations that bats use socially.

The most well-studied “songsters,” as the author, Virginia Morell, calls them, are songbirds. In species like canaries, zebra finches and starlings, the male sings a courtship song that he learns from his father to woo females.

Coordination Between Motor and Sensory Systems

One interesting problem in systems neuroscience is how the nervous system’s motor output interacts with its sensory systems. Sensory inputs that result from motor commands must be either filtered out or used to guide future motor actions. In other words, the organism must distinguish between sensory inputs that are self-generated and those from the outside world. In the juvenile songbird, for example, motor commands for song generation must be sent to some internal critic (likely basal ganglia) so the bird can compare the actual song output to some internal tutor model and improve subsequent renditions.

Milk Does Not Cause Autism

The radical organization whose supposed mission is to protect animal welfare now says that cow milk not only worsens autistic symptoms but can actually cause autism too. PETA’s campaign to stop people from using animal products latched on to obscure studies of dietary influences on autistic symptoms. A PETA blog post refers to two studies that found a link between autistic children’s behavior and consumption of cow milk (or proteins found in cow milk), and jumps to conclude that "dairy foods may worsen or even cause autism.”

Using the Brain to Treat the Body's Diseases

There’s an article in New York Times Magazine about using electrical signals in the nervous system to signal to the rest of the body to somehow alter molecular signaling outside the nervous system. Neuroscientists have known for a while that neurons transmit messages by electro-chemical signals: at each synapse, an electrical impulse arrives from a cell body, is converted to a chemical message via neurotransmitters. The chemical message jumps across the synapse, where it is again converted into an electrical signal at the next (postsynaptic) neuron. For some reason though, the thought that electrical signals interact with non-nervous system elements (like the immune system) has not been very popular; the idea that one could manipulate the electrical signals to “hijack” downstream molecular signaling without affecting neural communication itself seems like magic. 

How does sensory experience change cortex?

The neocortex is an evolutionarily new part of the brain unique to mammals and is responsible for high level sensation, movement and cognition. It wouldn't be fair to summarize in a sentence or two what cortex "does," but it is clear that it is an important part of the brain. Korbinian Brodmann famously divided the human cortex into about 50 areas based on histology of the six cortical layers in different parts of the brain; Brodmann's areas are still used today because their functions follow their histological structure. While cortical areas have largely stereotyped wiring patterns, some connectivity “motifs” are thought to be area-specific, varying based on the type of input the area receives. It is unknown whether the type of input (i.e. statistics of incoming activity that vary with types of sensory stimuli) to a given cortical area determines the types of connectivity motifs present in that region. And while classical cortical “rewiring”experiments from Mriganka Sur’s lab have shown that primary sensory cortices are somewhat tolerant to process foreign inputs, it is not clear to what extent those circuits constitute basic computational units or if foreign inputs cause reorganization of connections within the circuit.

Connectomic Reconstruction of Direction-Selective Circuit in the Retina

Connectomics is the area of neuroscience that aims to collect and curate the entirety of the connections made by all neurons in a brain (the product being called a “connectome”). For the human brain, that would be a data set of 100 billion neurons, each of which is estimated to make 1000-10000 synapses with other neurons (on the order of 1017 connections). The roll-up-your-sleeves-this-will-get-really-messy way of collecting that kind of data is to slice the brain into nanometers-thick sections and to image each slice with an electron-microscope, which has resolution below the nanometer range, and can reveal the structure of cells on a fine scale. In the image from Kristen Harris's lab below you can see a part of a neuron’s dendrite making a synapse with an axon filled with neurotransmitter vesicles; EM images however cannot show individual proteins or molecules).

Oklahoma's Torture-execution

With the world in shock over the botched execution of Clayton Lockett in Oklahoma last week, rather than questioning the morality of capital punishment, we should reevaluate America’s prison system as a whole. With an ever-growing population of inmates, America’s prisons are operating under the arcane notion that punishment deters crimes, while ignoring a growing body of scientific work that could be used to understand why people commit violent crimes and how to reinstate criminals into society successfully. On the question of what causes people to commit horrible crimes, we know that damage to the frontal lobes of the brain (the areas responsible for impulse-control, reasoning, foresight and other “higher” cognitive functions) can cause severe behavioral problems and violent outbursts. 

Congress to Peer Review Science Funding?

There is a bill circulating in the House of Representatives, sponsored by Lamar Smith of Texas, that aims to give Congress the power of oversight over government grants for scientific research. Grants from the National Science Foundation are given out to basic research projects based on their scientific merit, as determined by a system of peer review. Lamar Smith's legislature hopes to "improve" science funding (= reduce government spending) with this proposal:

The President's BRAIN Initiative

At three pounds, 100 billion cells, 10,000 as many connections, the human brain makes Facebook look like child’s play of a network, not without reason: our brains are solely responsible for our every thought, emotion and action. The human brain is the most complicated machine in the known universe. It is fitting then, that President Obama announced this week that the state of our knowledge of brain function is in a sort of swamp despite tremendous progress in the past century, and it is time to pave our way out in an effort to solve how the brain functions.

Idolatry in Science

Gary Marcus recently celebrated Noam Chomsky in an essay about the famous linguist’s life and influence on the field of linguistics over the past fifty years. There is no doubt that Chomsky has had tremendous impact on American intellectual life over the years, from work on language to political and philosophical ideas. However, Gary Marcus’s description of Chomsky’s influence on the field and his colleagues is somewhat troubling and unfortunately not unique to Chomsky but prevalent in the sciences. In every scientific sphere, it seems, a handful of individuals have excessive sway; these one-percenters are revered to an extent that their opinions go unquestioned (unchallenged) at best or as dogma, at worst. As Marcus points out, young linguists have a hard time studying what Chomsky finds uninteresting, the tragedy of which manifests itself in those people either not getting jobs and recognition in the field, or abandoning their interests in favor of Chomsky’s: “A good way for a young linguistics graduate student to make a name is to develop an intriguing idea that Chomsky mentions in one of his footnotes; it’s a riskier move to study something that Chomsky doesn’t find to be important.”

Runaway Selection in Birds of Paradise

I watched a program on PBS the other night about birds of paradise – exotic birds from New Guinea with elaborate displays. To attract females, males have evolved these intricate feathers and courtship dances and rituals. A Parotia male, for example, will clear out a dancing ground and when a female is in sight, he will puck up feathers around his chest into a sort of collar similar to those of Italian nobility of the Renaissance (or perhaps closer to a ballerina’s skirt) with bright iridescent feathers forming a shield below his neck, the long quills on his head that usually point lazily toward his rear will stick straight up in a semicircle around his head. 

A couple of weeks ago in the New York Times, David Ewing Duncan wrote an article, “How Science Can Build a Better You,” describing a brain-machine interface called Braingate that supposedly uses a tiny bed of "electrons" to read out brain activity. Scientists recently described this device’s ability to decode neural signals to control a prosthetic arm; this and other devices promise to restore mobility in paralyzed or tetraplegic patients. However, the Braingate device actually used an array of electrodes rather than electrons. An electron is a subatomic particle that carries negative charge; the flow of electrons is the basis of electrical stimulation. Electrodes, on the other hand, are wires that measure changes in electrical potential.

While the spelling difference is trivial, the semantic error is significant. Writing about science is a challenge for those who have no training in science, as is copy-editing; the complexity of science should require journalists to reach a level of expertise in their field before bringing their reports to the world. On the opposing side, American readers should have the basic education in science to know the difference between electrodes and electrons, and should not be at risk of being branded as nerds for pointing out such mistakes. Investment in early childhood education is critical for basic science knowledge, and the upcoming presidential election will determine if Americans choose “electrodes” over “electrons”.

Lost Thoughts in the Wake-Sleep Transition

I've been meaning to write about this curious phenomenon I experience every time I go to sleep. Lying in bed last night, I was thinking about a movie I had just finished watching - The Aviator, a great movie! - and was overcome by a sudden frustration: some idea that was running through my mind had simply vanished, to be replaced by something silly and mundane. Trying desperately to remember what I had just been thinking about, I could find no trace of my thoughts. It was as if they were never recorded. This happens several times, until I finally give up and fall asleep. Even more perplexing is that I am aware of those lost thoughts, I know something is missing. I just can't remember what it was. If these aren't freak phenomena, one can imagine something in the awake-sleep transition that messes with short term memory. It's as if whatever network or assembly representing the would-be memory doesn't undergo short term plasticity necessary to "solidify" those connections. This is of course overly simplistic and probably misleading language, but a way to think about it. Perhaps this can (or has been?) analyzed in rats, as in the "replay" or reactivation activity in hippocampus of experienced events, during sleep, as in this paper by Matt Wilson of MIT. One could examine lost thoughts in the awake-sleep transition by looking at the temporal structure of activity during that transition vs. same activity during experience on a maze, for example. Perhaps this loss of thought depends on some subcortical "kick" that's absent during sleep. Just a thought.

The Daily Show aired a special report by Aasif Mandvi on "an expensive lesson about bringing fish back to life," or the dangers of leaving children with the capability to make purchases on the Apple App Store. The point of this story is that children can't inhibit behavior as well as adults can due to their underdeveloped frontal cortices; and are therefore vulnerable targets to those whose sole purpose is to make easy money, not unlike drug dealers selling to addicts who just can't help themselves:

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Christopher Hitchens writes in the January edition of Vanity Fair about what he believes to be a nonsensical maxim: "What doesn't kill me, makes me stronger." Hitchens is suffering from esophageal cancer, the primary reason for the sentiment that he is not becoming "stronger," but is rather on a terminal decline. The phrase is attributed to Nietzsche, whose mental decline late in life, Hitchens notes, probably did not make him any stronger. Nor did the philosopher Sydney Hook consider himself stronger after a terrible experience in a hospital. Hitchens considers himself to be among the many who don't conquer illness to come out stronger. But there is a flaw in this reasoning - the first condition to becoming stronger is to not be killed. Hitchens is thankfully still alive and kicking (i.e. writing), but he hasn't defeated his cancer (yet, hopefully); it is only after the cancer is over with that Hitchens can say he's stronger or weaker. Now is premature. The more important qualification is that "stronger" should mean mentally stronger, not physically. Diseases that target the mind specifically, like Nietzsche's syphilis, should be discounted; all others should hopefully be an exercise for the power of will and mental fortitude.

Whenever you think life is hard, remember Hitchens and countless others who brave horrible diseases. Stay stark, Hitch!

Hitchens's essay may be found here.

Science, Religion and Values: Magisteria Redefined

Science and religion have been archenemies for some time now, with one on a quest for knowledge and truth, and the other seeking to fill a perceived void of meaning in lives. Logical inspection confirms the two systems are incompatible with one another, since science requires evidence for all claims, whereas religion insists on faith when there is no evidence whatsoever. But many do have both science and religion in their lives. How do they deal with the conflict? Stephen Jay Gould wrote in a 1997 essay on the non-overlapping magisteria, NOMA, that there actually is no conflict between science and religion:

Brainy Computers

“We’re not trying to replicate the brain. That’s impossible. We don’t know how the brain works, really,” says the chief of IBM's Cognitive Computing project, which aims to improve computing by creating brain-like computers capable of learning in real-time and consuming less power than conventional machines. No one knows how the brain works, but have the folks at IBM tried to figure it out? It seems strange to say that it's impossible to replicate the brain, especially coming from a man whose blog's caption reads, "to engineer the mind by reverse engineering the brain." Perhaps I'm picking at his words - replicating and reverse engineering are totally different things; to replicate is to copy exactly, while reverse engineering isn't as strict, since it's concerned with macroscopic function rather than microscopic structure. But of all the things that seem conceptually impossible today, it's the "engineer the mind" that's the winner, especially if one can't "replicate the brain." The chances of engineering a mind are greater the closer the system is to the brain; that's why my MacBook, to my continual disappointment, does not have a mind.

These little trifles haven't stopped Darpa from funding IBM and scientists elsewhere. IBM now boasts a prototype chip with 256 super-simplified integrate-and-fire "neurons" and a thousand times as many "synapses." This architecture is capable of learning to recognize hand-drawn single-digit numbers. Its performance may not be optimal, but still impressive considering the brain likely allocates far more neurons (and far more complicated neurons) to the same task. On another front, the group reported using a 147,456-CPU supercomputer with 144TB of main memory to simulate a billion neurons with ten thousand as many synapses. Now if only they could combine these two efforts and expand their chip from two hundred to a billion neurons.

Dancing for Science

Science is difficult to understand and even more difficult to explain. John Bohannon thinks that words are inept at explaining scientific concepts, and should stay out of the way. Powerpoint is useless too. Instead, Bohannon argues, scientific concepts should be explained with dance. He foresees a boost to the economy if dancers were to be hired as aids to presenters, not only because those dancers would have jobs, but because science would be communicated more effectively, leading to more innovation. Bohannon presents these ideas in an engaging TEDx talk, with the help of the Black Label Movement dance team.  No doubt, seeing people dance out cellular locomotion is fun and more straightforward than hearing a verbal description of the same thing. I wonder though if such concepts would be more accurately portrayed and easier to understand through animations. Perhaps there is something about seeing people perform live that is more engaging than seeing animations or the same performance on a screen. If that's true, then having dancers at one's presentations would be very helpful (it would also make that presentation stand out, if no one else has dancers).