Archive for: October, 2011

Way to go!

Oct 24 2011 Published by under Uncategorized

Thanks for all those that donated to our Donor's Choose classroom drive! Apparently this drive raised a total of about $50,000 and there's still the matching funds to come! Well done everyone and thanks for supporting education.

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Big Head

Oct 20 2011 Published by under Uncategorized

Meandering through Wikipedia during my lunch break I came across this list of animals sorted by number of neurons. And learned that elephants have about twice as many neurons than people (200 vs. 100 billion). And pilot whales have about three times more neurons in their cerebral cortex than people have. So why aren't they smarter than us? Maybe they just have less synapses. Or maybe they are secretly plotting to take over the world. Clearly there's not a direct correlation between intelligence and neuron number since cats have about twice as many cortical neurons than dogs, and we all know that dogs are way smarter than stupid cats. I also find it remarkable that octopuses have 300 million neurons, about 20 times more than a frog. Of course these are not necessarily in its brain.

This list took me to an even more interesting set of lists of brain facts, where I learned that our brain weighs about as much as that of a dolphin and slightly more than a walrus' brain. Of course I was not surprised that our brain weighs more than 40 times as that of a stupid cat. Furthermore, the surface area of our cerebral cortex is about 2/3 smaller than a dolphin's and 30 times larger than a stupid cat's. I also learned that we lose about 85,000 cortical neurons a day, or about 1 per second. You just lost about sixty reading my stupid blog post. Pop! There goes another one...

Did you know that we can hear sounds between 20 and 20,000 Hz when we are young, but when we are old our range is reduced to 50 to 8,000 Hz? So if you want grandpa not to hear your conversation, speak in a really squeaky voice. Mice hear between 1,000 - 40,000 Hz and our hearing range is closest to that of elephants (1-20,000Hz). But elephants can pick up very low frequencies. They would make good bass players.

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Owl Puke

Oct 20 2011 Published by under Uncategorized

So I've been remiss about urging my readers to donate to our Donor's Choose campaign where we (scientist bloggers) convince you to donate your pesos to a variety of schoolchildren who need your help. How does this work? You can click on this link, or on the little gidget-thing-a-ma-bob on the margin of this blog, and this will take you to my giving page.

I would really like to thank those reader's who have contributed via my giving page, but for those of you who have procrastinated, you are in even better luck. Apparently, if you give now until the end of the campaign (Saturday) the Donor's Choose organization will double your donation. After saturday you will receive an email asking you where you want to donate the matching funds. So it's like giving twice as much.

If you are undecided as to what project to donate to, I would suggest giving to Ms. DeFelice's 5th grade class, who needs some funds to buy some owl pellets. For those of you not "in the know", owl pellets are basically dried up owl puke. Why do they want owl puke? Because by going through it's contents you can learn tons of what the owl has been eating. So you can find little mice skeletons, gold coins, elves and whatever other crap the owls eat.

So go, give them some money.

Image source: D. Petersen

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Oct 19 2011 Published by under Uncategorized

So today I've been making some revisions on a paper we have been struggling to publish for over a year. Granted it's been a low priority publication and the student who did the work is long-gone, but still, its not too bad. What struck me about the last round of reviews is that it was sent to ONE reviewer, who proceeded to write a five page critique with more than eighty, specific comments. Typically papers go out to two or three reviewers, each with a handful of major comments and a few minor ones. So I didn't know what to do with eighty comments. Mind you this was also not a particularly high-caliber journal, to put it generously. The comments ranged from the petty:  "I can't find reference X, could you cite something newer?", or "I don't like your axis labels in figure 2B"; to the somewhat useful: "statistical test X would be more appropriate that statistical test Y"; to ones which to me bring up a grey area in terms of what to do with them, and that if I were to follow them I think the paper would be worse off. These usually have to do with writing style.

Most scientific papers follow the same basic organization: summary, introduction, methods, results and discussion. But how one treats these sections varies a lot from person to person. In my view, the most straightforward approach is also the most dogmatic and makes for some pretty dry, snooze-inducing reading. In this approach, after your introduction, the results are basically a pure description of the experimental findings, with no room for interpretation or background, these are saved for the discussion and introduction. The results become a list of findings to be discussed later in the paper. In  a second approach, which is the one I take, I split the results into sections describing the different experiments. Then for each subsection I first describe the rationale for the experiment, with a citation or two if needed and recapitulate briefly the method to be used. This may sometimes spell out expected outcomes as in "if such a hypothesis is true, we would expect that this and that would be observed when we manipulate these other things." Then I go through the actual findings. Finally, at the end of each subsection I summarize the interpretation of the data as in "the results from this experiment suggest that blah, blah, blah." This helps the reader understand not only why you did the experiment you just did, but also how you interpret it, and facilitates the transition to the next logical experiment. In this way you hold the reader's hand through the results and build your conclusion as you go along, adding helpful bits of interpretation. Then in the discussion, you summarize your findings and their interpretation and go on to discuss the larger context of your study. I find that this type of results section makes for much easier reading and better flow.

Now back to the reviewer with the eight-hundred comments. In many of the comments he or she kept saying "this line belongs in the discussion" or "move this to the methods". In other words "please make this paper so dry and boring so that my ego can be stroked and my terse writing style will prevail". They must have made about fifteen or so of these types of comment. And here is the crux of the dilemma, is it worth bowing to a reviewer's demand which you know will make your paper worse? Are stylistic comments valid criticisms? As for me, we're not sending the paper back to that crazy journal, so I'm just going to ignore the comments, its not even worth trying to address them all. How about you, reader, what do you do in this situation?

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Grad Rites

Oct 13 2011 Published by under Uncategorized

Recently I've been having a lot of conversations about graduate school "rites of passage." I've heard many people echo the sentiment that the purpose of being intensely quizzed by professors during things like journal club presentations (when you present the findings of a recent journal article of interest) or oral exams, is to humble the grad student, to make him or her feel bad about how little they know, and that surviving this is one of the rites of passage that all grad students must go through. As if it were some type of hazing ritual to help thicken your skin. But if that is what you are taking away from this exercise, then you are missing the whole point. Being quizzed to the edge of your knowledge, in front of your peers, is not done to make a grad student feel bad about themselves, or to toughen them up. It is serves two purposes. One, is for faculty to evaluate the breadth and depth of your knowledge, and be able to identify weaknesses that you might have to work on. For example, become better acquainted with the inner workings of a specific experimental method, or to familiarize yourself better with a certain body of scientific literature. In other words, to help guide in which directions you need to grow in. The second purpose is to help you identify holes in your critical thinking abilities and teach you how to question even the most basic assumptions. Why are you using a specific experimental preparation and not another? Why do you use a certain concentration of calcium in your buffers? What is the big question you are addressing? Why does this control experiment matter?

These type of things are good for you, not because they help you develop thick skin, but because they are an opportunity to learn and think about your science in some depth. It is common to join a new lab and start doing experiments the way everyone else does them. And probably this is the optimal way since people before you have been troubleshooting these techniques for years. But that's no excuse for not knowing why and how you do the things you do in lab. One should take all the lab protocols and go line-by-line in order to understand the logic and the reason behind each step.

So my advice to a fledgeling new grad student (any out there who read my blog?), is that, after you complete each of these milestones, before you go off to drink and celebrate surviving being buffeted by professors questions, take fifteen minutes to write down a list of things you were not able to answer, and figure out what your weaknesses were and what you need to work on. Then you can go to the bar and get shitfaced.


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As in cool.

Oct 13 2011 Published by under Uncategorized

My son, who is 6, just told me he wanted an electric guitar, because "electric guitars are SO sick!". Then he added, pointedly, that "sick also means cool", in case I didn't know. Thanks, dude.

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Zombies, WTF?!?

Oct 04 2011 Published by under Uncategorized

Dear Second Grade Music Teacher, Do you really think its a good idea to teach your class a song about zombies rising from the dead so that my daughter can be up for two hours at night crying and refusing to go to sleep because the zombies give her nightmares? Why not follow it up with a screening of The Exorcist?

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Gimme an "S"... gimme a "C"... gimme an "ience", help kids learn "Science" (and other stuff)

Oct 03 2011 Published by under Uncategorized

Alright, listen up peeps: Today is the kickoff for the Science Blogs Donor's Choose campaign, where we (scientist bloggers) convince you to donate your pesos to a variety of schoolchildren who need your help. How does this work? You can click on this link, or on the little gidget-thing-a-ma-bob on the margin of this blog, and this will take you to my giving page. Look at the projects that I have selected for help, or search some of your own and then give them some money. If the project raises enough funds, then that classroom will get their money. That's all!

Why should you donate? Because its a good thing to do. Plus if you don't I shall unleash this giant squid upon your ships:

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Schmatta Central

Oct 03 2011 Published by under Uncategorized

I hate those little fucking bags they give your kids when they leave a birthday party. Why do parents feel the need to inflict other families with a bag full of junk that your kids claim has things that they absolutely need and must collect, but in reality will just clutter your house, making it so that anywhere you step there's a little broken car, beaded necklace, faulty kazoo, deflated balloon, plastic whistle, paper party hat, and fairy stickers underfoot ready to make you trip and fall? Then they are full of candy that you have to fight your kids so that they don't eat it all in one sitting and become sugared-up maniacs, with cavities. NOBODY likes these bags, why do people keep handing them out? Perhaps revenge for making them invite your kid over to eat cold pizza and stale cupcakes at the bowling alley. Why can't my kids just go to a birthday party and that's it? Why does the party have to follow them home? In fact all kids birthday parties should be abolished. Nobody wants to have them at home to avoid the disaster that will ensue from 10 kids trashing the place, and places that hold parties are for the most part fucking depressing, with their sticky tables and dirty walls in their "party room" with peeling murals of little bears and Pac-mans and booger-covered broken toys "for the little ones". And those fucking little bags of junk you take home. I hate those.

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The Roaches Spike Back

Oct 02 2011 Published by under Uncategorized

This is a post I started about a year ago, but never got around to finishing it, so here it is in due time.

Every so often I teach an undergraduate course which deals with some of the seminal experiments done in the field of neuroscience, and how they shape the way we understand contemporary neurobiology. I usually contrast these to modern versions of the experiment which then either support or overturn the established dogma. Sometimes we try and replicate some of these experiments in class. I've written about my experiences in having my students replicate some of Cajal's original findings about neural structure by doing some of their own neural drawings under a microscope. Today I'm going to tell you about our experiences in replicating some seminal findings by neuroscientist (and nobleman) Lord Edgar Adrian. Adrian did some experiments in the 1920's that described how the nervous system encodes information. What he did is he basically hooked an isolated frog leg muscle with an attached sensory nerve to a device that amounts to a series of vacuum tube amplifiers. These amplifiers are able to record electrical impulses from the frog nerve and then cause a little bit of mercury inside a capillary tube to bob up and down in proportion to the amount of voltage recorded. This was then captured on film, which allowed him to have a continuous record of electrical activity in the nerve as it changes over time. Here's a schematic of the device from one of Adrian's papers (click to enlarge):


Adrian 1926, 1929 - Valve amplifier and capillary electrometer


Adrian then hung little weights from one end of the muscle —thus stretching it— and recorded the output of the sensory nerve. What he then found is one of the central principles in nervous system function. He found that when the muscle was stretched the nerve would fire discrete electrical impulses, and the heavier the weight (meaning the muscle is stretched more) the faster the rate of these impulses was. These impulses are known as action potentials and the phenomenon is known as rate coding. Rate coding basically means that the rate of action potential generation is proportional to the strength of a sensory stimulus. Larger stimuli result in a faster rate of action potentials. This finding is shown below:


Rate Coding, as described by Adrian (click to enlarge). Top graph shows the responses resulting from different weights hung from the frog muscle. The squiggles show changes in voltage over time. Those bumps are the action potentials. Notice that it isn't that clear cut that these are discrete units, but whatever. The bottom graph shows the relationship between response strength (x-axis) and stimulus strength (y-axis) for several experiments.


The other important observation was that action potentials were discrete units with similar size and shape. So stimulus strength was not represented as larger acton potentials, but rather as more action potentials, as shown here:


These are voltage recordings showing spikes as discrete units. In this example both rate coding and unit consistency is much more evident.


Finally, Adrian also observed that the rate of action potentials tended to slow down if the duration of the stimulus was sufficiently long. Thus, if he pulled the muscle for several seconds, the nerve would fire rapidly, but then would eventually slow down. Adaptation is the reason why you don't continuously feel your clothes, or why you can still see changes in brightness in bright daylight or have a conversation in a noisy street. The nervous system tends to adapt to continuous stimuli and is better at detecting change (like in Jurassic Park when the dude gets eaten by a T-rex when he makes a run for it, while the guys that stay put don't get eaten). Adrian's demonstration is shown below:


Adaptation of spike rate. Here spike rate is in the Y-axis, while the X-axis is time. The bar on the top shows the duration of the stimulus. Notice that the rate of spiking decreases after several seconds.


So now the question was, could we replicate these seminal findings in our classroom? Enter Backyard Brains. Backyard Brains is a nifty little company that makes these somewhat inexpensive amplifiers called spiker boxes, a modern and el-cheapo version of Adrian's valve amplifier. Rather than vacuum tubes a spiker box uses what most modern amplifiers use, which is a series of differential amplifiers, in order to amplify electrical signals in the nerve of a cockroach leg. A schematic is shown here. You can then poke the little hairs on the leg, which the roach uses for touch, to generate a sensory stimulus and record the resulting activity in the nerve in the leg. We had some trouble at first with the spiker box. The first one didn't really work, we could hardly get a signal, but they promptly sent us a replacement and we were on our way. Using free audio-processing software we were able to record the waveforms resulting from the neural activity.

Adrian's main findings were: action potentials as discrete units, rate coding, and adaptation. How did the spiker box hold up? As soon as we stuck the metal pins (known as electrodes in the local parlance) in the leg we observed little spontaneous action potentials, also called spikes, and indeed these seemed to be of roughly uniform shape and size. Here are some examples:



Notice how some of the spikes are big and some are small. Could Adrian be wrong? Probably not, more likely we are picking up activity from a couple of different sensory nerves and the size of the spikes depends on how close we are to the nerve itself. How about rate coding? Below is an example of a response resulting from gently blowing air onto the leg hairs compared with when you blow air vigorously. A weak and strong stimulus:


Rate coding and adaptation in cockroach leg nerve. The horizontal bar shows the duration of the sensory stimulus, a puff of air. The top response is to a gentle puff, while the bottom one is to a vigorous puff.


Notice how the weak puff of air causes the nerve to spike at a slower rate. Also, look at how the stimulus adapts after the puff of air has been going on for a while. This is more noticeable with the strong stimulus. Rate coding and adaptation!

So there we have it, the nervous system still works as we thought it did. This type of experiment is part of a field which neuroscientists call electrophysiology, and it is what I spend a lot of my time doing, but with much more expensive machines. I think it was a nice way to show the students how one can design an experiment to find specific principles and also to give them some first hand experience into how noisy data can look. Although we found the observations we had predicted, it took quite a bit of finesse to get the responses to look just right and to find good examples, and to sort these out from all the noise that goes on in the nervous system. And this is the kind of thing you get only from experience and from fiddling around with your equipment and preparation. Definitely not from a textbook. So go, get yourself a spiker box and see what you can learn.


Further Reading

Adrian, ED. The impulses produced by sensory nerve endings: Part I. J Physiol. 1926 Mar 18;61(1):49-72.

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