Category Archives: geek stuff

Primer: Electrophysiology

These posts, tagged “Primer,” are posted for two reasons: 1). to help me get better at teaching non-scientists about science-related topics; and 2). to help non-scientists learn more about things they otherwise would not. So, while I realize most people won’t read these, I’m going to write them anyway, partially for my own benefit, but mostly for yours.

It’s been awhile since I posted one of these, but as I’m working on radically different science than I have in years past, and people ask me “what I do,” I figured I should take the time to explain, to some degree.

Wikipedia defines “electrophysiology” in the following way:

Electrophysiology (from Greek ἥλεκτρον, ēlektron, “amber” [see the etymology of "electron"]; φύσις, physis, “nature, origin”; and -λογία, -logia) is the study of the electrical properties of biological cells and tissues. It involves measurements of voltage change or electric current on a wide variety of scales from single ion channel proteins to whole organs like the heart. In neuroscience, it includes measurements of the electrical activity of neurons, and particularly action potential activity.

So, in the most general sense, I’m “listening to neurons talk to each other,” and occasionally, “interrupting their ‘conversations’” in various ways. When I talk about “conversations,” I’m referring to the act of neurotransmission, whereby one neuron sends a chemical signal across a synapse to another neuron, resulting in the propagation of that signal (an action potential), or sometimes the inhibition of another signal.

As I talked about in a previous primer, in order for an action potential to occur, various ion channels in the membrane of a neuron must open, allowing sodium (Na+) from outside the cell to come in, and potassium (K+) to go out. Other ions will play roles as well, including chloride (Cl-) and calcium (Ca2+).

Using electrophysiology, it is possible to measure the movement of these ions across a cell membrane using relatively simple principles of physics. Specifically, [V=IR], or [voltage = current X resistance]. If you hold two of the terms of this equation constant, it is possible to determine the third term. Effectively, we do this using a “patch pipette,” a small, sharp, glass tube that has a wire electrode running through it. If you know the resistance of the pipette, and you hold the electrode at a constant voltage, you can measure the current across the membrane of a cell (i.e. the flow of ions).

In short, this diagram describes the actual process of making this measurement, using a technique called “patch clamp“:

Looking through a microscope (like the one pictured above), you move one of these glass electrode pipettes to be just touching the membrane of a cell. You have to be very careful so you don’t puncture the cell, thus damaging the cell membrane to the point where you can’t make accurate measurements. You then apply a small amount of suction using a syringe to actually suck some of the cell membrane inside the pipette. Once you have a strong seal formed (typically termed a “gigaseal”), you can apply a brief, large amount of suction with your syringe to rupture the membrane of the cell, where now, the inside of the cell is being exchanged with whatever you put on the inside of the pipette. The internal solution of a pipette is usually something like potassium, basically trying to recreate what the inside of a cell would be, aside from all the organelles, however you can add compounds or drugs to manipulate the actions of channels you are trying to study. Typically, though, you apply drugs to the outside of the cell, as well.

So, a real-world example of how this technique is used would be in my study of NMDA channels. The NMDA receptor is a sodium channel and is very important in neurotransmission, but especially in memory. When I have a cell “patched” like in the diagram above, I can apply the drug, NMDA, to the cell and see a large sodium current on my computer screen, kinda like this one.

So, over time, when a drug like NMDA or this “Blocker” is applied, you can see a change in the current (measured in “picoamps”) across the membrane of the cell. In this case, we would read these data such that NMDA opens its channel and sodium ions flood inward, then that current is reduced by the “Blocker” that was applied for a few seconds, and then once the application of the “Blocker” was stopped and NMDA alone was applied to the cell, the inward sodium current increased again.

These traces allow you to get information about how channels are opening, what ions are flowing in what direction, and to what degree drugs like this “Blocker” are affecting channels. It is work like this, for example, that led to characterization of benzodiazepines and barbiturates, drugs that interact with the GABA receptor, a chloride channel. Without these techniques, it is difficult to know how a drug is affecting a channel at the cellular level. Just about every cell in your body has channels of some kind, as they are very important for maintaining the function of that cell. Neurons are just highly specialized to require ions more than some other cells do, though heart cells are also studied in this way, among others.

Effectively, these techniques allow you to determine how a cell works.

Protip

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"Hello. My name is 'Google Reader.'"

I’m fully aware that many believe I sit in front of a computer all day and stare at Facebook, posting articles and comments and shirking actual “work.” In actuality, I’d argue that I only have “http://www.facebook.com” on my web browser 15 min per day, on average. On a “busy” day, when I’m in the middle of a conversation/argument, more like 30 min.

How is this possible, you ask? Why, it’s the power of RSS readers!

“RSS” stands for “Really Simple Syndication,” and the idea for it goes back as far as 1995, though the first official version was integrated into Netscape in 1999. In many ways, RSS is what gives blogs the power they have today: the ability for the headline and a brief description of an article or posting to be “aggregated” for easy digestion by the reader.

Note: This very blog has and has always had an RSS function. That’s what the cute little orange icon in the upper-right corner that pops up does.

So here’s the secret: I’ve got 45 different blogs aggregated into my Google Reader account. This means that my phone, my Kindle Fire, my Chrome web browser, and the Reader website itself all tie into a single repository that collects new posts from each of these sites almost immediately after a new article is posted. I’ll wake up in the morning and have 75+ articles to wade through, to see if there’s anything interesting, and I can do this easily on my phone, swiping with my finger to scroll through the list.

Any articles I think may be interesting (based on the title, usually, but sometimes after checking the description), I will press to add a “Star,” effectively bookmarking it for later reading. Then, I can just click “Mark All Read” and my list is cleared out, ready for re-population. Once I sit down at a computer somewhere, or with the tablet, I will then skim the articles I found to be most interesting. And sometimes, I’ll share relevant articles on Google+ or Facebook.

So, quite rapidly, I can skim through articles from the St. Louis Post-Dispatch or the Columbia Daily Tribune without ever having to actually visit the sites themselves, thus avoiding ads and thus saving me time.

And furthermore, you can share articles to Facebook or Google+ directly from most of these blogs, as this is how they generate their traffic. You just have to click “Share” from the page in question, or from within Google Reader. A little box shows up and you write what you want to post, along with the link. And you never have to actually go to Facebook.com to do this.

So yeah, a little “protip:” use an RSS reader of some kind to make your blog reading more efficient. You are more than capable of getting information throughout the day without getting bogged down in Facebook or on blogs themselves. You can, in fact, get work done and still provide useful information on subjects that interest you. It really isn’t that hard…

Pirates on the High Seas (of the Internet)

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I read a pretty spectacular article from Forbes.com today about how the MPAA and RIAA are fighting a losing battle against piracy. The article echoes statements I’ve made in the past, though not on this blog (…that I can find, anyway…).

The author is blunt and to the point: the movie industry is being dragged kicking and screaming to a future that practically all their customers want, and they’re losing revenue in doing so. They could make their money back on volume by making their movies a). easier to access, and b). cheaper.

The primary problem movie studios have to realize is that everything they charge for is massively overpriced. The fact that movie ticket prices keep going up is astonishing. How can they possibly think charging $10-15 per ticket for a new feature is going to increase the amount of people coming to theaters rather than renting the movie later or downloading it online for free? Rather than lower prices, they double down, saying that gimmicks like 3D and IMAX are worth adding another $5 to your ticket.

They have failed to realize that people want things to be easy. Physically going to the movies is hard enough without paying way too much for the privilege. Going to a store and buying a DVD instead of renting or downloading is generally an impractical thing to do unless you A) really love a particular movie or B) are an avid film buff or collector.

Here’s the part I’ve been most concerned by: rising ticket prices. Why go to a movie theater to spend $10-$15 on a ticket, plus an additional $10+ on “food?” Granted, I have a toddler so my movie viewing in theaters has decreased tremendously in the past few years anyway, but with the advent of Netflix, I have all kinds of things to watch, and now I have the will to wait until a movie comes out on DVD. Especially when the summer blockbusters are looking more and more like that “Battleship” ad you saw during the Super Bowl. Now, if I could see a non-IMAX, non-DTS movie in the theater and get a medium-sized non-refillable soda for $10? I’d do that. No question.

Finally, the author suggests a solution to this problem: the movie industry needs their equivalent of the gaming industry’s digital distribution platforms (e.g. Steam). Heck, they need Apple’s iTunes. Make buying the product so stupid simple that it takes less effort to buy it than it does to steal it. As he points out, it takes 7 steps to download a movie illegally, and depending on your internet connection, you could have an HD-quality movie in a half hour. If the movie industry would just get behind an Apple or Amazon model of 1). find movie, and 2). click “buy” (for a reasonable price).

Let us recall music piracy of the late-90s/early-2000s for a moment. Back then, you could go on Napster or Kazaa and search to find music you wanted, but you’d easily find tens or hundreds of the same track, each one with different sound qualities. You could easily download a track you thought was good, but after downloading, you’d find actually had multiple “hiccups” in the file. iTunes streamlined the process. Search to download one song that you knew was of relatively high quality and was consistent with the rest of your iTunes library. Moreover, you’d see that you could get a song for $1, but the entire album for $10, undercutting what was easily $15 at most brick-and-mortar retailers. So in many respects, at least with iTunes, there was a chance you’d “up sell” your customer on getting the whole album, rather than just a single song.

iTunes made it easy and people flocked to it. Does music piracy still happen? Absolutely, but now, people have a reasonable, viable alternative that I’d argue most people consider before pirating albums.

Steam did the same thing for the gaming industry, making it stupid simple to download a digital copy of a computer game without having to search through seedy sectors of the internet looking for a pirated copy (that could include viruses or other malware). They can even upgrade your graphics drivers and more for you when you install the game, streamlining the process further to make life for the consumer that much better. Many PC games are released day and date with their “physical media” counterparts. In many cases, you can actually have the game downloaded and then get it “unlocked” at midnight on its release day. For PC games, you can’t get much more convenient. You don’t even have to get out of your pajamas…

If piracy has taught us anything it’s that the movie industry thinks that an audience watching their movies on a computer or TV screen, while that same movie is still out in theaters, is important. If this is really the case, the movie industry should do the smart thing and release movies online day and date with their release in theaters. Charge $10 to rent it, making the cost comparable with a ticket to the theater (though that $10 is then divided up among the number of people watching the movie in your living room).

Obviously, some people don’t care if the movie is in IMAX or has super-duper Dolby Digital Sound or smell-o-vision: they just want to watch the damned movie. They don’t want to deal with crappy popcorn prices. They don’t want to deal with screaming kids or people talking through the whole thing. They don’t want to fight for a decent seat in a packed theater. They don’t want to drive their car and park in a lot. They don’t want to pay upwards of $30 to see a movie on a Saturday afternoon. There are any number of reasons folks don’t want to go to a movie theater, while others still like going. There’s no reason the movie industry can’t cater to both demographics and make money doing it.

So, take heed, Movie and TV Industry. You’re being surpassed by other content purveyors. Make it easy to access your content and I assure you, people will return to you and buy more of your stuff.

And stop taking your anger out on Netflix…that isn’t helping anything…

Internet Bi-Partisanship

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By now, surely you have read and/or heard plenty about the Stop Online Piracy Act (SOPA) and the Protect IP Act (PIPA). These two bills were heading through the U.S. House and Senate (respectively) and seemed destined for passage as recently as last week, with the first votes coming up next week.

Also, as you probably know, a shutdown of Wikipedia, Reddit, and other popular websites (as well as a host of other “In Solidarity” messages on homepages across the web) managed to galvanize support against the bills that has never been seen before. In a single day, Google.com collected over 7 million signatures on an online petition. Rather than the English-version of the website, Wikipedia redirected you to a list of your Congressional representatives and senators so you could either phone or e-mail them (I sent e-mails to all of mine; heard back from two of them, so far).

I don’t want to belabor how bad the bills are (or now were). They were pretty bad. They were so vague as to allow for entire websites to be brought down, or at least to make it so cost-ineffective to host any interaction with users and consumers (for fear of copyrighted material being posted) that an entire industry of user-generated content would die. I highly suggest you watch the video above if you want to understand the issue fully. If you’re an internet user in any capacity, it’s an important 13 minutes for you to spend.

Mostly, I wanted to address how ridiculously cool it was to see the entire internet united, even if for only one day. For that 24 hr period, this is all anyone was talking about across social networking. For that 24 hr period, people were engaged in the politics of what was going on with an issue that applied to them directly. For that 24 hr period, it didn’t matter if you were a Democrat or a Republican posting on some message board: both political parties supported the bills, and both party’s voters were against it.

For that 24 hr period, the internet and its users had more political power than the lobbyists from the motion picture industry and the music industry. And that’s saying something.

We’ve seen something like this before, in the form of the Arab Spring nearly a year ago, where social networking and the internet helped spawn a revolution across the Arab world, in multiple countries, casting down dictators long thought to be invincible by their people. Their citizens got organized, coalesced behind a belief that they could make a difference in their lives, and decided to take action. And in some small way, the internet did the same thing for the people of the United States this week.

And I just think that’s kinda cool.

Trying Out A New Toy

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A little snow won't dissuade the determined brewer.

For mid-January, yesterday ended up being a pretty gorgeous day for brewing. The sun was shining (occasionally) and the temperature held in the mid-40s for most of the afternoon. Thus, with Brooke and Meg out of the house, I opted to make the Chinook IPA Mom and Dad got me for Christmas.

This time, however, I also got to try out one of our new immersion wort chillers, so I figured I’d take the time to explain what this thing does and how to use it. Generally, you boil your wort (i.e. unfermented beer) for about an hour, and you add hops and other components during that period. However, you can’t add the yeast until the beer has cooled to below 100 F, though preferably closer to 80 F. You need to cool it down as rapidly as possible, so you can hopefully get it into your sealed fermentation vessel as soon as possible, including yeast.

For previous batches, we’ve always just put that big 5 gal. pot in an ice bath, though we’d have to add additional ice and cold water throughout, frequently taking well over an hour to cool down. Here’s where a wort chiller comes in: you run cold water through its copper tubing to act as a heat exchanger, removing heat from the wort quickly as cold water takes it away.

As this was my first time using said device, I had to do a few things first, namely, clean it.

Wort chiller, bathing in diluted white vinegar.

In the process of manufacturing, the copper tubing tends to have coatings of various oils and oxidized gunk that you don’t really want in your beer. Reading from John Palmer’s “How To Brew,” I found that before you use the chiller for the first time, you need to clean it with some kind of industrial copper cleaner, or alternatively, just use distilled white vinegar. The oils and oxidation products tend to come off the tubing in acidic solutions, and as beer is slightly acidic, all that stuff would end up in the beer. Thus, bathing the chiller in diluted vinegar (the stuff from the store is 5% acetic acid) shines it up nicely.

After soaking for maybe 20 min in vinegar, I rinsed it off well and let it air dry while the beer was boiling. When there’s about 10 min left in the boil, I then put the chiller in the brew pot, so the act of boiling would help sanitize the chiller. Though I’d just cleaned it in vinegar, there could still be some “bugs” on the outside of the tubing, so the boiling should take care of it.

Once I’d reached the end of the boil, I carried the pot and chiller down to the basement and hooked it up to a sink using an old washing machine hose.

Looks appetizing, eh?

Cold water going in and through the tube, then coming out the other end. I didn’t have a hose that fit that end of the tubing, so I just make sure to only keep the water pressure at something manageable, so it would stay within the sink.

The wort cooled down in about 20 min. Good deal!

Now that the chiller’s been cleaned before, I shouldn’t have to soak it in vinegar again, though forum posts on the interwebs will tell you that some people insist on cleaning it every time. In theory, all you should have to do is rinse it with water, then put it in the wort for 10 min while it’s boiling, then rinse it once you’re done.

All in all, it was remarkably easy and cut down on some of the total time spent brewing. Now, we’ll just have to wait another month or so to see how the beer turned out!