tag:blogger.com,1999:blog-28991657828642263632024-03-12T20:38:46.242-04:00The Junction PotentialNat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.comBlogger94125tag:blogger.com,1999:blog-2899165782864226363.post-65317303939919246052014-01-27T09:36:00.000-05:002014-01-27T09:36:26.224-05:00Academic protest songs@EvoNeuro added some new Academy-inspired lyrics to classic 60s era protest songs, <a href="http://evoneuro.org/2014/01/27/academy-protest-songs/">which were just awesome</a>. It inspired me to reword another song—classic, though not from the 60s.<br />
<br />
<div style="text-align: center;">
<span style="font-size: x-small;">Old profs oh yes they rob I</span></div>
<div style="text-align: center;">
<span style="font-size: x-small;">Sold I to the post-doc ship</span></div>
<div style="text-align: center;">
<span style="font-size: x-small;">Minutes after they passed me</span></div>
<div style="text-align: center;">
<span style="font-size: x-small;">from the Ph - D pit</span></div>
<div style="text-align: center;">
<span style="font-size: x-small;">But my brain was made strong</span></div>
<div style="text-align: center;">
<span style="font-size: x-small;">by the boot of the Academy</span></div>
<div style="text-align: center;">
<span style="font-size: x-small;">We forward this grad generation</span></div>
<div style="text-align: center;">
<span style="font-size: x-small;">Sorrowfully</span></div>
<div style="text-align: center;">
<span style="font-size: x-small;">Won't you help to sing</span></div>
<div style="text-align: center;">
<span style="font-size: x-small;">these songs of vain hope</span></div>
<div style="text-align: center;">
<span style="font-size: x-small;">Cause all I ever have</span></div>
<div style="text-align: center;">
<span style="font-size: x-small;">Rejection songs</span></div>
<div style="text-align: center;">
<span style="font-size: x-small;">Rejection songs</span></div>
<div style="text-align: center;">
<span style="font-size: x-small;"><br /></span></div>
<div style="text-align: center;">
<span style="font-size: x-small;"><br /></span></div>
<div style="text-align: left;">
<span style="font-size: x-small;">Almost feels wrong to use this particular song. But, I think the greatness of the real song can easily survive this silliness.</span></div>
Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com1tag:blogger.com,1999:blog-2899165782864226363.post-30092545701439291052013-11-02T23:26:00.000-04:002013-11-02T23:27:50.466-04:00AcWriMo13<div style="text-indent: 36px;">
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="font-size: 12pt;">November is the month of <a href="http://nanowrimo.org/">NaNoWriMo</a></span><span style="font-size: 12pt;">, a project that gets writers together with the aim of completing a full novel in 30 days. Sure, it’s not intended to be a perfect final version, but rather an exercise to force out a crappy first draft. If you’ve co-authored something with another person, you know that it’s often much easier to do the editing than to set down the initial draft.</span></span></div>
<div style="text-indent: 36px;">
<span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;">NaNoWriMo helps with motivation by connecting authors with one another for encouragement and with tools for keeping track of your progress. The concept has gone beyond the novel writing goal, being coopted by many different communities. One such is AcWriMo, which is geared for academic writing projects. It’s described <a href="http://www.phd2published.com/2012/10/15/announcing-acwrimo/">here</a> </span></div>
<div style="text-indent: 36px;">
<span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;">For me, this is a perfect time for such a writing push, as I have multiple projects that need transforming into papers. I have one that really just needs an introduction and discussion, so that’s first up. But the other projects maybe still need an experiment or two. What better way to see what’s truly needed than writing them up- and getting the inevitable “why didn’t I do THAT experiment then?” feeling? </span></div>
<div style="text-indent: 36px;">
<span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;">I tried something similar back in 2009, which crashed and burned- add another notch to my failure case (must be room somewhere). No matter, it’s a new year, and I’m in a much different place personally now. So, let’s see what I can really do. How much writing I can produce in a month? </span></div>
<div style="text-indent: 36px;">
<span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;">An important part of NaNoWriMo is to set clear goals, but make them lofty. For the novelists, it’s fifty thousand words. For AcWriMo, it’s more personalized, given the variety of academic disciplines involved. Whatever your goals, try and push the limit. Looking through my writing output that I’ve tracked in the past few months, I’m in the range of 300-400 words per day. That’s not full-time writing, as I’m doing experiments as well. But I think a goal of 750 words per day is good- ambitious yet attainable. </span></div>
<div style="text-indent: 36px;">
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="font-size: 12pt;">I’ll keep track of my progress among nine different files, each for the writing software <a href="http://www.literatureandlatte.com/">Scrivener</a></span><span style="font-size: 12pt;">. It’s a great program, and I’ve been using it for about 6 months. Probably it’s worth a later post on how it’s improved my writing output- and my experimental output). And yes, I said nine different files. That’s what’s currently in my open-loop writing wise. I did say it’s a good time for AcWriMo. I’ll prioritize them of course, but progress on any of them will count towards my goal. Everyday I write, I’ll tweet my word count, with the #AcWriMo hashtag. Maybe I’ll also post periodic updates here. And, I’ll take all the high-fives and hells-yeah folks can spare. So if you’re on Twitter, or here, I’ll take any and all kind words.</span></span></div>
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<div style="text-indent: 36px;">
<span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;">Oh, and how many words did I write today? Well, including this post (hey, it counts. It’s my goddamn AcWriMo, and I say it counts) I wrote 744 words. Not bad, considering I also raked fifteen 30 gallon bags worth of leaves, played Wii with the boy, hung out with the girl, and went to the movies with the family. I got this.</span></div>
Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com0tag:blogger.com,1999:blog-2899165782864226363.post-91595245174520413472013-10-16T11:12:00.000-04:002013-10-16T11:12:01.606-04:00Where IS my outrage?<blockquote class="twitter-tweet">
<a href="https://twitter.com/drisis">@drisis</a> you know you're the only person that actually re blogged Monica's? Rather depressing to me.<br />
— ScientistMother (@ScientistMother) <a href="https://twitter.com/ScientistMother/statuses/390353582358138880">October 16, 2013</a></blockquote>
<br />
[<i>note- this is a bit rambling, but I think it's important to get these thoughts out, ill-formed as they may be. And on the off-chance that you haven't read about Monica Byrne's experience, go do so <a href="http://monicacatherine.wordpress.com/2012/10/09/this-happened/">now</a> ]</i><br />
<br />
I want to thank ScientistMother for her <a href="http://sciencemommy.wordpress.com/2013/10/15/standingwithdnlee-and-im-standingwithmonicabyrne/">post</a> last night, and for noting that only Isis explicitly <a href="http://isisthescientist.com/2013/10/15/this-happened/">reblogged</a> Monica Byrne's story. I couldn't stop thinking about how my own response to DNLee's experience and Monica Byrne's experience differed so much. Why was that? It felt pretty easy to stand with DNLee when some two-bit online marketer called her an "urban whore." Didn't require a second thought. Why not the same response for Byrne's story?<br />
<br />
Because Bora has been a science blogger for so long? Well, I've never interacted with Bora online, and honestly I never did follow his blog.<br />
<br />
Because he's an editor at SciAm blogs? Maybe, though I don't have any aspirations for deliberately trying to widen my blog's audience (if I did, posting something, anything, would be a step).<br />
<br />
Because after what he did to Monica Byrne, he apparently didn't continue making sexual advances to her? Ok, but other women writers say he did the same to them (see comments on her post), and honestly, his <a href="http://blog.coturnix.org/2013/10/15/this-happenned/">apology</a> is weak.<br />
<br />
Because I didn't want to be seen as a trouble maker, or 'activist' in this regard? Whatever I write here may be read by people I'd want to hire me, and is this how I'd want them to see me?<br />
<br />
Because I know of times where I <i>know</i> I've acted badly, and recognize there are surely times where I've acted badly without knowing it. So, who am I to judge?<br />
<br />
It's been bothering me all night, and that's good- it should. Because it's not consistent to stand up loudly for DNLee and not for Monica Byrne. And because my thoughts above place the center on the incorrect location: either Bora, or me. The attention should be on Byrne, and then what is the best response<br />
<br />
Monica Byrne wanted to talk to Bora about writing on science- Bora thought of Byrne (and the other women he did this to) purely as a potential sex partner. "I'm a very sexual person," he said. There's no way to see that as anything other than a disgusting and outrageous comment in a work setting. I still can't grasp what it would feel like to meet with someone about a cool new opportunity to write an article, a blog post, whatever- and then have that person make it clear that they don't give a shit about that. They just want to go to bed with you. And then integrate that over a lifetime of similar experiences? I have no words, cause I cannot conceive of it. Need more concrete examples? Read about Kathleen Raven's <a href="http://sci2morrow.com/2013/10/16/mixed-up/">experiences</a>.<br />
<br />
This pisses me off. Any right thinking person knows these actions are horrendous and unacceptable. Behavior like this shouldn't be tolerated anywhere. I'm pissed off as a man, who is judged, <b>reasonably</b> so, as a possible creep by people who don't know me. I'm pissed off thinking about what experiences the women in my life (my mom, my wife, my daughter) have endured. But that's too narrow a focus. I'm pissed off that other people have to experience this. I don't really know what to do to address it. But the response overall has been somewhat muted, when more outrage is in order.<br />
<br />
I want to thank Monica Byrne for her bravery in speaking up. I don't know what it feels like, but can only imagine it's incredibly difficult to do so.<br />
<br />
Relevant links:<br />
Priya Shetty has an excellent <a href="http://www.huffingtonpost.co.uk/priya-shetty/sexual-harassment-in-science_b_4102449.html">piece</a> about the relative silence of the community's response.<br />
Dr FreeRide's <a href="http://scientopia.org/blogs/ethicsandscience/2013/10/15/this-is-not-a-post-i-want-to-write/">post</a><br />
DrugMonkey's <a href="http://scientopia.org/blogs/drugmonkey/2013/10/15/i-miss-my-sisters/">post</a><br />
Odyssey's <a href="http://scientopia.org/blogs/blather/2013/10/15/power-and-bad-times-in-your-life/">post</a><br />
<br />
<script async="" charset="utf-8" src="//platform.twitter.com/widgets.js"></script>Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com5tag:blogger.com,1999:blog-2899165782864226363.post-68485605726643510182013-10-13T15:36:00.000-04:002013-10-13T15:36:00.116-04:00A bit late, but still time to stand with DNLeePerhaps you've heard of this through others in the science blogging commuity, but it needs to be said over and over again: this behavior is never acceptable, and must be called out as such. If you offer a science writer a change to blog at your site, and she refuses you, you don't call her whore. <div>
<br /></div>
<div>
Go read about it at Isis's place <a href="http://isisthescientist.com/2013/10/11/tell-someone-no-get-called-a-whore-standingwithdnlee-batsignal/">here</a> (after Scientific American removed DNLee's post), and also check out her follow up <a href="http://isisthescientist.com/2013/10/12/an-open-letter-to-scientific-american-and-why-youve-lost-a-reader-boycottsciam/">here</a>. </div>
<div>
<br /></div>
<div>
[it's another example showing the value of the web to learn about experiences of people different than you. As a white male in science, it's not likely someone would call me a whore if I refused their offer to do something. What would that feel like, especially when it's one more thing in a long line of similar experiences?]</div>
Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com0tag:blogger.com,1999:blog-2899165782864226363.post-70545949404923296512013-10-06T18:32:00.001-04:002013-10-06T18:32:54.099-04:00Yum!After a long, cold day of apple picking in the rain, not much can beat the first beef stew of the season.<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8gBGjtdxPxetQtLQ8seEPsHOL-bnAe7Krsi7w-AKzpR5cW3F_pB_RF9MZuGQf1Xsdwp2O12f4bY7yPbMvjE-lE7g2ATnMlftk2cTLQ0oiUSPwCSnqWlNITY-dGzybtwKPAgyHM-QYkFw/s1600/photo+(1).JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="239" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8gBGjtdxPxetQtLQ8seEPsHOL-bnAe7Krsi7w-AKzpR5cW3F_pB_RF9MZuGQf1Xsdwp2O12f4bY7yPbMvjE-lE7g2ATnMlftk2cTLQ0oiUSPwCSnqWlNITY-dGzybtwKPAgyHM-QYkFw/s320/photo+(1).JPG" width="320" /></a></div><br />
Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com4tag:blogger.com,1999:blog-2899165782864226363.post-5064304097457389752013-09-16T13:37:00.000-04:002013-09-16T13:37:31.577-04:00Cleanliness is next to godlinessNoise- electrical noise. One of the banes of the electrophysiologist. It turns your recordings to laughable 60 cycle garbage, that you'd be embarrassed to publish. It turns your days into fruitless searches for impossible to find ground ground loops.<br />
<br />
Some of the most pernicious sources of noise I've had resulted from old spills of salt solutions that I thought I'd cleaned up. One time the saline seeped between the air table and a post holding the manipulator and headstage. That created a weird acoustic pickup that was near my voice's natural frequency. Took me a long time to find that one.<br />
<br />
Another annoying place that salt can build up is the pipette holder itself. A little excess internal solution at the non-tip end of the pipette can get into the holder, causing havoc. I haven't seen that lead to overt 60 cycle noise, but rather an increased RMS noise that makes single channel recording more annoying that it already is.<br />
<br />
To get around that, a good dip in the ultrasonic cleaner can do wonders. I fill up the cleaner with a solution with some detergent (1% ContRad works well). The detergent improves wetting of the objects you're cleaning, and reduces microbubbles-which prevent effective cleaning. Degas the solution by running the cleaner for 10-15 minutes, then immerse your disassembled holder and bath in the solution. Let it run for ~10 minutes, wash your stuff a few times in dH20 and you're good to go.<br />
<br />
A cool way to test if your cleaner is working well is with a pencil mark drawn on the frosted end of a glass slide:<br />
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<br />Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com0tag:blogger.com,1999:blog-2899165782864226363.post-63063509872098204212013-08-29T11:09:00.002-04:002013-08-29T11:11:44.231-04:00Patch-clamp playlist<span style="font-family: Arial, Helvetica, sans-serif;">This playlist has been killing it for the past few weeks. </span><span style="font-family: Arial, Helvetica, sans-serif;">I share it with you all in case </span><span style="font-family: Arial, Helvetica, sans-serif;">you need inspiration. I left off 'The Who', lest you go all Pete Townsend/Keith Moon on your rig.</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<span style="font-family: Arial, Helvetica, sans-serif;">1 - Working Man - Rush</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">2 - Space Truckin' - Deep Purple</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">3 - Ace of Spades - Motörhead</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">4 - Pain and Pleasure - Judas Priest</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">5 - Highway to Hell - AC/DC</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">6 - Crazy Train - Ozzy Osbourne</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">7 - I Wanna Be Sedated - The Ramones</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">8 - Whipping Post - The Allman Brothers Band (20+ minute live jam preferred)</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">9 - The Mob Rules - Black Sabbath</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">10 - Symphony of Destruction - Megadeth</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">11 - Fade To Black - Metallica</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">12 - Tom Sawyer - Rush</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">13 - We're Not Gonna Take It - Twisted Sister</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">14 - The Prisoner - Iron Maiden</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">15 - God Save the Queen - Sex Pistols</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">16 - Seek and Destroy - Metallica</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">17 - We Will Rock You/We Are the Champions - Queen</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com4tag:blogger.com,1999:blog-2899165782864226363.post-22177889543174198862011-06-06T11:53:00.002-04:002011-06-06T11:56:13.451-04:00Guest blogging over a ScientopiaI'll be spending the next two weeks blogging at the Guest Blogge at Scientopia. <a href="http://scientopia.org/blogs/guestblog/">Here</a>. <div><br /></div>Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com0tag:blogger.com,1999:blog-2899165782864226363.post-62424901225571629972011-04-22T15:55:00.000-04:002011-04-22T15:55:00.517-04:00I love it, just love it!<div><br /></div><div><br /></div><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEixvksiDu4QzrK22mx_6FXvOrVxV-0JaUlNL7HFRaQix-GQGmQ_bMkXqJx0mluxsbtFwXUz_FFHklL3RI2VHy0rmZDKnyOvf5HppQqaQGHYrRjTxFJriQ6IRqE1QNDowtfLxDzpGyCm8w0/s1600/rigjockey.jpg" onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 254px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEixvksiDu4QzrK22mx_6FXvOrVxV-0JaUlNL7HFRaQix-GQGmQ_bMkXqJx0mluxsbtFwXUz_FFHklL3RI2VHy0rmZDKnyOvf5HppQqaQGHYrRjTxFJriQ6IRqE1QNDowtfLxDzpGyCm8w0/s320/rigjockey.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5598497554020542706" /></a><div style="text-align: center;">Doesn't matter how long I've been doing it, I love being a rig jockey.</div>Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com7tag:blogger.com,1999:blog-2899165782864226363.post-51095727088590467022011-04-08T08:48:00.002-04:002011-04-08T08:49:13.267-04:00LET'S GO YANKEES!!!!!Here we go Yankees, here we go!<div><br /></div><div>Here we go Yankees, here we go!</div><div><br /></div><div>Beat those goddamn mouthbreathers! WOOHOO!</div>Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com2tag:blogger.com,1999:blog-2899165782864226363.post-57601601778576703462011-03-03T14:08:00.002-05:002011-03-03T14:10:58.218-05:00Some things shouldn't go togetherLike ball-peen hammers, screwdrivers, and microscopes. <div><br /></div><div>The first two would be much better served striking the head of whatever ingrate spilled solution all over the scope and then DIDN'T WIPE IT UP. </div>Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com2tag:blogger.com,1999:blog-2899165782864226363.post-43366707547960844572010-10-27T15:30:00.001-04:002010-10-27T15:31:00.713-04:00How do I measure the liquid junction potential?And so it emerges from the depths.....<br /><br />For years innocent readers thought they had escaped...<br /><br />A horror so horrible it inspires screams...of horror<br /><br />It is...the...long awaited post on how to measure a junction potential!!<br /><br />It's clear from the search terms that bring people here, plenty of folks are curious about this topic. The "<a href="http://junctionpotential.blogspot.com/2009/04/what-is-junction-potential.html">What is a Liquid Junction Potentia</a><a href="http://junctionpotential.blogspot.com/2009/04/what-is-junction-potential.html">l</a>" post is one of the most read. So allow me to finally follow up with how to actually measure it. Although there are the standard descriptions about junction potentials in various texts and <a href="http://junctionpotential.blogspot.com/2008/07/what-are-bibles-of-your-field.html">bibles</a> of the field, a step by step 'how-to' is lacking. Seeing as I bridge these two in real life lab,why not here?<br /><br />Ok, you have some internal solutions, and you want to report the correct voltages in your paper.<br /><br />You've got to account for the junction potential between the internal solution and the bath solution present when you first stick in the pipette. Now, you can calculate it if you want; there's a program built into Clampex. But, are you sure that the constants are correct for what's in your solution, especially if it has something weird in it? TEA-methanesulfonate for example. Or NMDG-aspartate - a killer internal for recording sodium current by the way. Are you even sure you made the solution correctly?<br /><br />It's easy, so measure it!<br /><br />When I measure junction potentials, I follow the advice of my old <a href="http://junctionpotential.blogspot.com/2008/07/genealogies-of-academic-variety.html">granpappy</a>, as discussed in E. Neher, Methods Enzymol. 1992;207:123-31.<br /><br />Here's what you want to do:<br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpxUAOLlzFXjVfApMeD3jxwawiPhlO2b3AMRbM7pe1eQx48bnhXkyU8Asb5bMYWd0XN7CHFRi1x-olH1xhxYxGRzlhCJX_UqiOAEY3EFDhcZFw85tARXEekKxYi8hSu07gp07wg7DafZg/s1600/IMG_3058.JPG"><img style="display: block; margin: 0px auto 10px; text-align: center; cursor: pointer; width: 320px; height: 240px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpxUAOLlzFXjVfApMeD3jxwawiPhlO2b3AMRbM7pe1eQx48bnhXkyU8Asb5bMYWd0XN7CHFRi1x-olH1xhxYxGRzlhCJX_UqiOAEY3EFDhcZFw85tARXEekKxYi8hSu07gp07wg7DafZg/s320/IMG_3058.JPG" alt="" id="BLOGGER_PHOTO_ID_5532807458103766226" border="0" /></a>1) Get your stuff together: battery powered chlorider (don't tell me you're using bleach - GAH!!), silver wire, 3 M KCl, 5+ mL of each of the internal solutions, plus a few mL of the typical bath solution, a few patch pipettes.<br /><br />2) Make a 'flowing KCl' bridge, by taking a patch pipette, breaking off most of the tip, and filling it with 3 M KCl. Chloride a silver wire and use this as the bath ground. The high concentration of KCl, and the similar mobility of K+ and Cl- will help keep the junction potential at this electrode constant, even as the bath solutions changes. I fashioned a little jig to hold the bath pipette (on left below, a piece of plexiglass on a piece of white teflon).<br /><br />3) Rechloride your silver wire on the headstage, fill a normal resistance patch pipette with one of the solutions. If you're measuring only a single internal/bath pair, then you can put the internal in the pipette. But since setting this up is somewhat annoying, I often measure multiple internals relative to the same bath solution. In that case, I put the bath solution in the pipette.<br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi2YU4_zdzBcHVVryB4Q60usX3dhbjgxojNOqcSWnf38pjhICwzoKY-YP3GxJvoAKmppjUCpxNef20Sh94ik6PxZvNPh2UU75cS9SqI5LR28HvON-D1NjXUTpBd8kuXcLw51muNw_kuLaQ/s1600/IMG_3059.JPG"><img style="display: block; margin: 0px auto 10px; text-align: center; cursor: pointer; width: 320px; height: 240px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi2YU4_zdzBcHVVryB4Q60usX3dhbjgxojNOqcSWnf38pjhICwzoKY-YP3GxJvoAKmppjUCpxNef20Sh94ik6PxZvNPh2UU75cS9SqI5LR28HvON-D1NjXUTpBd8kuXcLw51muNw_kuLaQ/s320/IMG_3059.JPG" alt="" id="BLOGGER_PHOTO_ID_5532808052700360370" border="0" /></a>4) Whatever solution you put in the pipette, add it to the bath.<br /><br />5) Put your amplifier in current clamp mode (slow versus fast doesn't matter), set the 'meter' to 'Vm', make sure that there's no external command signal coming into the amplifier.<br /><br />6) lower pipette in<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3DXSTMUY4TRKGQtgT7pF-ZEXzyetp2nT_gtnGKnvP1zCUHs6JypIaeJqAOBhiPMKgqud-zEy9Ay7WhyphenhyphenwmoySOJxwiNk77TXS4-SYrwZSk525w-EHptRk-z8y_1_eQKO0fTfk9r0ygDF8/s1600/IMG_3060.JPG"><img style="float: left; margin: 0pt 10px 10px 0pt; cursor: pointer; width: 200px; height: 150px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3DXSTMUY4TRKGQtgT7pF-ZEXzyetp2nT_gtnGKnvP1zCUHs6JypIaeJqAOBhiPMKgqud-zEy9Ay7WhyphenhyphenwmoySOJxwiNk77TXS4-SYrwZSk525w-EHptRk-z8y_1_eQKO0fTfk9r0ygDF8/s200/IMG_3060.JPG" alt="" id="BLOGGER_PHOTO_ID_5532808646747668290" border="0" /></a>to solution.<br /><br />7) Use the "pipette offset" potentiometer until the meter reads zero mV. Wait a minute or so; if the voltage drifts by more than a few tenths of a mV, then you might need to rechloride the wires.<br /><br />8) Completely exchange the bath solution with the solution to be measured.<br /><br />9) Read the meter, which shows the junction potential.<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhndtodst42dB8cmEXPrq6b8dRJyKsiaLokPQRvdkS1U-5-v-4dauG8WBZy9IcM8dhHUfVH4yFdr5eYDdpFcAjNPkqjmGOEIqlevs1uu3grrUfCQ-ul_PyPIVDx1Tl86dhmvs_eolYjgJs/s1600/IMG_3061.JPG"><img style="float: right; margin: 0pt 0pt 10px 10px; cursor: pointer; width: 200px; height: 150px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhndtodst42dB8cmEXPrq6b8dRJyKsiaLokPQRvdkS1U-5-v-4dauG8WBZy9IcM8dhHUfVH4yFdr5eYDdpFcAjNPkqjmGOEIqlevs1uu3grrUfCQ-ul_PyPIVDx1Tl86dhmvs_eolYjgJs/s200/IMG_3061.JPG" alt="" id="BLOGGER_PHOTO_ID_5532808931678994514" border="0" /></a><br /><br />10) Replace the bath with the same solution as in the pipette, check that Vm is back close to zero. After that you can measure any other solutions.<br /><br />11) Now, to get the total transmembrane voltage in your experiments, you have to add your command voltage (or recorded in the case of a current clamp expt) to the measured junction potential. NOTE: If you switched the bath and pipette locations, then you MUST reverse the polarity. So, in the 8.2 mV above, that's actually a junction potential of -8.2, and is added to the command (e.g., a step from -80 to 0 in Clampex becomes -88 to -8 mV). If you're an anal retentive scientist *whistles innocently*, then you already account for the junction potential in your voltage protocols, resulting in nice round numbers.<br /><br />There you go, and hope that helps. Questions? Let em rip in the comments.Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com75tag:blogger.com,1999:blog-2899165782864226363.post-61491036868530574632010-10-01T11:40:00.001-04:002010-10-01T11:40:00.411-04:00Damn I love being a scientist!Even though most times it's difficult, experiments don't cooperate (cells, I'm looking at you), the future isn't certain, there's NOTHING ELSE IN THE WORLD I would do rather than be a scientist. I love it.<br /><br />I also love the actual <span style="font-style: italic;">doing</span> of the experiments. There are many postdocs out there who are counting the days until they can stop doing experiments (well, no one forced you to be a Western jockey), and let other people do it. Not me. I get an inordinate amount of satisfaction from craft of experiments.<br /><br />So, off to patch clamping. The soundtrack to <span style="font-style: italic;">Conan The Barbarian</span> is blasting. We'll see if the <span style="font-style: italic;">Wheel of Pain</span> has me or the cells as its subject.Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com3tag:blogger.com,1999:blog-2899165782864226363.post-5093615266255391062010-09-22T14:55:00.003-04:002010-09-22T14:57:16.511-04:00Sometimes being a science dad...means leaving your experiments early because your son has been having lots of pee pee accidents, so they're worried about UTIs, and your daughter is coughing up a lung, so might have a pneumonia.<br /><br />*sigh*<br /><br />At least the cells weren't great, cause it's easier to leave them. Anyways, the kids need their daddy!Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com6tag:blogger.com,1999:blog-2899165782864226363.post-46979779645183767302010-09-21T11:00:00.000-04:002010-09-21T11:00:01.053-04:00Falling to AutumnNot too much blogging going on obviously. Things aren't bad, just kinda meh. Why? Let us count the ways:<br /><br />1) Return of illin'. No, I don't mean harkening back to early hip hop, I'm talking viruses. Day care center strength viruses. Day cares where the vast majority of parents are health care workers, shipping their gunk into school, letting it percolate among the young'uns, whereupon it descends upon fresh victims. I've already had one GI bug (seriously, WTF is that? They never tell you that before you have kids), and we're all getting over a head cold. Luckily though, the little girl fought it off well, didn't progress to an ear infection. *knocks on wood*<br /><br />*knocks on formica*<br /><br />*knocks on cinderblocks*<br /><br />2) Watching young scientists get chewed up and spit out by their so called mentors. I've been in this business long enough to see some ugly stuff, and I realize that's the way of the world. But why does it seem to happen to women more than men? Maybe I shouldn't let it drag on me. What's the phrase? "Not a fucking Care Bears tea party?" There, now I feel better.<br /><br />3) I have to sit through 8 one hour ethics training sessions, to fulfill some new NIH requirement. This is a total waste. No one in their right mind believes this will really change behavior, do they? It's just window dressing. I have a feeling I'm gonna be a pain in the rear in this class.<br /><br />4) The filament in the pipette puller just broke, so now I get to make a new program. *sigh*Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com8tag:blogger.com,1999:blog-2899165782864226363.post-85780092434648454762010-08-27T10:20:00.004-04:002010-08-27T10:27:59.692-04:00Friday Morning Quick Hits<span style="font-style: italic;font-size:85%;" >(Ed. - Sorry about the accidental posting clogging up your RSS tubes)</span><br /><br />I am about to start patching some cells this morning. The cells have been a tad obstreperous and ornery these days. I want to warn them though, this crap's gotta stop. So here's your heads up you little buggers:<br /><a target="_blank" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiO58d92wgV3_wwo0rspMRs4DuGP1-MSELFZlpFUloJZNgUOrT6H1KBsiPldHQkbm_iId58aD7efIYPu9RrSVeDoqpUWhZlKpJPbsyiEimhxJOkR_IN3ipkDs3FVOD89QlRCewa7-x9slg/s1600/earp.jpg"><img style="display: block; margin: 0px auto 10px; text-align: center; width: 300px; height: 170px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiO58d92wgV3_wwo0rspMRs4DuGP1-MSELFZlpFUloJZNgUOrT6H1KBsiPldHQkbm_iId58aD7efIYPu9RrSVeDoqpUWhZlKpJPbsyiEimhxJOkR_IN3ipkDs3FVOD89QlRCewa7-x9slg/s320/earp.jpg" alt="" border="0" /></a><span style="font-size:85%;"><span style="font-weight: bold;">Figure 1</span>: YOU TELL I'M COMING!!! AND PIPETTES WITH VARIOUS AND SUNDRY INTERNAL CONSTITUENTS ARE COMING WITH ME!!! PVSINCses ARE COMIN WITH ME!!!</span><br /><br />In other news, DrugMonkey is highlighting an <a href="http://scientopia.org/blogs/drugmonkey/2010/08/25/online-commentary-on-papers-allows-scooped-authors-to-argue-their-priority/">online comment on a recent Nature paper</a> that point to possible GlamourMagz shenanigans: did a Nature editor string along one group working to refute a recent paper, only to publish a second group's similar work (thus scooping the first group)? And was this Nature editor friends with the 2nd group? Check it out.<br /><br />Lastly, your Science Soundtrack for the week:<br /><object width="480" height="385"><param name="movie" value="http://www.youtube.com/v/M8L4C0IXNC8?fs=1&hl=en_US&rel=0"><param name="allowFullScreen" value="true"><param name="allowscriptaccess" value="always"><embed src="http://www.youtube.com/v/M8L4C0IXNC8?fs=1&hl=en_US&rel=0" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="480" height="385"></embed></object><br />Yes, I just compared science to S&M. Dog upon a leash indeed.<br /><br /><div><img src="https://blogger.googleusercontent.com/tracker/2899165782864226363-3059045712376473068?l=junctionpotential.blogspot.com" alt="" width="1" height="1" /></div>Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com3tag:blogger.com,1999:blog-2899165782864226363.post-27252175366452583142010-08-20T09:30:00.001-04:002010-08-20T09:38:50.480-04:00Friday Morning Science SoundtrackTo coincide with<a href="http://www.labspaces.net/blog/profile/596/Genomic_Repairman"> Genomic Repairman's</a> daily music postings, and the awesome grad school blog carnival Samia is hosting over at <a href="http://im-geiste.blogspot.com/">49 Percent</a>, I present my own top pick on my personal Science Soundtrack. Though it doesn't actually convey my grad school experience (which was on the whole quite good), it sure nails the post-doc.<br /><br />Here it is, arguably the greatest metal song ever:<br /><br /><span style="font-size:130%;">MASTER OF PUPPETS - METALLICA</span><br /><br /><object width="480" height="385"><param name="movie" value="http://www.youtube.com/v/tPWlzBsJfxA?fs=1&hl=en_US&rel=0"><param name="allowFullScreen" value="true"><param name="allowscriptaccess" value="always"><embed src="http://www.youtube.com/v/tPWlzBsJfxA?fs=1&hl=en_US&rel=0" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="480" height="385"></embed></object><br /><br /><br />A perfect meditation on the at times abusive relationship I have with Science.<span style="font-style: italic;"><br /><span style="font-style: italic;"><br /></span></span><span style="font-size:85%;"><span style="font-style: italic;"></span><blockquote><span style="font-style: italic;">Master of puppets I'm pulling your strings</span><br /><br /><span style="font-style: italic;"> Twisting your mind and smashing your dreams</span><br /><br /><span style="font-style: italic;"> Blinded by me, you can't see a thing</span><br /><br /><span style="font-style: italic;"> Just call my name, 'cause I'll hear you scream</span><br /><br /><span style="font-style: italic;"> Master</span><br /><br /><span style="font-style: italic;"> Master</span><br /><br /><span style="font-style: italic;"> Just call my name, 'cause I'll hear you scream</span><br /><br /><span style="font-style: italic;"> Master</span><br /><br /><span style="font-style: italic;"> Master</span><br /><br /><br /> <br /><span style="font-style: italic;"> Master, master, where's the dreams that I've been after?</span><br /><br /><span style="font-style: italic;"> Master, master, you promised only lies</span><br /><br /><span style="font-style: italic;"> Laughter, laughter, all I hear or see is laughter</span><br /><br /><span style="font-style: italic;"> Laughter, laughter, laughing at my cries</span><br /><br /><br /> <br /><span style="font-style: italic;"> Hell is worth all that, natural habitat</span><br /><br /><span style="font-style: italic;"> Just a rhyme without a reason</span><br /><br /><span style="font-style: italic;"> Neverending maze, drift on numbered days</span><br /><br /><span style="font-style: italic;"> Now your life is out of season<br /><br /></span></blockquote><span style="font-style: italic;"></span></span>My fellow masochists are invited to contribute their own picks for the Science Soundtrack.Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com2tag:blogger.com,1999:blog-2899165782864226363.post-29816570333477949632010-08-06T14:15:00.002-04:002010-08-06T14:16:15.423-04:00Science Dads Reporting for Duty!<a href="http://scientistmother.blogspot.com/">ScientistMother's</a> recent post about a new article in Science Careers (<a href="http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2010_08_06/caredit.a1000077">Scientist Dads Step Up</a> by Vijaysree Venkatraman), was welcome, extending the Work-life balance theme that the bloggers at <a href="http://www.labspaces.net/index.php">LabSpaces</a> have been exploring recently.<br /><br />Let me first make a big fat disclaimer: I don't know anything about work-life balance, because mine has been broken ever since the second baby came into our lives (hey, who knew a 4 1/2 lb preemie could bust that up?). I ain't no role model, as I'm far from doing either the work thing well, or the parent thing well. In fact, if I had to say which I was better at, right now it'd be the parent thing.<br /><br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj5OhmMGyZIJirskqCZhADLH350LsTLyLjy4e4yZYgVx2elyG-Iud6CqXAjASgdqjB95LDB2wPAmhknVRSIQ9akg5c4LD2j8T_M92fBjrJ5a3LDOXq13rEj63rPr2rPglF8gNMs7omJTdQ/s1600/kids_slide.jpg"><img style="display: block; margin: 0px auto 10px; text-align: center; cursor: pointer; width: 238px; height: 320px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj5OhmMGyZIJirskqCZhADLH350LsTLyLjy4e4yZYgVx2elyG-Iud6CqXAjASgdqjB95LDB2wPAmhknVRSIQ9akg5c4LD2j8T_M92fBjrJ5a3LDOXq13rEj63rPr2rPglF8gNMs7omJTdQ/s320/kids_slide.jpg" alt="" id="BLOGGER_PHOTO_ID_5502359790500038994" border="0" /></a><span style="font-size:85%;"><span style="font-weight: bold;">Figure 1</span>: The Blair spawn frolick. I'm not in the picture cause Mom had to work on both weekend days. We all survived, the house survived, and I think I even got some laundry done. Can't remember if it was folded though.<br /></span></div><br />Normally I don't think of blogging about my role as a parent. As most parents will tell you, parenting is by and large boring and repetitive tasks, punctuated by both incredibly heart warming and incredibly terrifying moments. So who cares when I have to stay home with a sick kid? Or that I made dinner last night - as I have just about every night for the past 11 years of our marriage? Or when night terrors in a 4 1/2 year old return us to the sleepwalking zombies of the infant stage? Or that I left the lab early to go to a parent-teacher conference at daycare? I already lived it, what's the point to discussing it further? Plus, god forbid it be seen as cookie-begging.<br /><br />Well, maybe it isn't obvious that a lot of science dads are doing the hard grunt work of parenting. Maybe because there just aren't actually do do it. Or maybe those who do feel they need to hide or diminish it, for fear of not being taken seriously. In that case, having science dads talk about their involvement would help make it more normal.<br /><br />And reading between the lines of the Science Careers article suggest we need to go even farther, as these quote suggest:<br /><br />"<span style="font-style: italic;">...his lawyer wife, who works part time...</span>"<br /><br />"<span style="font-style: italic;">Currently, his wife stays home to care for their two young children </span>-- "<br /><br />"<span style="font-style: italic;">But women avail themselves of those [parental-leave] policies more often than men do because men fear they may not be regarded as serious, competitive scientists if they take parental leave...</span>"<br /><br />[now, each couple makes the decisions that are best for them. I get that. But the best we got from the men for staying away from work was Chad Nusbaum and his two months. Which is definitely great. Still, can't we do more? Shouldn't we?].<br /><br />And some other quotes:<br /><br />"<span style="font-style: italic;">Maybe pick two hours each day on Saturday and Sunday” to balance the needs of science and home life.</span>" (F*** you dude).<br /><br />"<span style="font-style: italic;">Maybe you should have married a more supportive wife</span>" (one male postdoc to another regarding long hours spent in the lab)<br /><br /><br />---<br /><br />So, should I do more of daddy blogging? Like I said, I'm not a role model for someone doing well at parenthood and work. I wouldn't call myself a successful scientist; I'm just kinda getting by as well as I can (though things are improving). So in that case, maybe it's worse to do more daddy blogging?<br /><br />Final note: we're on vacation next week, having family time on the beach. So whoever out there is reading (not that any of you lurkers would step up and respond to <a href="http://junctionpotential.blogspot.com/2010/07/belatedly-and-memely-yours.html">this</a> - naughty naughty), no posts.Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com1tag:blogger.com,1999:blog-2899165782864226363.post-14158047518428177972010-08-05T14:00:00.001-04:002010-08-05T14:00:00.975-04:00Team Fox or Team Hedgehog?<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjrImO1FbUtaV5LYv-pKdJ2kmmMzhiD2kEaupIOqOp2UzjkVS8VfZailS2qEaowtNnP4TaPqFp2a0FLqajhNqW5Bsu4pKZIn0-RivrlGN2YOFbNkswdfitP8q-V4bbGwEQvtP4tQi8-guc/s1600/Photoxpress_1084019.jpg"><img style="display: block; margin: 0px auto 10px; text-align: center; cursor: pointer; width: 320px; height: 214px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjrImO1FbUtaV5LYv-pKdJ2kmmMzhiD2kEaupIOqOp2UzjkVS8VfZailS2qEaowtNnP4TaPqFp2a0FLqajhNqW5Bsu4pKZIn0-RivrlGN2YOFbNkswdfitP8q-V4bbGwEQvtP4tQi8-guc/s320/Photoxpress_1084019.jpg" alt="" id="BLOGGER_PHOTO_ID_5501983448083252130" border="0" /></a><span><span>Team Hedgehog, all the way!<br /><br />In case you haven't been following, <a href="http://girlscholar.blogspot.com/">Notorious Ph.D</a>. posted about the differences in academic approaches between “foxes” and “hedgehogs”:<br /><br />"<span style="font-style: italic;">The fox knows many tricks; the hedgehog knows only one, but he does it well.</span>"<br /><br />I’ll admit it, I am and have always been, a science hedgehog. There’s nothing like a nice 10+ figure paper, replete with detailed, technically exce</span></span><span><span>llent experiments, explicit consideration of other explanations (negative results, and their controls go here) to get me all hot and bothered. It’s what attracts me, what I find compelling science, and after enough time, I’ve realized that it’s not something I can easily change about myself (part of Notorious’s post concerns exactly that: changing from a <a href="http://girlscholar.blogspot.com/2010/07/fox-and-hedgehog-part-1.html">hedgehog into a fox</a>, and also how <a href="http://girlscholar.blogspot.com/2010/07/fox-and-hedgehog-part-2.html">other scholars respond</a>).<br /><br />And yet, I realize the limitations of such a hedgehogia</span></span><span><span>n approach. Sometimes, a mix of approaches is required to get an answer; hedgehogs might miss this. Sometimes, you get so deep into something that you lose perspective, seeing only the trees, and not the forest. I get that. Still, there are ways as a hedgehog to evolve without completely changing species. You can be a serial hedgehog, going deep into different topics over time (I’d put my thesis advisor in this category). Or, you could</span></span><span><span> be a topic hedgehog: sticking to one topic, going </span></span><span><span>very deep into it, but bringing in other techniques as needed. I’d put the guy I started grad school with in that group.<br /><br />But in all the discussion on this, which has largely been pro-fox, there hasn’t been much focus on what the limitations of the fox approach is. Sure, the best foxes are out there seeding fields with new approaches, new techniques, and both answering old questions while raising new ones.<br />There’s another species of fox too:<span><span><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgvsZEe556PQRHuF7uN0FuWgswgliJeFT6QKEK6I_xze_QMhz4GXeE3eN4liIlneBi-ATKzdsjhCAXMnSjgHCpWt5Ln8hGfrzY5IyoJ6wapKnmKk6f48IhHEHREWZTD04YlqfpZJ791FnM/s1600/swiper.jpg"><img style="display: block; margin: 0px auto 10px; text-align: center; cursor: pointer; width: 306px; height: 320px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgvsZEe556PQRHuF7uN0FuWgswgliJeFT6QKEK6I_xze_QMhz4GXeE3eN4liIlneBi-ATKzdsjhCAXMnSjgHCpWt5Ln8hGfrzY5IyoJ6wapKnmKk6f48IhHEHREWZTD04YlqfpZJ791FnM/s320/swiper.jpg" alt="" id="BLOGGER_PHOTO_ID_5501983045291063858" border="0" /></a></span></span><br /><br />We all know them. Shitty experimentalists who flit from project to project, or people with a new fancy trick that they get the same answers people in the field had already gotten (BUT LOOK, IT’S PRETTIER!). Or they ignore the previous results that their "great new technique" doesn't replicate (probably because they don't really understand the earlier results, as they never engaged them seriously).<br /><br />True, there’s fewer of these kind of foxes around for long, being selected against over time. In this vein, the idea/suggestion that younger scholars must start out as hedgehogs has a lot of merit. But I've seen young foxes; it often ain't pretty.<br /><br />In the end, instead of <a href="http://physioprof.wordpress.com/2010/08/01/foxes-and-hedgehogs/">pigeonholing hedgehogs</a> as boring old, narrow minded, one trick ponies, and foxes and shallow, incompetent, jacks of all trades, I’d rather people agree that, when well done, BOTH approaches have their merit, and that it’s important to maintain a healthy equilibrium between the two.<br /></span></span>Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com1tag:blogger.com,1999:blog-2899165782864226363.post-16499931632753723422010-08-02T15:45:00.000-04:002010-08-02T15:45:00.718-04:00I am the Norge Repairman of the primary literature<span style="font-size: 11pt; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; font-weight: normal; font-style: normal; text-decoration: none; vertical-align: baseline;" id="internal-source-marker_0.919369922884668">In one of those strange coincidences of the blogosphere, Chad (at <a href="http://scienceblogs.com/principles/2010/07/two_cultures_defining_research.php">Uncertain Principles</a>) and Janet (at <a href="http://scientopia.org/blogs/ethicsandscience/2010/07/29/research-methods-and-primary-literature/">Adventures in Science</a> - now in her new digs are <a href="http://scientopia.org/blogs/">Scientopia</a>) are discussing the role of the primary literature in the sciences, at exactly the same time as I was plumbing the depths of the primary literature.</span><br /><span style="font-size: 11pt; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; font-weight: normal; font-style: normal; text-decoration: none; vertical-align: baseline;"></span><br /><span style="font-size: 11pt; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; font-weight: normal; font-style: normal; text-decoration: none; vertical-align: baseline;">See, for the past few weeks I myself have been conducting an extensive expedition through the literature on the M current. M current stands for muscarinic current, which is a potassium current in various neurons that is closed by muscarinic agonists (among others). This reduction leads to enhanced neuronal excitability and more action potentials. The current has been most widely studied in sympathetic neurons, which do something to pumps or plumbing or something. Go ask <a href="http://scientopia.org/blogs/nobrain/">her</a>.</span><br /><span style="font-size: 11pt; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; font-weight: normal; font-style: normal; text-decoration: none; vertical-align: baseline;"></span><br /><span style="font-size: 11pt; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; font-weight: normal; font-style: normal; text-decoration: none; vertical-align: baseline;">This sort of detailed review is something I’ve been meaning to do for some time, but never forced myself to start. But the life-work balance has been recalibrated recently (hence the increased posting here - more on that later?), so I’ve finally begun. I’ve been tracing back through the literature and cited references, checking reviews, and also reading what I can find about the scientists who contributed to the field. I find this a great way to engage in the literature, because tracing the development of the ideas helps .e put them in a context that I find much easier to remember. I’d hazard a guess that this would be a lot more useful to undergraduates engaged in research, than simply throwing the “primary source” of a bunch of ganglia at them while telling them to “do research.”</span><br /><span style="font-size: 11pt; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; font-weight: normal; font-style: normal; text-decoration: none; vertical-align: baseline;"></span><br /><span style="font-size: 11pt; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; font-weight: normal; font-style: normal; text-decoration: none; vertical-align: baseline;">I find the M current story compelling for a couple reasons. The first relates to why studying the primary literature can be an important part of doing science. The excitation resulting from muscarinic stimulation was obvserved as far back as the early 1950s, yet it wasn’t until the mid 2000s that a pretty complete picture of the entire process, including receptor proteins, ion channels, signalling molecules, was developed. And in that time, as you might imagine, there were a lot of missteps, and numerous errors. That lesson, that wrong things get published all the time, is a crucial lesson. Another lesson is that science doesn’t develop as a neat and tidy, linear march to more and more understanding. Both of these are rarely discussed in science textbooks. he only counterexamples I can come up with are Newtonian versus quantum mechanics, and Lamarck’s theory of evolution). Most of the rest of science in textbooks is so boring. Message to undergrads: Science can be a whole lot more fun than that.</span><br /><span style="font-size: 11pt; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; font-weight: normal; font-style: normal; text-decoration: none; vertical-align: baseline;"></span><br /><span style="font-size: 11pt; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; font-weight: normal; font-style: normal; text-decoration: none; vertical-align: baseline;">The second reason is that the 55 odd year trip from initial observation to final signalling molecules gives me hope on my own research topic. In my day job I’m studying how G protein coupled receptors activate a particular transient receptor potential (TRP) channel, TRPC5. But it’s been a bear, because we’ve exhausted the usual suspects, and haven’t yet nailed down the culprit. (Also, the channel is just a pain in the f***ing ass, clearly being a devotee of Marquis de Sade.) In fact, it’s entirely possible that we’re on the wrong path entirely (I said “possible”. Not “likely”). Still, seeing as this channel was only cloned in 1996, and “real” recordings of its activity date from 1999-2000, I figure we still have some time to go before making a run at the title of “Longest duration from ion channel to signalling pathway elucidation.” </span><br /><span style="font-size: 11pt; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; font-weight: normal; font-style: normal; text-decoration: none; vertical-align: baseline;"></span><br /><span style="font-size: 11pt; font-family: Arial; color: rgb(0, 0, 0); background-color: transparent; font-weight: normal; font-style: normal; text-decoration: none; vertical-align: baseline;">I plan to do some blogging on the seminal papers of the field, as well as the its overall development. </span>Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com3tag:blogger.com,1999:blog-2899165782864226363.post-55133349592681777132010-07-29T14:30:00.001-04:002010-07-29T14:30:00.903-04:00Good olden tyme science (now with Squid Axon videos!)Isis posted an <a href="http://scienceblogs.com/isisthescientist/2010/07/how_physiology_was_cooler_40_y.php">awesome video</a> of physiologist John Severinghaus discussing his work on altitude and...um...physiology, while working on White Mountain Research Station. Very interesting, and from this neurogeek's perspective, a part of physiology that I know little about.<br /><br />It got me thinking about the great old experiments in my own subfield of ion channels and electrical excitability. I'm a big fan of going back and actually, you know, reading the foundational literature in the field. That's just me, I don't expect everyone to love it, but I always wonder at how clearly those greats viewed things, and how much their work shapes the later development of the field (especially with regards to what questions are considered important).<br /><br />For electrophysiology, this leads to One Prep, One Prep to Rule Them All:<br /><br /><span style="font-size:130%;"><span style="font-weight: bold;">THE SQUID GIANT AXON!!!!!!!!1!!ELEVENTY!</span></span><br /><br />As most biologists likely learned at some point in school, the <a href="http://en.wikipedia.org/wiki/Squid_giant_axon">squid giant axon</a> provided the system that Alan Hodgkin and Andrew Huxley used to analyze the basis of the action potential. Nowadays though, I'd gather there aren't many electrophysiologists who have actually seen the axon or it's beautiful action potential in real life. I know I haven't.<br /><br />Luckily, we have our own kick ass old science videos. Back in the 1970s, J.B. Gilpin-Brown at the <a href="http://www.mba.ac.uk/nmbl/index.htm">Marine Biological Laboratory</a> in Plymouth, England, filmed a movie called "The Squid and its Giant Nerve Fiber". Now, the entire work has sadly been lost, but there are some parts which have been saved. These videos are available at the <a href="http://www.science.smith.edu/departments/NeuroSci/courses/bio330/squid.html">Bio 300 course site</a> taught at Smith College, and they include J.Z. Young dissecting out the giant nerve (which he was the first to describe). If you're interested in this kind of stuff, I highly recommend you go check them out (Quicktime needed).<br /><br />My favorite video is the one aboutvoltage clamping the squid axon. Here are some stills I captured from it:<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjSeBGwodapNdjqXjjsb0iFsCATAlMGY7WEHjZZ4BnFYE_PYJJA8KVxoJzZgNsgW2sypdAMaLxjNo9-z7Y-xt67RPTW_nBPwSqf-qgxntAyGrM9JmRH0-xU0zyCa1ADZaM8oBeJPBKeE-c/s1600/SquidAP.jpg"><img style="float: left; margin: 0pt 10px 10px 0pt; cursor: pointer; width: 320px; height: 301px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjSeBGwodapNdjqXjjsb0iFsCATAlMGY7WEHjZZ4BnFYE_PYJJA8KVxoJzZgNsgW2sypdAMaLxjNo9-z7Y-xt67RPTW_nBPwSqf-qgxntAyGrM9JmRH0-xU0zyCa1ADZaM8oBeJPBKeE-c/s320/SquidAP.jpg" alt="" id="BLOGGER_PHOTO_ID_5499389395465446610" border="0" /></a><span style="font-weight: bold;">Figure 1</span>:The squid axon action potential. A thing of beauty, no doubt. Complete with hot oscilloscope action (yeah, that ain't digital!). Note the afterhyperpolarization.<br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><span style="font-weight: bold;">Figure 2</span>:<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEia3fQRJ5kKGwWJ4tSn1jbJC4_eBfHeNdZIMgFvfPYGurX88DP92a1o8D5hKCAopvNYP8ck8ubxoRB5pWzyvdiWrPy0ZEOj7zXDhkW-M8k4hK5cbKRwyRp_fgsfqUtdowDK7zvV2B2xyj8/s1600/HodgkinAxon.jpg"><img style="float: left; margin: 0pt 10px 10px 0pt; cursor: pointer; width: 320px; height: 293px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEia3fQRJ5kKGwWJ4tSn1jbJC4_eBfHeNdZIMgFvfPYGurX88DP92a1o8D5hKCAopvNYP8ck8ubxoRB5pWzyvdiWrPy0ZEOj7zXDhkW-M8k4hK5cbKRwyRp_fgsfqUtdowDK7zvV2B2xyj8/s320/HodgkinAxon.jpg" alt="" id="BLOGGER_PHOTO_ID_5499390480130682658" border="0" /></a> Here, Alan Hodgkin, Nobel Laureate, prepares to ACTUALLY DO AN EXPERIMENT ZOMG!!! He's picking up the axon and getting ready to insert the electrode. I know, sorry, it's an old white d00de, wearing a vest and tie ferchrissakes. But I'll admit that I love his papers.<br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgF60PTyLGD44mmNmFULnsKuSapX7zttS-b5iI95_fASyGz53dwhyS8xiQAJ_ESfEYmv4jmv1XKahHN23SXx50FSQTmosvvHw-S652920sD1c7ZadIHsTK9FBUTKACfN8-AB0WzUzu7ZLk/s1600/VoltclampCurrents.jpg"><img style="float: left; margin: 0pt 10px 10px 0pt; cursor: pointer; width: 319px; height: 291px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgF60PTyLGD44mmNmFULnsKuSapX7zttS-b5iI95_fASyGz53dwhyS8xiQAJ_ESfEYmv4jmv1XKahHN23SXx50FSQTmosvvHw-S652920sD1c7ZadIHsTK9FBUTKACfN8-AB0WzUzu7ZLk/s320/VoltclampCurrents.jpg" alt="" id="BLOGGER_PHOTO_ID_5499391256758177426" border="0" /></a><span style="font-weight: bold;">Figure 3</span>: A family of voltage step currents, showing the early inward sodium current followed by the delayed outward potassium currents (responsible for the membrane depolarization and repolarization, respectively). IT'S EXACTLY LIKE THE DAMNED TEXTBOOKS! Hell, I think it might <span style="font-style: italic;">be </span>the textbook figure. Note the slight deviation in the voltage clamp (pesky series resistance; now that's a post for another day), and the potassium tail currents.<br /><br /><br /><br /><br /><br /><br /><br />Phew, ok, sorry to get all hot and bothered. Beautiful currents will do that to me. Now I need to get to my own electrophysiology. But these are awesome. Anybody got any more old science videos to share? I love this stuff.Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com1tag:blogger.com,1999:blog-2899165782864226363.post-83780456490688757692010-07-29T10:15:00.001-04:002010-07-29T10:15:00.168-04:00Belatedly, and memely, yoursEarlier this month the "<a href="http://scienceblogs.com/notrocketscience/2008/07/spread_the_word.php">Who are you, what are you doing and why do you keep looking at me!!??!</a>" meme came back with a vengeance worse than the West Nile virus fears in Eastern Massachusetts. I saw it on <a href="http://scienceblogs.com/drugmonkey">Drugmonkey</a>, wherein I cringed at my old age.<br /><br />Two years ago, Ed Yong at his Not Exactly Rocket Science blog (currently living <a href="http://blogs.discovermagazine.com/notrocketscience/">here</a>) posted this question to his readers, asking them why they come to the blog. From there it spread to various other science blogs.<br /><br />Since my own return to blogging, I thought I'd ask my readers out there why they follow these ramblings, and what brings them here. What posts do you find most interesting. I'm especially interested in hearing from any lurkers out there. Besides, DM tagged people, and who am I to ignore that?Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com2tag:blogger.com,1999:blog-2899165782864226363.post-91473465689962060352010-07-28T16:10:00.001-04:002010-07-28T16:10:00.203-04:00It starts earlyThe Patriarchy that is.<br /><br />The other day my 4 1/2 year old son told his mother the following:<br /><br />boy: "But you can't be a doctor, you're a girl, and girls aren't doctors. They're nurses. Only boys can be doctors."<br /><br />Which is of course odd, because not only is his mother very much a doctor, but so are the vast majority of mothers of the kids we hang out with (as well as a large majority of the mothers at his daycare). And he had no problem saying that Daddy is a scientist, and "does science." <br /><br />It's also a big odd, because when my wife was admitted to the hospital before our second kid arrived, he referred to all the nurses and doctors as "doctors" - male or female. Even though he knew what a nurse was, as his aunt is one. <br /><br />So what was it that turned the tide, and sent him to the DarkPatriarchy side?<br /><br />A buncha stupid flashcards at school that show a doctor as a man, and a nurse as a woman. WTF?!? <br /><br />Of course his parents reacted in the way all good generally socially progressive types would: His mother gave the daycare folks a stern talking to, while his father beat him.<br /><br />Case closed!<br /><br />Seriously though, how much of this can we counteract in his little brain? We're just going to have to teach him to see it as well. <br /><br />(Disclaimer - if you need a disclaimer to inform you which part of this post not to take literally, you really oughta move along elsewhere.)Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com2tag:blogger.com,1999:blog-2899165782864226363.post-19726167151690477102010-07-27T13:30:00.001-04:002010-07-27T13:32:40.203-04:00juniorprof's #painresearchmatters campaignIn case any of you readers out there missed <a href="http://juniorprof.wordpress.com">juniorprof's</a> roaring back into the science blogosphere, I thought I'd take a moment to highlight his <a href="http://juniorprof.wordpress.com/2010/07/23/painresearchmatters-campaign/">campaign</a> to improve the awareness of pain and pain research, in all its facets, from the toll it takes on those who suffer from it, to current and new therapies, to new basic science. If you have a story to add to the discussion, from whatever perspective, head over to his blog to contribute. Or check out his <a href="http://twitter.com/JUNIORPROFBLOG">Twitter feed</a> if you're into that sorta thing.<br /><br />From a neuroscience standpoint, I can attest to the fact that although pain is an incredibly interesting topic, it isn't up there front and center with the Big Questions of Neuroscience. Off the top of your head, how many Nobel prizes have been awarded for pain related research? I got nothing (OTOH, there's a number of ion channel and synapse related prizes I can name). During out intro to neuroscience course in grad school, I think we had one, count 'em ONE, <span style="font-style: italic;">guest</span> lecture about pain. Try and guess how many we had about synapses, or the visual cortex? Nothing against those systems; I love them too, and some of my best friends are synaptic physiologists. It just serves to illuminate the priorities of the field.<br /><br />Come to think of it, this is reflected in my own bias as well. See, during grad school I did <a href="http://junctionpotential.blogspot.com/2009/03/its-beautifulpair-of-sodium-currents.html">research</a> on nociceptors, those ornery little neurons that convey signals about injury to the central nervous system. And yet, I never did call myself a "pain researcher," nor do I know think back on that as "pain research." Why is that?<br /><br />I'll admit that some of that it to prevent being labeled as "too applied" or "too disease oriented" in my research question. I liked to believe my research had broader applicability to questions of excitability and action potential electrogenesis, so I shied away from it. Now that I think about it, that personal bias is counterproductive when it extends throughout the community. I'd hazard a guess that you probably know the feeling, that applied research is somehow lesser, or done by "those <span style="font-style: italic;">clinical </span>people (<span style="font-size:85%;">and we all know how good they are, knowwhatImeannudgenudge, aren't we great, high fives</span>) leads to a situation like juniorprof tweeted yesterday:<br /><br />"<span class="status-body"><span id="msgtxt19666310714" class="msgtxt en">Pain <a title="#1" class="tweet-url hashtag" href="http://twitter.com/search?q=%231" onclick="pageTracker._setCustomVar(2, 'result_type', 'recent', 3);pageTracker._trackPageview('/intra/hashtag/#1');">#1</a> reason people seek medical attention but pain rsrch less than 1% of NIH budget</span></span>"<br />(reference for that <a href="http://bit.ly/dqYoT6">here</a>)<br /><br />That's just crazy. Crazy crazy crazy. It makes me regret how I characterized both my research and myself as a scientist.<br /><br />So I'll say it loud, and say it proud, I was, and still am (<span style="font-size:85%;">for about ~35% of my time depending on which project I'm currently focusing on and don't even get me started about that last grad school paper but don't forget I had two kids so cut me some slack</span>) a PAIN RESEARCHER!<br /><br />I think in the near future I'll write up a few posts on nociceptor excitability and ion channels. Thanks for the inspiration juniorprof!Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com3tag:blogger.com,1999:blog-2899165782864226363.post-52990336792008041482010-07-23T12:29:00.002-04:002010-07-23T12:30:02.627-04:00You know what else sucks?Blogger.<br /><br />But I'm guessing all you on Wordpress already know that.<br /><br />Somehow the block quotes in the previous post are screwing up the text color. Any ideas?Nat Blairhttp://www.blogger.com/profile/12684196915592792806noreply@blogger.com0