tag:blogger.com,1999:blog-312267102024-03-07T08:54:13.566-05:00She Blinded Me with ScienceRuminations on science news and science minutiae.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.comBlogger52125tag:blogger.com,1999:blog-31226710.post-29191161943848855222007-04-28T12:18:00.000-04:002007-04-28T12:58:40.630-04:00A dream is a wish your blog makes<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhpaY_CN4yp0nzGVTF2wsEPM1QTi-Wy-2cv_bStq17I45DOi-8bmbg_ZlEnI-XItv3hu2m98oOKMlclzzA9urkHcM3ko0SxqmCv5WU7dMZFgGqD1VClNiR3PtesVoYsMtbNgf3K/s1600-h/Little-Black-Dress-VIII.jpg"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhpaY_CN4yp0nzGVTF2wsEPM1QTi-Wy-2cv_bStq17I45DOi-8bmbg_ZlEnI-XItv3hu2m98oOKMlclzzA9urkHcM3ko0SxqmCv5WU7dMZFgGqD1VClNiR3PtesVoYsMtbNgf3K/s200/Little-Black-Dress-VIII.jpg" alt="" id="BLOGGER_PHOTO_ID_5058516659117996722" border="0" /></a>I've really let this blog go over the last while, haven't I? There are so many great new blogs out there that I haven't had the chance to link to. First off, I wanted to thank everyone who commented on my <a href="http://blind-science.blogspot.com/2007/03/will-doi-cure-what-ails-me.html">DOI post</a>; the tips have made thesis-ing go a tad more smoothly. Second, I wanted to let everyone know what I'll be up to next. Soon, I'll no longer be qualified to write from the point of view of a grad student. I've been offered an Assistant Editor position with <a href="http://pubs.acs.org/cen">Chemical and Engineering News</a>. I'm looking forward to getting started, even though the production schedule will mean that the bloggers will scoop me more often than not. :) It's likely that from now on, I'll be posting from meetings, and in another forum. So for now, "She Blinded Me with Science" will be on an indefinite hiatus, while I format margins, apartment hunt in <a href="http://www.culturaltourismdc.org/information2550/information.htm?area=2522">DuPont Circle</a>, and hone my craft at C&EN.*<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhMpgXb0ctMjCYuC4noeFwq3lIa-UUvNw87dp7E3luUa4wqeJqnQF19Wx4CMUZ0KgkaclF9kA0TZzaiJa3nRwxr1TR6YjWXPsQ8Zvd2UO3dvmaMZi6HDM7UcpoTNowEV_9gu1An/s1600-h/cen1scrop.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhMpgXb0ctMjCYuC4noeFwq3lIa-UUvNw87dp7E3luUa4wqeJqnQF19Wx4CMUZ0KgkaclF9kA0TZzaiJa3nRwxr1TR6YjWXPsQ8Zvd2UO3dvmaMZi6HDM7UcpoTNowEV_9gu1An/s320/cen1scrop.jpg" alt="" id="BLOGGER_PHOTO_ID_5058516461549501090" border="0" /></a>I'll leave you with a deconstruction of one of the more hilarious commercials I've seen lately. <a href="http://www.zoomnow.com/">Go to this link</a>, then click the "see the Zoom! TV commercial" box, and prepare to be blown away.<br />Choice quotes:<br /><span style="font-weight: bold; color: rgb(255, 255, 0);">"..an advance so profound, it took a team of scientists years to create."</span><br />This was noteworthy because apparently, a lot of scientific advances can be sorted out in a fortnight.<br /><span style="font-weight: bold; color: rgb(255, 255, 0);">"the patented Zoom! light"</span><br />Can you really patent light? Can you forbid, say, the use of the 254nm wavelength without paying extensive royalties? My guess is that they've patented whatever lamp generates the UV light at a controlled intensity that's used in the procedure, but feel free to correct me if I'm wrong.<br /><span style="color: rgb(0, 0, 0);"></span><span style="color: rgb(255, 255, 0); font-weight: bold;">"breaking down the stains' double bonds"</span><br />I love how they threw that in there just to be sciencey. Evidently, the radicals generated by the <a href="http://en.wikipedia.org/wiki/Fenton_reaction">Fenton reaction</a> (which means the gel contains hydrogen peroxide and some kind of iron or other catalyst) are changing the structure of the stains so they no longer appear colored.<br /><br />aside: I just did some demonstrations yesterday for 8th graders. Among other things, we bleached shredded <a style="color: rgb(255, 153, 0);" href="http://en.wikipedia.org/wiki/Carotene">carrots</a><span style="color: rgb(255, 102, 0);"> </span>(aka, got rid of some of the double bonds.)<br /><br />I'm really just concerned about the fallout for double bonds everywhere. I hope no one starts a smear campaign. (Double bonds aren't all bad, people! <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=123596">Gleevec's</a> got 'em, hey, even <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=62853">Viagra's</a> got 'em.)<br /><br />Lastly, I know that when I go to the dentist's office, I wear my slinky little black dress. The black dress is, after all, <a href="http://www.msnbc.msn.com/id/17804986/">a wardrobe staple</a>.<br /><br />Thanks for reading, everyone.<br /><br /><span style="font-size:78%;">* If you do a Google Image Search for C&EN, you will find pictures that appeared in <a href="http://blog.chembark.com/">Chembark</a>, <a href="http://coronene.blogspot.com/">Carbon-Based Curiosities</a>, and the <a href="http://cmliris.harvard.edu/">Lieber group</a> webpage in the top hits.</span>Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com9tag:blogger.com,1999:blog-31226710.post-16202532174136034362007-04-05T11:57:00.000-04:002007-04-28T12:54:11.066-04:00Just try it.<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgE8-YKTteXodSQSlQyZzdo-EMuHy8orPfry_5UF9Ksj3YG-Z20aGlp5YudzT94up63GUkNSTZ0r0t_D5CO72iqU0xI1n7A2FstMWCVUKmaqnearJkD8o9z48jmINdF-Q-cpkZ4/s1600-h/magneticsculpturebig.jpg"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgE8-YKTteXodSQSlQyZzdo-EMuHy8orPfry_5UF9Ksj3YG-Z20aGlp5YudzT94up63GUkNSTZ0r0t_D5CO72iqU0xI1n7A2FstMWCVUKmaqnearJkD8o9z48jmINdF-Q-cpkZ4/s200/magneticsculpturebig.jpg" alt="" id="BLOGGER_PHOTO_ID_5050292877254429538" border="0" /></a><br />Try googling "masamune effect". It has to be in quotes for this to work. I was looking for a specific reference and was too lazy to go to Web of Science right away. I got a good chuckle for my efforts, but little else.<br />Sorry I haven't blogged in a bit. I'm recovering from an unfortunate turn of events that I'd prefer not to post about, and my computer time's being eaten up by other things these days.<br /><br />..when you're done with that, read the real references, if you're so inclined. (I did have to go outside of Google to find them, since this work is mentioned offhand in many more recent papers.)<br />(a)<a href="http://dx.doi.org/10.1021/jo00155a053">W. Choy, L. A. Redd III., S. Masamune, <span style="font-style: italic;">J. Org. Chem</span>. <span style="font-weight: bold;">1983</span>, <span style="font-style: italic;">48</span>, 1137-1139; </a><br />(b) <a href="http://dx.doi.org/10.1021/jo00171a072">S. Masamune, L. A. Reed III., J. T. Davis, W. Choy, <span style="font-style: italic;">J. Org. Chem</span>. <span style="font-weight: bold;">1983</span>, <span style="font-style: italic;">48</span>, 4441-4444.</a><br /><br />Satoru Masamune, while a professor of chemistry at MIT, made many contributions to the field of chemical synthesis. These two papers describe some of his contributions to the <a href="http://nobelprize.org/nobel_prizes/chemistry/laureates/1950/">Diels-Alder reaction</a>, one of my adviser's favorites.<br />The Diels-Alder reaction is artistic (it can let us sculpt 3D molecules out of flat precursors), it's <a href="http://en.wikipedia.org/wiki/Environmental_movement">green</a> (no waste atoms lying around after the reaction, with just a few exceptions), and chemists have gotten pretty good at controlling and predicting its power. <br /><br />Back to Masamune's papers. This work describes a small reactant with a defined 3D structure, which reacts very well at low temperatures, catalyst-free (green again, low energy requirement) with a variety of partners. The best part about this reactant was that one could predict the 3D structure of the products for the reaction. Masamune surmised that this was made possible by <a href="http://en.wikipedia.org/wiki/Hydrogen_bonding">hydrogen bonding</a> interactions occurring over the course of the reaction. That's a strategy taken straight out of the <a href="http://en.wikipedia.org/wiki/Enzyme">enzyme</a>'s playbook.<br /><br />I picked the picture because I've always been fascinated by those desk toys. If you could turn the magnet on and off at will, I think it's a pretty decent basic illustration of the concept of building 3D things from flat things.<br /><br />*UPDATE 4/28/07. Apparently, "She Blinded Me with Science" is now the top hit when you try googling "masamune effect". Neat.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com3tag:blogger.com,1999:blog-31226710.post-45012596102181457462007-03-21T15:58:00.000-04:002007-03-24T14:38:08.862-04:00Whither the protecting group?<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiURnA5AD0o0ptqC3uSj9YS03Rowz1a20dxIyzt4lOtrdoZKqy4xbr0LetzLzdvJtujQNADUlehWE29eSGgh6fwmjFPVV2T2LjzPz2mcBetVJOSb9ncTEA1XtTWoun_2Jm_xLWl/s1600-h/shield.JPG"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiURnA5AD0o0ptqC3uSj9YS03Rowz1a20dxIyzt4lOtrdoZKqy4xbr0LetzLzdvJtujQNADUlehWE29eSGgh6fwmjFPVV2T2LjzPz2mcBetVJOSb9ncTEA1XtTWoun_2Jm_xLWl/s200/shield.JPG" border="0" alt=""id="BLOGGER_PHOTO_ID_5044473145345127090" /></a><br />Kudos to <a href="http://www.scripps.edu/chem/baran/html/home.html">Phil Baran's group</a>, who have just published in the journal Nature describing protecting-group (PG) free syntheses of members of the hapalindole, fischerindole, welwitindolinone and ambiguine families.<br /><span style="font-weight: bold; color: rgb(255, 255, 0);">the ref</span>: <a href="http://dx.doi.org/10.1038/nature05569"><i>Nature</i> <b>2007</b>, <i>446</i>, 404-408.</a><br />His group has published the enantioselective total synthesis of some of these compounds before (see, for instance, <i>JACS</i> <b>2005</b>, <i>127</i>, 15394-96.) but I'm guessing Nature deemed this worthy because of its unified application of a few big philosophies of organic synthesis (ie, <a href="http://www.stanford.edu/group/bmtrost/">atom economy</a> and <a href="http://en.wikipedia.org/wiki/Convergent_synthesis">convergency</a>) while trying to evaluate the pros and cons of going PG-free, as well as its overarching call for hearkening back to the early days, when <a href="http://nobelprize.org/nobel_prizes/chemistry/laureates/1947/robinson-bio.html">men were men</a> and syntheses were PG-free. That, and they optimized the routes to welwitindolinone and fischerindole to get higher yields.<br />So what is a protecting group? For organic chemists, they are a way of reining in the more unruly sections of the molecule you happen to be making. To be more specific, it's necessary to mask parts of the molecule that are likely to behave in some way other than what you'd like, or that refuse to "go along quietly" when some other part of your molecule needs attention.<br />For a great description, take a look <a href="http://www.rsc.org/chemistryworld/Issues/2007/February/OpinionBenchMonkey.asp">here</a> for Dylan Stiles' (aka Tenderbutton's) rather prescient article about the protecting group and some classic examples thereof.<br />Is the "PG-free way" really Mother Nature's way? If not, is her favorite protecting group the MOM group?<br />I think that some masked chemical reactivity exists in the biological world. I hope that my more scientifically inclined readers won't take offense at my stretching an analogy just a bit for the sake of a blog entry.<br />Take enzymes like proteases. Proteases break the bonds that link up the fundamental building blocks in proteins, and they're involved in many important roles in the body, from blood clotting to cell death. It's extremely important that proteases be exquisitely regulated, so that they don't start chopping up proteins willy-nilly. The "protecting groups" for proteases are in place at the beginning, during their production. Proteases are built as inactive forms known as <a href="http://en.wikipedia.org/wiki/Zymogen">zymogens</a>, and in order to reveal the active protease, there's a little sliver of protein (called a peptide) that's got to get lopped off.<br /><span style="color: rgb(255, 255, 0); font-weight: bold;">the ref</span>: <i>Nature</i> <b>1999</b>, <i>402</i>, 373-376.<br />That isn't the only mechanism for regulating proteolysis. You can imagine that if a protease somehow gets activated at the wrong time, or in an out-of-control way, there would be dire consequences (ie, too much protease activity could contribute to stroke or alzheimer's).<br />When that happens, one natural defense mechanism is the <a href="http://en.wikipedia.org/wiki/Serpins">serpin</a> class of proteins. Serpins permanantly (covalently) inhibit proteases, mostly the serine type.<br /><br />Incidentally, this is the most chemistry I've ever seen in an issue of Nature. Besides the Baran paper and the intro to it by Porco, there's a great piece by Bergman on C-H activation and a review by Toste. Plus, there's an article about chemistry in the NatureJobs section.<br />UPDATE 3/24: I should've realized Nature did that <a href="http://blogs.nature.com/thescepticalchymist/2007/03/editors_choice.html">to coincide with the ACS national meeting</a>.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com2tag:blogger.com,1999:blog-31226710.post-47960709597526788012007-03-20T22:55:00.000-04:002007-03-20T23:55:38.282-04:00Will DOI cure what ails me?As I mentioned on my last post, I've been busy reformatting tons of references, adapting something I've written before to satisfy a slightly different format.<br />Non-scientists, non-scholarly types: It's like writing that 8th grade term paper all over again, times 100. You know, the one where each of your sources for your bibliography had to be on a separate index card, and you had to get your mom to drive you to the <a href="http://www.goes.com/hfplinfo/">Hackettstown Library</a> to search (are you ready now?) the <a href="http://lib.northern.edu/infolit/tablesversion/lessons/lesson5/readersguide.htm">Readers' Guide to Periodical Literature</a> for information on The Manhattan Project. I can't remember why I chose to write a term paper about the A-bomb at the tender age of 14, but a lot of what I read about for that paper still comes up. <br />But I digress. <br />The point is that reformatting references is unbelievably mundane work.<br />There is some computer software out there that's meant to take care of all that for you. The one I had started using is called <a href="http://www.endnote.com/">EndNote</a>. Endnote interfaces with Word, and it's smart enough to know that when you move text around, the numbers of your references will change if the order's been changed. It has templates for bibliographies in many different journals and can (supposedly) instantly reformat your references to a new journal. <br />Endnote didn't work well for me at all. I was working with a library of a couple hundred references for this review paper back in 2005. Unfortunately, I couldn't figure out a way to make the software format my references according to the specifications of the particular journal. So, once I was sure I was done shuffling text around, I switched my references to text-only and reformatted them manually, and now I'm reformatting once again. <br />Is there other, better software out there?<br />The biggest difference between now and when I was in eighth grade is the ease of access to the internet. One of the handiest technologies for keeping track of the scholarly literature is The Digital Object Identifier System, or <a href="http://www.doi.org/">DOI</a>. DOI is like a homing device for a journal article, so that no matter where the content moves on the web, looking it up using a DOI locates it and retrieves it. <br />Recently, some Elsevier journals changed their web and old links no longer worked. If I'd set those links to the DOI of the journal article, they'd still be intact. That reminds me; I need to change my research group's "Publications" page so that everything is indexed by DOI. <br />What I'm wondering is whether there will come a point where DOI will become the universal reference citation standard, including in print. If that happened, I'd never have to worry about whether I should be using bold or italic font, or whether the authors' surnames come first or last, ever again. Just a simple URL would be all I'd need. However, part of me thinks that if journals (or is it the <a href="http://www.oup.com/us/samplechapters/0841234620/?view=usa">ACS Style Guide</a>people?) were ever going to adopt uniform, URL-based standards, they would have done it a few years ago, at the relative "dawn" of the internet age. <br />What are the barriers to this, if any? Is it a content searching issue?<br />If you were going to pick a universal reference style, what would it be and why?Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com6tag:blogger.com,1999:blog-31226710.post-21930191866932319302007-03-20T19:58:00.000-04:002007-03-21T16:16:03.050-04:00If I were going to Chicago...If I were going to <a href="http://acswebcontent.acs.org/nationalmeeting/chicago2007/home.html">Chicago</a>, I'd probably be inspired to post something a little more imaginative. <br />I've been working on a research proposal (read: reformatting references) all week. My brain hurts.<br /><br />It won't surprise anyone who knows me that I'd want to attend talks that walk the chemistry-biology tightrope. (Read: Jon Clardy, Dale Boger, Laura Kiessling, Sam Gellman, Carolyn Bertozzi, Anna Mapp, Xiaowei Zhuang, etc.)<br />Here are some of my less obvious go-to talks.<br /><br />Sunday all day (intermittently): AGFD: Natural Products, Diets and Cancer Prevention. A friend from my last lab always made time to go to the talks from the Ag. and Food chemistry division. I like them, too, because, to me, they have a more "generalist" vibe, and sometimes there are some really interesting chemical structures that they throw up on a slide. You never know where the inspiration for the next target will come from. Not too long ago, there was a postdoc in my group who spent part of his Ph.D. synthesizing a molecule found in <a href="http://www.straightdope.com/mailbag/mbluecheese.html">Roquefort cheese</a>.<br /><br />Monday AM: MEDI: Drugs from Academia: Marketed Drugs Discovered in Academic Labs<br />I'm curious what Bob Holton's going to do with the taxol <span style="font-weight: bold;">$$</span>. That, and I have to cheer on Princeton's own <a href="http://www.princeton.edu/%7Estcweb/html/pope06essaya.html">Edward C. "Ted" Taylor</a>.<br /><br />Monday lunch: CHED: Undergraduate Research Poster Session: Organic Chemistry<br />Mad props to Mike, my little bro, for being the first in the family to present a poster at an ACS meeting. I should probably have gotten more work done.<br /><br />Monday PM: CHED: Research in Chemical Education<br />My friend Angie is a <a href="http://sciencecareers.sciencemag.org/career_development/previous_issues/articles/2006_05_12/postdoctoral_teaching_savvy_career_move_or_distraction_from_research">teaching postdoc</a> and she's giving a talk about how to keep a lecture hall's worth of sophomores engaged in the organic chem course's subject material. My favorite quote from her teaching experiences is on my Facebook wall. "Sigh....I'm introducing the concept of "backside attack" to 260 college sophomores today. Pray for me." At her postdoc interview she had a week's notice to prepare a lecture on her assigned topic for another ~300 students.<br /><br />Tuesday AM: PHYS: Xiaowei Zhuang's talk in ACS National Awards in Physical Chemistry<br />I know I said I wouldn't discuss an obvious one, but I've always really been intrigued by the idea of single molecule imaging studies. I was too afraid of math to take the plunge in a group like that, though. I like to think that one day we'll be able to make movies like <a href="http://www.studiodaily.com/main/technique/tprojects/6850.html">this one.</a> I don't think I've linked to that movie yet.<br /><br />Wednesday AM: <br />9:55-10:35 ORGN: Biomimetic Natural and Unnatural Products Synthesis<br />Not a surprise that I'd go here. :)<br />I think the boss is talking about some new alkaloid-related work, but I'm not sure.<br /><br />Wednesday PM: INOR: Coordination Chemistry: Characterization and Application <br />I want to listen to my friends Karl and Eli give talks about <a href="http://electronics.howstuffworks.com/oled.htm">their work</a> (or at least, my rudimentary, pop-science understanding of their work, judging by the link).<br /><br />At some point: run up to Lincoln Park to get breakfast at <a href="http://www.bpigcafe.com/">The Bourgeois Pig</a>, followed by research on, um, surface science at the <a href="http://www.blissworld.com/category/spa.do">Bliss Spa</a>, paid for by my imaginary money.<br /><br />Thursday PM: Nanoparticles: Synthesis, Passivation, Stabilization, and Functionalization<br />Nanotubes, biosensors, and a talk from someone in Chad Mirkin's group. What's not to like?<br />Chad Mirkin was here at Princeton a while ago and I regret skipping his talk because of labwork. His science reaches in so many directions.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com1tag:blogger.com,1999:blog-31226710.post-22006029500133136482007-03-14T08:20:00.000-04:002007-03-14T09:18:23.709-04:00Note to Anonymousthis started as a reply to a comment on my last post, but it got so long i figured it deserved a post of its own. paul, excuse the lack of caps. i wrote this in the heat of the moment. i know how to diagram sentences, i swear. :)<br />anonymous,<br />i do agree with you that for grads busting their asses to pass quals (or get into a good group, or just getting stuff to work for once), the wining and dining days of recruiting are a distant memory. it's definitely true that fewer and fewer upper year students take part in the festivities, and with good reason... <br />i think that potential chemgrads need to go in well-informed about <span style="font-weight: bold;">precisely what you said</span>, and be open to (gasp!) <a href="http://www.amazon.com/Alternative-Careers-Science-Cynthia-Robbins-Roth/dp/0125893752">other options</a>. if you really really really want an industry job, they are tough to get these days. maybe the pendulum will swing back, maybe not. <br />and you're right, a survey can't be comprehensive if everyone isn't polled or doesn't respond, and they're reporting on survey data, so hopefully people trained as scientists know to take it with a grain of salt. <br />"The 2006 survey involved mailing questionnaires<br />to a random sample of 24,000<br />ACS members who were most likely to be<br />in the domestic workforce. They all resided<br />in the U.S., were under 70 years of age, and<br />were not in the emeritus, retired, or student<br />member categories." -C&EN 9/18/2006<br />The ACS has over 150,000 members, and it's been discussed at length in the blogs that many chemists don't join ACS at all, or their employers pay for it, so there's some overrepresentation there.<br />without real poll data, you risk jumping into that nebulous trend story fad. see <a href="http://www.nytimes.com/2005/09/20/national/20women.html?ei=5090&en=6a8e0c413c09c249&ex=1284868800&pagewanted=print">here</a> and <a href="http://www.nytimes.com/2007/03/11/us/11separate.html?em&ex=1174017600&en=f87a31f8b9d94ab0&ei=5087%0A">here</a>. so maybe their hands are tied to some extent. i don't think the stories on the survey data should be portrayed as indicative of anything wider. the question is, how could a good poll be properly conducted? with the status of postdocs being different almost everywhere, to cite one example, it would require extensive red-tape wading to reach everyone. on the other hand, since a lot of the job market stuff comes through word of mouth anyway, we could argue about where the best place is to disseminate this information in the first place. federal labor statistics?<br />i hear about industrial sites that are only hiring one person or two a year, and everybody has a fantastic pedigree. so, what happens to the others? some people are having to take a risk and take a job at a tiny company where they'd really need to stand out to ever be hired by a big guy.there are probably some success stories there, but i don't know as many working chemists as other bloggers. <a href="http://pipeline.corante.com/">derek's</a> situation is difficult, as well. it's economics driving that, plus perhaps preferring to train someone with less experience in your company's particular way of doing things? <br />when i got to grad school, i had blinders on. it's partially due to the fact that i went to a small school and didn't know any grad students, and that i had my "eyes on the prize" and didn't stop to think about the fact that i might be good at more than chemistry. my academic work was inextricably linked to my self-esteem back then. i think you can still go to grad school and work in a lab because you like chemistry. that's perfectly OK, but i think that people in this modern economy have to realize that a ph.d. in chemistry can be useful in plenty of different jobs, despite the traditionalists who regard those careers as "alternatives". i struggled with that idea for some time, but i keep hearing about my friends in the grad program that are going to go into consulting or work as a patent agent, two jobs i didn't know existed till grad school. some of them think that they might miss the lab, but maybe not. i even know someone who returned to the lab from an editorial position. it's tough, and you need to work hard to get back into the groove, but it's possible. reading "<a href="http://www.amazon.com/World-Flat-Updated-Expanded-Twenty-first/dp/0374292795/ref=pd_bbs_sr_1/103-5299210-3050212?ie=UTF8&s=books&qid=1173875654&sr=1-1">the world is flat</a>" made me realize that everyone's going to have to work smarter and be creative in order to stay afloat. <br />the easiest jobs to look at are the ones for which you are supposedly directly trained. med school-> doctor. business school-> executive. law school-> lawyer. <a href="http://www.thequarter.org/issue10/page06.php">sally struthers school->medical assistant, electrician, business management, or accounting</a>. chemistry grad school-> professor or lab chemist? yes, it's true that the other professions don't have the same kind of supply/demand issue in their job markets, but it's not something individuals have much control over, so i went for something different. maybe that's why when i hear about disgruntled grad students first thinking about other professions, those are often the things they gravitate toward at first. it takes real soul-searching to look beyond that. months and months of it, in my case, and if i'm not happy when i start working, i'm not afraid to start the process all over again.<br />i think the hardest part of the problem is that it's hard to explain this to the young-uns, because they think they have the answers and it won't happen to them, because we have somehow "failed" as chemists. i doubt i would have listened if "future me" went back in time to warn "young, idealistic, slightly cocky me" about such things. <br /><br />whew. that's a manifesto-length post. speaking of which, if you haven't read <a href="http://orgprepdaily.wordpress.com/2007/03/11/milkshake-medicinal-wisdom/">milkshake's post, get thee to org prep daily</a>. i learned a lot from it.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com1tag:blogger.com,1999:blog-31226710.post-40727680304856561192007-03-04T20:46:00.000-05:002007-03-04T20:58:04.037-05:00My favorite dog and pony showIt's recruiting season at Princeton. <br />Typically, prospective students don't actually visit our department until they're already admitted, meaning that the department pulls out all the stops to bring in plenty of great people. I was admitted in the first year that Princeton started having a full recruiting weekend, instead of ad hoc visits to the department, and it made a huge difference (we had 1.5 times more people start than what had been common for the past 5 or 6 years). Every department does recruiting differently and presumably tries to do something distinctive/memorable, although I feel like most students come for a certain faculty member or two, not the department as a whole. Back when I was a senior in college, I remember that I had dinner at <a href="http://www.yale.edu/peabody/exhibits/greathall.html">Yale's Peabody Museum (with the dinosaurs)</a>, but I think I heard that that hasn't been done in recent years. True? Also, does anybody know whether MIT still does the lobster bake? I've been told that <a href="http://www.scripps.edu/phd/index_external.html">TSRI</a> does interview its students before admitting them, so the process is a little different there. What are some of the other well-known/ unique/ offbeat recruiting traditions? <br />The really interesting stuff happens after recruiting, when students commit to the university and then have to join a group. This tends to fuel the gossip for the better part of the fall semester. Who's going where, how many people is so-and-so taking, and the like. The department doesn't allow anyone to officially join a group until the end of November, although many students will start working in their lab of choice the summer before. During the fall semester, all first years attend all the research talks given by the faculty in one of our lecture halls. Unfortunately, as my years here have progressed, I've started to notice that the department's been providing less and less food at these events (we got free lunch and baked goods, the next year it was just baked goods, the year after that nothing at all.) My understanding is that at some places, the research talks are more of an "open house" setup, where interested parties listen to the faculty member discuss what's going on in the group. I've seen some of <a href="http://evolve.harvard.edu/OHPoster2003.jpg">David Liu's open house posters</a>, for instance. I understand why the department asks everyone to attend every talk, since there have been several occasions where students have switched fields completely at the beginning of grad school, and it's important to know what's going on outside of your field, but I also think that in an open house situation, there's likely to be more lively discussion, because everyone who's attending wants to be there.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com5tag:blogger.com,1999:blog-31226710.post-57686958504058562352007-02-22T13:52:00.000-05:002007-02-22T13:55:05.503-05:00Too bad Apple's got that name locked up<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjXf7-_nTKOvnSBCxK06ywz0mvQjxVr6GEw41KdYJsi0T9vVfgNY8XdPW5Zm9xUtq2_4xCA95mpto2lWbtpiKqoL2Sboe86NjeiUFTNzUzUIs7mit4bxUgQK6hQpPOCpuJoJhDM/s1600-h/rotaxane.jpg"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjXf7-_nTKOvnSBCxK06ywz0mvQjxVr6GEw41KdYJsi0T9vVfgNY8XdPW5Zm9xUtq2_4xCA95mpto2lWbtpiKqoL2Sboe86NjeiUFTNzUzUIs7mit4bxUgQK6hQpPOCpuJoJhDM/s320/rotaxane.jpg" alt="" id="BLOGGER_PHOTO_ID_5034433948387405666" border="0" /></a><br />I gravitated toward this paper's title, "Reversible, Erasable, and Rewritable Nanorecording on an H2 Rotaxane Thin Film".<br /><span style="font-weight: bold; color: rgb(255, 204, 0);">the ref</span>: <i>JACS</i> <b>2007</b> <i>129</i>, 2204-2205.<br />This paper's about a new material that makes a promising step toward atom-scale data storage devices. As computers store more and more large files (and I don't just mean home movies from your family trip to <a href="http://www.roadsideamerica.com/attract/MNDARtwine.html">the world's largest ball of twine</a>, I'm talking government use, scientific number crunching, and the like), the logical progression points to further miniaturized data drives.<br /><br />Computers store data in bits and bytes, and the system boils everything down to <a href="http://computer.howstuffworks.com/bytes.htm">a string of digits</a> with only two possible values: <span style="font-weight: bold;">zero</span> or <span style="font-weight: bold;">one</span>. Because of this, the fundamental storage unit needs to be capable of switching reversibly between two different forms.<br /><br />The authors of the paper pulled that feat off by making their new material from a molecule called a <a href="http://en.wikipedia.org/wiki/Rotaxane">rotaxane</a>, which is mechanically interlocked, like those <a href="http://www.brainpuzzles.com/difficult.html">metal toy puzzles</a> that drive me crazy. Basically, the ring can move to each side of the dumbbell.<br /><br />The "recording device", a <a href="http://en.wikipedia.org/wiki/Scanning_tunneling_microscope">scanning tunneling microscope</a>, reminds me of a tiny turntable needle. This kind of microscope is a little different from the ones in every high school science classroom. It's used to measure properties at surfaces down to the nanometer (billionth of a meter) scale, and with an applied voltage, it can manipulate material down to individual atoms and molecules. Those school microscopes couldn't come close to being able to "see" something that small, and there's no voltage involved with them, either.<br /><br /><br />Put those two things together and the tiny tip can "move" the ring on the dumbbell molecule reversibly, which would translate to recording and erasing.<br /><br />These researchers published a similar paper last year, but the new work tweaks the molecular structure of the dumbbell that makes erasing "data" easier. The next questions are ones of lifetime (how long-lasting is this material and how stable is the switch once it's put in position? etc.)Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com0tag:blogger.com,1999:blog-31226710.post-75404730974245151242007-02-18T21:58:00.000-05:002007-02-18T22:08:17.067-05:00Death, Taxes, and Grad SchoolOne of the many differences between me and my friends who got "real jobs" after college is how Uncle Sam (and his state- and city-level brethren) decide we should be classified in the tax code. Since it's getting to be that time of year again, I figured I'd try to relate some of the confusion I've experienced because of the non-intuitive-ness of it all.<br />Back in high school and college, I got a W-2 at the end of the year for any job I held, listing how much had been withheld from my paycheck for federal and state tax, etc. All it took to do my taxes (and get my refund!) was the aptly named 1040-EZ.<br />In grad school, I was lucky enough to be awarded a <a href="http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=6201">fellowship</a>. There is a difference in the way the federal government regards the various forms of grad-student income.<br />Princeton required me to TA for one semester, and that year I had a combination of fellowship and salaried income, so I remember that mess particularly fondly.<br /><span style="font-style: italic; font-weight: bold; color: rgb(255, 255, 0);">Permit me to explain:</span><br />If you're TA'ing a class (or, as Princeton calls it, acting as an <a href="http://www.princeton.edu/%7Eaiteachs/">AI</a> or a <a href="http://www.princeton.edu/pr/pub/precept/Precept.pdf">preceptor</a>), that is considered salaried work, so you still receive a W-2 and have federal and state taxes withheld. There is no money withheld from fellowship income at Princeton. (Is this different anyplace else?) That means I don't get a W-2.<br />Instead of the 1040-EZ, I have to use the tax tables to estimate what my tax will be for the coming year and send in a stub with a check to the U.S. Treasury quarterly. Then, I have to use a 1040-A form to report my estimated payments and deduct that from my calculated tax. There's a fine if you don't pay a certain amount of estimated tax in advance, so that's why I don't just pay up in one chunk on April 15th. The state-level taxes have the potential to add another layer of complexity, but I've been lucky because fellowship stipends are not taxable in the state of NJ, so I'd always get a little bit of a refund there. I grew up in NJ, so I didn't bother changing my residency or anything, either. (Now that I live in PA, I need to look into whether I'll owe tax at state level). City-dwelling grad students, how complicated is the tax situation for you?<br />Just for kicks, I'll link to <a href="http://gradschool.princeton.edu/about/docs/financial/taxrequirement.pdf">Princeton's tax requirement sheet</a>. I don't think you need to have an on-campus IP address to access it.<br />You always hear tell of random grad students who don't pay their taxes, figuring that it isn't worth the government's time to audit someone who only makes 19K a year. Good luck with that. I don't have the cojones for it.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com0tag:blogger.com,1999:blog-31226710.post-86070934461369983552007-01-28T19:18:00.000-05:002007-01-28T19:26:41.028-05:00The Grad Student ExperienceI've been out on the left coast for a while, indulging my desire to use a <a href="http://en.wikipedia.org/wiki/Pipettor">Pipetman</a>, run <a href="http://sdspage.homestead.com/">pretty gels</a>, and generate boatloads of <a href="http://en.wikipedia.org/wiki/Tandem_mass_spectrometry#Tandem_MS">mass spec. data</a>.<br /><br />While I've been here, I've started thinking about the differences in the graduate student experience at a university and at a research institute or a medical school. I applied to all three when I was an undergrad, although that probably doesn't happen often unless you have a biological bent in your research interests.<br /><br />I'm floored by the facilities out here. They're really conducive to getting things done quickly. I've been to three or four other labs here to use some random instrument, and everyone's been very helpful. This equipment-sharing must just vary widely from department to department depending on how collegial a place is or how many levels of bureaucracy you need to get past to accomplish anything.<br /><br />A couple years back, our department was actively recruiting a faculty member from a university that had a medical school campus. I can understand the challenges that would come with relocating to a university like Princeton with no professional schools at all. (The fictitious hospital <a href="http://www.answers.com/topic/frist-campus-center">where House works</a> doesn't count). Even little things like access to the right set of journal articles can become a real hassle.<br /><br />So why'd I go to a university? At the time I picked Princeton because it had the most PI's I'd want to work for. (Funny that none of them are there now.) I think that the shared experience my incoming class had (living in the grad dorm, working out at the gym on-campus, problem sets in the coffeehouse) gave us a real sense of community, which as a grad student is nice.<br /><br />It's also important to me to socialize with nonscientists. I didn't know (or perhaps I should say didn't respect) very many humanities people in college, but the people I meet here are almost uniformly brilliant.<br /><br />Maybe being a grad student outside of a university feels more like a real job, which is exactly what I was trying to put off?Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com4tag:blogger.com,1999:blog-31226710.post-63535262661004461622007-01-08T21:52:00.000-05:002007-01-08T21:58:18.215-05:00Triangle Club**<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhkrQIa_9_Zmsy_dWRvxsA0wWS85FZ3KBG6Ye0JL_AuUFwztjidSolqIHSxgvmrPlc3JlWGeQ6TZ-JEUvDgsbOdLlDg8GJTaXyqF0nSA2_siObAPvH7a9r1-jIPJYLC_UrvpiSC/s1600-h/naloxnaltrex.bmp"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhkrQIa_9_Zmsy_dWRvxsA0wWS85FZ3KBG6Ye0JL_AuUFwztjidSolqIHSxgvmrPlc3JlWGeQ6TZ-JEUvDgsbOdLlDg8GJTaXyqF0nSA2_siObAPvH7a9r1-jIPJYLC_UrvpiSC/s320/naloxnaltrex.bmp" border="0" alt=""id="BLOGGER_PHOTO_ID_5011021674178816978" /></a><br /><br />I wish I had the opportunity to learn more about concepts that are important to understand in developing a functioning drug. <a href="http://pipeline.corante.com/">Derek's blog</a> will have to suffice for now.<br />Today I'm posting about <a href="http://en.wikipedia.org/wiki/Naloxone">Naloxone</a> and <a href="http://en.wikipedia.org/wiki/Naltrexone">Naltrexone</a>. They came up in a conversation about drug addiction (more on that later). These two molecules are <a href="http://en.wikipedia.org/wiki/Opioid">opioid</a> receptor antagonists that are strikingly similar in structure, but they're used in the clinic in different ways. An antagonist in the drug sense is something that binds to a receptor and stops the events/actions set in motion by another drug called an agonist. By itself, an antagonist doesn't do anything to the receptor.<br />(If you're lost and haven't read the links, suffice to say that the word "opioid" sounds like the word "opium" for a reason.)<br /><a href="http://www.moleculeoftheday.com/2006/07/12/85/">See here</a> for Molecule of the day's entry on Naloxone.<br />Naloxone clears your system more rapidly. It's given to patients who have overdosed on things like heroin or morphine. (I think the wikipedia entries I cited above may be confused here..) Naloxone essentially kicks the heroin/morphine off of the opioid receptor, and what you get is a rapid detox, complete with all the very painful symptoms of withdrawal. The detox process is almost instantaneous; the patient goes from completely passed out to completely awake in seconds. The process can also be done under anesthesia.<br />After detox, patients in rehab may take a once-daily pill of Naltrexone, which is much longer-acting. It'll keep any other opiates they may try to sneak from working.<br />The difference between the structures is actually really subtle. Note the cyclopropane Naltrexone substitutes for the Naloxone olefin. One extra carbon. Hmmm.<br />It's known in the literature that <a href="http://chemistry.furman.edu/profile.php?shortname=goess">cyclopropanes can possess alkene-like reactivity</a>.<br />What I'm not sure of (and don't have the time to look into in depth) are the differences in how they're metabolized. But here's something about metabolism of cyclopropanes that you can dig out of the literature pretty quickly:<br /><span style="font-weight: bold; color: rgb(255, 204, 0);">The ref</span>: <i>Chem. Rev</i>. <b>2003</b>, <i>103</i>, 1625-1647.<br /><br />** and if you're into musical comedy and Ivy League tradition, see the <a href="http://www.princeton.edu/~triangle/">Princeton Triangle Club's website</a>.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com4tag:blogger.com,1999:blog-31226710.post-6002407862456776752007-01-06T15:38:00.000-05:002007-01-06T15:43:38.595-05:00More a hackneyed grad student joke than a science thing...The inventor of Instant Ramen and Cup Noodles <a href="http://news.bbc.co.uk/2/hi/asia-pacific/6237013.stm">has passed away</a>. I actually haven't eaten the stuff in ages, because I have a kitchen now. When I was a first-year grad student, I had a case of ramen in my dorm room. I could never handle the whole "flavor packet", though, too salty. Usually I would add about half the packet. Oh, and Chicken Ramen was by far the best-tasting.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com1tag:blogger.com,1999:blog-31226710.post-30731297371387262682007-01-03T20:38:00.000-05:002007-01-07T15:32:38.107-05:00Acros starts 2007 off right (in my book, anyway)Today, we received an order from <a href="http://www.acros.com/">Acros</a> that a former postdoc in the group originally placed in 2004 or so. It was one of the lab's occasional multi-bottle orders of 2.5 M <a href="http://en.wikipedia.org/wiki/N-butyllithium">n-butyllithium</a> (n-BuLi) in hexanes. <br />(We order multiple 100 mL bottles, though some of our postdocs come from labs where one of the group jobs was to dole out the new n-BuLi into special sealed bottles from its big container. When I first joined the group, we had some shared 800 mL bottles, but that started to get unwieldy as we got more people.)<br />Anyway, soon after we placed that 2004 Acros order, we received a backorder notice, and the notices kept coming for a good while. We talked to our university's Fisher customer service rep to get to the bottom of the problem, and I believe we were told that because 2.5 M n-BuLi was manufactured in Europe, there was some new regulation on the books that made it very difficult to ship overseas. We had no problem getting 1.6 M Acros n-BuLi (anybody recall whether the suppliers are different for the two different concentrations?) and those that wanted it ordered 2.5 M n-BuLi from <a href="http://blog.chembark.com/2007/01/02/the-new-aldrich-catalog-is-almost-here/">Aldrich</a> (who I believe uses <a href="http://www.fmclithium.com/products/products_p.asp?ID=421">FMC Lithium</a>) as a supplier, so I guess that order was relegated to the back of our heads until now. I have no idea what changed. Maybe some new law took effect Jan 1st (or 3rd, because of <a href="http://video.google.com/videoplay?docid=-89770458144460734&q=gerald+ford">Gerald Ford</a>). (**updated that link**) Our Fisher rep is usually around on Thursdays, so maybe I'll run into him tomorrow and find out.<br />For a trip down memory lane, see <a href="http://archive.tenderbutton.com/?p=166">this post</a> at Tenderbutton for a high-yield primer on the many ways to use an Aldrich or Acros Sure-Seal. You all remember the password, don't you?Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com1tag:blogger.com,1999:blog-31226710.post-76907380132105594132006-12-22T19:22:00.000-05:002006-12-22T19:25:18.186-05:00Air out. Titanium tetrachloride in.<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgezOCDC4hJl8dmW68r-rElKormTzcaNsNuh42FjMTmO7QOqGgeiRsxGnKANL9YCnBQkUYhOHNgA8CJ5nid2K4jU5zclThVHb9L1m7IbNu8BAs93mAelLKl_pV1eyGzqxBgJ8kW/s1600-h/CIMG0555.JPG"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgezOCDC4hJl8dmW68r-rElKormTzcaNsNuh42FjMTmO7QOqGgeiRsxGnKANL9YCnBQkUYhOHNgA8CJ5nid2K4jU5zclThVHb9L1m7IbNu8BAs93mAelLKl_pV1eyGzqxBgJ8kW/s320/CIMG0555.JPG" border="0" alt=""id="BLOGGER_PHOTO_ID_5011511201666313186" /></a><br />I've been blogging sporadically lately; sorry about that. In the department of simple but really useful ideas, a postdoc in the lab next door is using a <a href="http://www.sealameal.com/">vacuum food sealer</a> to package up some moisture-sensitive reagents. I can understand that he probably doesn't want to bother <a href="http://blind-science.blogspot.com/2006/09/more-to-glove.html">using our glovebox</a> to store chemicals. Happy Chrismahannukwanzaakah to you all, and thanks for reading.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com1tag:blogger.com,1999:blog-31226710.post-85152682391276152022006-12-13T17:08:00.000-05:002006-12-13T17:30:35.874-05:00Busting out (cells) all overIn keeping with the theme of <a href="http://www.thechemblog.com/?p=336">Kyle's hilarious post</a>, I'll throw in my own two cents. A couple of weeks ago some friends from the lab next door went to a Starbucks coffee tasting. It was one of the windiest, rainiest, nastiest nights in a while, so they apparently were the only ones there. By the way, the "Christmas Blend" is the same as the "Holiday Blend", in case you were wondering. Yes, the Starbucks people used a <a href="http://www.ineedcoffee.com/99/05/frenchpress/">French press</a>. The only nagging question I have is whether there is some cutesy urban legend about the connection between the coffee French press and the <a href="http://www.thermo.com/com/cda/product/detail/1,1055,23695,00.html">French press biologists use</a> to gently crack open cells. Usually, when you want to recover a protein that you have manufactured in lab bacteria, you want a gentle method that won't damage your protein. You may also want to get at intact organelles, or something. In my very minimal protein purification experience, we would rapidly freeze, then thaw cells for a few cycles. For the proteomics I currently do, I use a <a href="http://www.bellcoglass.com/thumbs/1984-10002.jpg">Dounce homogenizer</a>.<br />Here's <a href="http://www.piercenet.com/Proteomics/browse.cfm?fldID=72F377CD-2581-438C-9B27-5360226EA128">a great basic reference</a> for the ways to bust open cells.<br />Incidentally, I love Starbucks's eggnog lattes, but going to Starbucks in this town sometimes seems taboo, like you're getting your coffee from the man. Locals seem to prefer Small World coffee, and it's growing on me. Once Starbucks cans its seasonal beverage I might try to make the change permanent. (But yes, Jack, Halo Pub still makes the best mocha.) The Small World coffee tee shirt is one of the default gifts that grad students seem to get when they finish, regardless of whether they frequented the place or even whether they like coffee.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com2tag:blogger.com,1999:blog-31226710.post-38679894243811649522006-12-08T15:34:00.000-05:002006-12-08T16:03:31.482-05:00Trying not to use the obvious title joke here..I think my favorite science to read about is the type where the central idea is so elegant, you wonder why no one had thought of it already. <a href="http://en.wikipedia.org/wiki/PCR">PCR</a> is like that, and in my mind, so is this recent JACS ASAP.<br /><br /><span style="font-weight: bold; color: rgb(255, 204, 0);">The ref</span>: <a href="http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ja0657307"><i>JACS</i> <b>2006</b>, DOI: 10.1021/ja0657307</a> (subscriber link)<br /><br /><span style="font-weight: bold; color: rgb(51, 255, 51);">The background</span>:<br />I was in a bioinorganic/ biophysical chemistry lab a few years back, and the topic of FRET came up a lot. If you're unfamiliar, FRET stands for Förster resonance energy transfer (you'll also see fluorescence resonance energy transfer), and it is a convenient visual tool for measuring distances. This comes in handy when you want to learn more about protein-protein interactions, receptor-ligand interactions, and conformational changes.<br /><br />You need 2 fluorescent dyes for a FRET experiment. In a simple case, you attach one dye to protein A and the other one to molecule B, and watch for changes in how they interact. If you did everything right, you'll see a different-colored glow depending on whether A is close to B.<br />Of course, you conscientiously selected your dyes so that their energy profiles overlapped just right. If A and B are close together, when you shine a light that would otherwise make A <span style="color: rgb(204, 51, 204); font-weight: bold;">glow</span>, what you see instead is mostly B <span style="color: rgb(255, 102, 102); font-weight: bold;">glowing</span>. That's because instead of glowing, A is able to hand off its energy to B in a way. That phenomenon is what's called FRET. <a href="http://probes.invitrogen.com/handbook/boxes/0422.html%22">Read this</a> if you're interested in more details. Also, <a href="http://www.amazon.com/Principles-Fluorescence-Spectroscopy-Joseph-Lakowicz/dp/0306460939">Lakowicz's Principles of Fluorescence Spectroscopy</a> is an excellent book that discusses the field.<br /><br /><span style="font-weight: bold;">The ACTUAL PAPER</span>:<br />The authors wanted an easy way to visualize a working enzyme in a living cell in real time. In other words, no additional prep time to wash out excess dyes, or having to bust the cells open to "see" the results.<br />Rather than bringing in two dyes on two separate molecules, the research team made a probe with two carefully chosen dyes built in.<br />When the target enzyme is catalytically active, it cleaves a protective group from a phenol to yield a quinone methide. There's a leaving group involved in generating the quinone methide. In this paper, the leaving group was one of the dyes. After the labeling event, the dyes aren't close together anymore, so no more FRET. (I can't remember where the liberated acceptor dye ends up, or whether that was mentioned.) The quinone methide that's left behind is a highly reactive alkylating agent that's known to latch onto any nearby nucleophile in a protein. Bingo, protein labeling and color change in one shot. <br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEizDjwIvTA49pgcKv7cLfnzSAN4RE0OhgHIElD6zSvGw3hCW5XBZyvUfcJ_j8LFqeRWcnmsnjoDmx0Us2w9k4D0KZchyZ382Wmn3dV8OKRzh2WWSfFyGB5y-Ty9LI8VCiMdoMiL/s1600-h/fret.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEizDjwIvTA49pgcKv7cLfnzSAN4RE0OhgHIElD6zSvGw3hCW5XBZyvUfcJ_j8LFqeRWcnmsnjoDmx0Us2w9k4D0KZchyZ382Wmn3dV8OKRzh2WWSfFyGB5y-Ty9LI8VCiMdoMiL/s400/fret.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5006258634156323794" /></a>Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com0tag:blogger.com,1999:blog-31226710.post-79075409894968387952006-12-06T23:30:00.000-05:002006-12-06T23:35:06.405-05:00Whaddaya think's in the tacos?**The <i>E. coli</i> outbreak that swept central Jersey and surrounding states now seems to have been traced to <a href="http://www.latimes.com/business/la-fi-taco7dec07,0,3168590.story?coll=la-home-headlines%22">green onions</a> distributed to local Taco Bell restaurants. So, no Jersey jokes allowed.<br />Cue the renaissance of <a href="http://www.amazon.com/Green-Onions-Booker-T-MGs/dp/B000002IR7">this 60's hit</a> off the American Graffiti soundtrack.<br />I'm just glad reporters mostly shied away from the obvious "<span style="font-weight: bold; color: rgb(255, 0, 0);">Run for the Border</span>" headline.<br />Nothing's been confirmed, but Taco Bell's parent company is pulling all green onions from its shelves. For a slightly propagandistic (is that a word?) briefing on <i>E. coli</i> O157:H7, the virulent strain behind the food poisoning, pick yourself up a copy of <a href="http://books.google.com/books?id=yNFN1OpnkBkC&dq=fast+food+nation&pg=PP1&ots=l_jhsB8s63&sig=ifVIMim7apXqPiC4eShPgUIAX7c&prev=http://www.google.com/search%3Fq%3Dfast%2Bfood%2Bnation%26start%3D0%26ie%3Dutf-8%26oe%3Dutf-8%26client%3Dfirefox-a%26rls%3Dorg.mozilla:en-US:official&sa=X&oi=print&ct=result&cd=1%22">Fast Food Nation</a>.<br />What I remember from college is that this particular variety of <i>E. coli</i> produces a toxin that inhibits protein synthesis in a way similar to <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17101666&query_hl=6&itool=pubmed_docsum">ricin</a>, and often results in substantial kidney damage.<br />When I was a college freshman, we had case studies in our general chemistry course, and the one in the nuclear chemistry chapter was based on the <a href="http://www.ou.edu/deptcomm/dodjcc/groups/02C2/Jack%20in%20the%20Box.htm">Jack-in-the-Box E. coli outbreak</a> of the 1990's. As I recall, we discussed the background of the case and debated the merits of beef irradiation.<br /><a href="http://www.mercola.com/article/irradiated/nuclear_lunch.htm">This link about irradiated beef</a> is pretty thought-provoking. Show me a guy who goes to McDonald's to boost his daily intake of essential vitamins, and I'll show you a doctor running a health website who <a href="http://en.wikipedia.org/wiki/Joseph_Mercola">does not believe in vaccinations or mammograms</a>.<br />Quite a bit of the news coverage for this Taco Bell incident refers to Jack-in-the-Box, more so than the more recent <a href="http://www.fda.gov/oc/opacom/hottopics/spinach.html">E. coli outbreak in spinach</a>. That doesn't make sense to me unless it's eventually demonstrated that the ground beef in the tacos is to blame. Maybe newswriters just think it's better to compare/ link fast food restaurants in their coverage.<br />I guess this is just a wake up call to me and any other non-red-meat eaters who are smugly thinking "this won't happen to me". I haven't eaten at Taco Bell in ages, but I got really cozy with <a style="color: rgb(51, 255, 51); font-weight: bold;" href="http://en.wikipedia.org/wiki/Best_Week_Ever">arugula</a> earlier this year.<br /><br /><br />** Hopefully a few people remember the TV show "<a href="http://www.ycdtotv.com/">You Can't Do That on Television</a>"....Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com2tag:blogger.com,1999:blog-31226710.post-51336923730776325462006-11-29T19:52:00.001-05:002006-11-29T19:56:46.302-05:00Pimp My InstrumentationWith the arrival of the <a href="http://www.princeton.edu/%7Edmacgr/">MacMillan group</a>, change is sweeping our lil' department. We are getting three new NMR spectrometers to complement what we currently have. They won't be ready to use for a little while, but I'm really looking forward to the day when I will no longer have to wait in line to use the instrument and get the data I need to move forward.<br /><br />NMR is short for Nuclear Magnetic Resonance. An NMR spectrometer is a machine that operates on the same principles as an <a href="http://en.wikipedia.org/wiki/MRI">MRI (magnetic resonance imaging)</a>. Don't get worried when you see the word <a href="http://www.cafepress.com/buy/nuclear/-/pv_design_prod/pg_1/p_storeid.21976510/pNo_21976510/id_7272348/opt_/fpt_fHBa__DB_________bSH_P___e/c_0/">"nuclear"</a>; this instrument's no more dangerous than an MRI (unless you wear a pacemaker). We organic chemists use NMR several times a day to help figure out the chemical structure of the stuff we make.<br /><br />Non-chemists, all you need to know is that compared to what we had before, this is <b style="color: rgb(255, 204, 0);">frickin' sweet</b><span style="color: rgb(255, 204, 0);">.</span><br /><br />Now, for specifics:<br />Our old NMR's are Varian's and the new ones are Bruker's. Having only used Bruker as a biochemistry undergrad taking phosphorus NMR's, I can't really compare the experience. It seems like most organic chemists feel strongly that one is better than the other, and that Jeol is a distant third.<br />We get a couple of <a href="http://www.bruker-biospin.com/nmr/products/crp.html">cryoprobes</a>, specifically Bruker's <a href="http://www.bruker-biospin.de/NMR/nmrsoftw/news/report/152/pdf/20-23.pdf">TCI probe</a> and <a href="http://www.bruker-biospin.com/nmr/products/crp_qnp.html">QNP probe</a>. The latter apparently allows users to switch by computer between 4 different nuclei without changing the probe tuning.<br />Also, we will have probes with heightened carbon sensitivity, meaning you can take a carbon NMR in the same time it would take for a proton (a couple minutes). <br />These instruments are actually located pretty close together and it's going to take some extra effort on Bruker's part to make sure everything works normally. Bruker may use our department to showcase their Ultrashield NMR's and the compact setup.<br />Each system is fully automated. We will just drop off our NMR tubes into the autosampler and the instrument will print out a spectrum and email the raw data and pdf of the spectrum to us.<br />There's a Bruker rep on campus every day setting up this instrument and its software, as well as the 2 other NMR's, which'll be in the next room. More as it develops.<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger2/6998/3811/1600/bestpicofwholenmrsystem.jpg"><img style="margin: 0pt 0pt 10px 10px; float: right; cursor: pointer;" src="http://photos1.blogger.com/blogger2/6998/3811/320/bestpicofwholenmrsystem.jpg" alt="" border="0" /></a><br />And here's one of our babies as it stands now. (A big thank you to Istvan Pelczer for this photo.) <br />If you haven't seen one of these instruments before, <a href="http://en.wikipedia.org/wiki/Superconducting_magnet#Use">the magnet in the instrument</a> needs to be kept <span style="font-weight: bold; color: rgb(102, 255, 255);">cold</span>, so it's encased in an insulating metal container that's filled with liquid nitrogen and liquid helium. That's really cold, far below zero.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com5tag:blogger.com,1999:blog-31226710.post-39917032359912396282006-11-22T19:44:00.000-05:002006-11-22T19:48:48.117-05:00The big brother I never hadEarly yesterday morning, a few people came by the lab to install temporary mats by some of the hoods. The general idea is to monitor how much time we spend working at the hood each day. The mats sense our weight and record a length of time in a networked "box" just outside the lab. The compiled data get downloaded later. <br />No, it's not some passive-aggressive move on the part of my funding agency. Princeton Chemistry <a href="http://www.princeton.edu/main/news/archive/S15/45/48I07/">is breaking ground for a new building</a> soon (our first new home since the <a href="http://en.wikipedia.org/wiki/Calvin_Coolidge">Coolidge</a> administration!) and an estimate of our time spent at the hood goes into choosing the best system of new hoods for the new building.<br />So let me back up a bit here and tell you what a hood is and why I use one.<br /><a href="http://en.wikipedia.org/wiki/Fume_hood">Fume hoods</a> are a mainstay of the organic chemistry lab. A hood is an enclosed workspace designed so that we can perform our experiments in a space that's fairly isolated from the air we breathe. Air flows up into the hood and away from the lab, sparing us from a lot of noxious fumes and small, potentially lung-coating particles. I work at the hood standing up, though I sometimes sit at a bar-stool height seat. The hoods in our lab are about 6 or 8 feet wide and pretty deep, longer than arm's length for me. They're outfitted with places to secure our flasks, vials, test tubes, whatever. Also in my hood are magnetic plates for stirring and heating, a couple of water taps, and a line for putting reactions under a vacuum or under an inert gas (see <a href="http://blind-science.blogspot.com/2006/09/more-to-glove.html">my entry on gloveboxes</a> for a reminder about why that's important.)<br />You can imagine that several hundred of these hoods constantly sucking away air makes it costly to heat and cool a building. There have been improvements in hoods' energy efficiency with new designs, and we will be getting these "improved" hoods in the new building. The MacMillan labs are already equipped with new, energy efficient hoods. I guess they just want to get an idea of the volume of airflow that the we use in a given day, hence the mats. <br />One problem I see is that I'm not sure whether they are assuming that everyone closes their hood to save energy when they aren't working at them. Wishful thinking in this building. I know I'm not always very good about that.<br />The mats are about the size of a welcome mat and nondescript gray in color. Not nearly as nice as what I currently have attached to my XBox at home for playing <a href="http://en.wikipedia.org/wiki/Dance_dance_revolution">Dance Dance Revolution</a>. (You laugh, but try playing the advanced level. Tell me that's not a good workout.) <a href="http://www.ab.com/safety/prod_directory/pres_sens_safe_devices/safety_mats/matguard_press-sens_safe_mats/index.html">This</a> is kind of similar to what we got.<br />Needless to say, the mats spawned a couple of creative strategies in the group for "enhancing" the hour count, from moving our argon tanks on top of the mats to offering extra credit to undergrads to stand there for you. <br />So basically, it looks like I might soon be able to construct a bar graph like the one Kyle made <a href="http://www.thechemblog.com/?p=298">here</a>.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com1tag:blogger.com,1999:blog-31226710.post-33037239754442204052006-11-17T17:01:00.000-05:002006-11-17T17:04:18.406-05:00A Shot in the ArmI got my flu vaccine for free last week through Princeton Health Services. To encourage us to get vaccinated, there was an ad blitz campuswide for "FluFest", a two-day event at the student center which featured performances by our <a href="http://en.wikipedia.org/wiki/A_cappella#Modern_a_cappella">a cappella groups</a> and free food.<br />I won't bother blogging about why you should get your flu vaccine, or complaining about misguided rants, because that's been done to death. Search blogger.com if you don't believe me. <br />For up-to-date information on the vaccine and the flu, <a href="http://www.cdc.gov/flu/">click here</a> to go to the Center for Disease Control's Website.<br />See <a href="http://www.cdc.gov/flu/professionals/vaccination/composition0607.htm">here</a> for more details about what's in the vaccine.<br />The two types of vaccine:<br />1) The trivalent inactivated influenza vaccine.--> I got this one.<br />"Trivalent" in this case means that the vaccine provides immunity to three different strains of the flu. The three strains in the vaccine change from year to year, depending on what health professionals have determined to be the most likely ones to be going around that particular flu season. <br />"Inactivated" means that the virus isn't infectious. You just get the parts of the virus that trick your immune system into doing its job. Mostly, that's the outer coating. It's like the story in the bible about how Jacob fooled his blind father Isaac into giving him the blessing intended for his hairier brother Esau, by <a href="http://www.cdc.gov/flu/professionals/vaccination/composition0607.htm">wearing hairy goatskins</a>.<br />2) The live, attenuated influenza vaccine.<br />"Attenuated" means weakened. <br />This vaccine is a nasal spray, not an injection.<br />The modified viruses for both types of the vaccine are grown in chicken eggs. This technology has been around since <a href="http://www.pubmedcentral.nih.gov/pagerender.fcgi?artid=169693&pageindex=1">at least as far back as the 1950's</a>, and it's why people with egg allergies shouldn't be given this kind of flu vaccine. <br />I searched PubMed for "embryonated hen's egg" and it looks like plenty of things can be grown in chicken eggs, like herpes simplex virus and hepatitis. I wonder why we still use this system. Seems to me like we should be able to make a synthetic, <a href="http://en.wikipedia.org/wiki/Hypoallergenic">hypoallergenic</a> cocoon for these things to grow by now.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com1tag:blogger.com,1999:blog-31226710.post-10811353188216562562006-11-10T18:04:00.000-05:002006-11-10T18:09:48.682-05:00I'll own up to itI shattered a dewar for a 500 mL round-bottomed flask today. I was wearing gloves and goggles, the dewar was in my hood at arm's length, and no one was hurt, but the <span style="font-weight: bold; color: rgb(204, 51, 204);">BANG!</span> was so loud that I was trembling for the next five minutes.<br /><a href="http://web.princeton.edu/sites/ehs/labsafetymanual/sec7h.htm#Dewar">Here's a link</a> to Princeton's lab safety website and its recommendations on dewars.<br />A dewar is an insulated container that I use for my cold baths in the lab. The most common cold bath I use is a mixture of dry ice and acetone, which has a temperature of 78 degrees below zero (Celsius). It's important to run some reactions in the cold to prevent uncontrolled reactivity.<br />Anyway, this particular dewar is made of glass that is lined with silver. The whole thing is surrounded by aluminum metal. The reason a dewar insulates so well is that it's a double layer flask with a space for a <a href="http://en.wikipedia.org/wiki/Thermos_bottle">vacuum between the walls</a>.<br />Dewars implode when they are broken, meaning that they collapse in on themselves instead of <i>exploding</i> outward. However, there's still a risk of small glass particles flying around and injuring someone.<br />The most famous dewar out there is the humble <a href="http://home.howstuffworks.com/thermos.htm">Thermos</a> that you took to lunch every day in grade school.<br />In homage to the <a href="http://blog.tenderbutton.com">Tenderbutton</a> style of blogging, I've posted pictures of the dewar so you can see the damage for yourself. I think I needed a better camera for this. The aluminum/ glass reflects light really well and is hard to photograph.<br />Here's a regular dewar.<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger2/6998/3811/1600/IMGP3076.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://photos1.blogger.com/blogger2/6998/3811/320/IMGP3076.jpg" alt="" border="0" /></a><br />Here's my shattered one.<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger2/6998/3811/1600/IMGP3075.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="http://photos1.blogger.com/blogger2/6998/3811/320/IMGP3075.jpg" border="0" alt="" /></a><br />Kids, don't try this at home. We're trained professionals.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com4tag:blogger.com,1999:blog-31226710.post-48591797417598525822006-11-10T17:27:00.000-05:002006-11-10T17:32:10.617-05:00Blogger BetaI finally made the switch to the beta version of the blogging website. There may be some bugs in the coming weeks (ie, in past weeks, other bloggers have not been able to see or post comments.)<br />So bear with me.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com0tag:blogger.com,1999:blog-31226710.post-1163003463292673432006-11-08T11:28:00.000-05:002006-11-10T17:25:59.151-05:00I Wish I Swore by Something with a Nice FragranceLate fall is upon us, and the inevitable cold weather chapping and cracking of the skin on my hands has begun. The situation is exacerbated by having to wear gloves and wash my hands repeatedly at work. <a href="https://www1.fishersci.com/Coupon?gid=173043&cid=1328">Proguard</a> is a moisturizer that's available from <a href="http://www.fishersci.com">the Fisher catalog</a>, which is a one-stop shopping depot for general lab supplies, as well as direct from the Princeton Chem. stockroom. It is <span style="font-weight: bold;">THE ONLY THING</span> that ever keeps my skin from cracking. I use a little every time I wash my hands and it's fantastic; I even bought one for home (Jason wears gloves, too.) I hate to waste money on one of the cute little travel size packages of scented lotion for my purse because I know it'd be purely ornamental. I just throw some Proguard in a travel size case. Ideally, I'd like to be able to take my Proguard to something like <a href="http://www.thebodyshop.com/bodyshop/browse/product_detail.jsp?productId=prod3650045&categoryId=cat4750003">The Body Shop</a> and just blend it with any fragrance oil to use outside of lab. Come to think of it, that's something I'll have to try, but I doubt they'd help me out unless I was buying their brand of lotion. Proguard will definitely be one of the things I miss when I graduate. Maybe someone on the inside will be able to hook me up.<br />Just for fun, I thought I'd do a quick comparison of the main ingredients in Proguard ("P") versus my favorite scented moisturizer (we'll call it "<span style="font-weight: bold; color: rgb(255, 204, 0);">WVS</span>" for short, but those of you who know me should know what I'm talking about). I don't really have any sense of the percent composition of either lotion, because the ingredients are listed in descending order of percentage with no concrete numbers, as they'd be on food. I never stopped to think about moisturizer formulation before. <a href="http://www.emedicine.com/derm/topic506.htm">Moisturizers</a> have to multitask on the outermost layers of the skin, repairing damage and sealing in water, without triggering allergies or any other adverse reaction.<br /><br />emollient (skin softener):<br />P = cetyl alcohol<br />WVS = cetyl alcohol, stearyl alcohol, petroleum jelly<br /><br />silicone oils: (<a href="http://www.snowdriftfarm.com/silicone_use.html">they form a protective layer</a>)<br />P = dimethicone<br />WVS = same<br /><br />humectant (hygroscopic substance, something that absorbs water):<br />P = sorbitol, propylene glycol<br />WVS = glycerin, propylene glycol<br /><br />preservatives:<br />P = diazolidinyl urea (formaldehyde-releasing goodness!), methyl and propyl paraben, tetrasodium EDTA<br />WVS = basically the same<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://photos1.blogger.com/blogger/6955/3367/1600/proguard.1.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="http://photos1.blogger.com/blogger/6955/3367/320/proguard.1.jpg" alt="" border="0" /></a><br /><span style="color: rgb(255, 255, 0); font-weight: bold;">the ref</span>: Characterization and chemistry of imidazolidinyl urea and diazolidinyl urea. <i>Contact Dermatitis</i> <b>2006</b> <i>54</i>, 50-58.<br />So all the key ingredients are nearly indistinguishable, but the scented stuff also contains vitamins, which I'm not sure would penetrate deep enough into my skin to do me any good anyway. (Anybody know about those properties for specific vitamins offhand?) The difference in cost is negligible when you factor in the size of the package and assume a little discount for buying in bulk.<br />With all this newfound knowledge of moisturizers, I'm not sure I buy into the <a href="http://www.cremedelamer.com/templates/products/sp_nonshaded.tmpl?CATEGORY_ID=CATEGORY5778&PRODUCT_ID=PROD2459">Creme de la Mer</a> craze, what with all their "miracle formula" sales pitch. "Even now, it is not entirely clear how Creme de la Mer works," they say. To me, it seems like the ingredients that work best in moisturizers are pretty cheap (dimethicone can be found in <a href="http://en.wikipedia.org/wiki/Dimethicone#Applications">Silly Putty</a>!). Anyhow, for some sciencey-looking stuff (fermentors!), I recommend you click the link labeled "The Miracle" and enjoy the movie.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com10tag:blogger.com,1999:blog-31226710.post-1162868643796415582006-11-06T22:03:00.000-05:002006-11-10T17:25:59.089-05:00Belated Halloween EditionPorphyrias are a family of relatively rare diseases that present symptoms reminiscent of the characters immortalized by <a href="http://en.wikipedia.org/wiki/Lon_Chaney,_Jr.">Lon Chaney, Jr</a>. and <a href="http://en.wikipedia.org/wiki/Bela_lugosi">Bela Lugosi</a>. There's ample discussion in the literature about whether these diseases spawned the myths we recognize today. Porphyria sufferers may have anemia, light sensitivity, and reddish colored urine, or excessive hair growth. The underlying problem has to do with how the body makes and utilizes porphyrin, part of an oxygen-carrying complex in our blood. The molecular underpinnings of the disease are largely unknown, but a recent Nature letter presents evidence that some porphyrias may be due to a defect in a specific protein. <br /><span style="color: rgb(255, 255, 0); font-weight: bold;">the ref</span>: <span style="font-style: italic;">Nature</span> <span style="font-weight: bold;">2006</span>, <span style="font-style: italic;">443</span>, 586-589.<br />This protein, called ABCB6, transports porphyrins to a place where they can bind to iron. This iron-porphyrin combo eventually ends up in <a href="http://en.wikipedia.org/wiki/Hemoglobin">hemoglobin</a>. This work points out that it isn't necessarily just the production of porphyrins that's the problem, that getting porphyrins where they need to be so that they can do their job is equally important.<br />This idea reminds me a little of the distinction between Type I and Type II diabetes. The underlying theme that diseases with the same symptoms could come from "manufacturing" or "distribution" issues must be more common than I realize.<br /><a href="http://en.wikipedia.org/wiki/Type_1_diabetes">Type I diabetes</a>: decreased or no insulin production<br /><a href="http://en.wikipedia.org/wiki/Type_2_diabetes">Type II diabetes</a>: insulin's around, but the body isn't responding to it properly<br />There was supposed to be a chemistry grad student with porphyria beginning in my year, 2002. The department spent a sizable chunk of change renovating an entryway so that she could turn off all lights when she needed to, and they built her a private office and everything. (I think she would've been a computational chemist). She deferred enrollment for a year and then never arrived. Not sure where she is today.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com0tag:blogger.com,1999:blog-31226710.post-1161920922625540092006-10-26T23:43:00.000-04:002006-11-10T17:25:59.027-05:00Look, Ma, I'm a Citizen-JournalistI drove to Baltimore after work today to attend the <span style="font-weight: bold; color: rgb(51, 204, 0);">National Association of Science Writers'</span> 2006 meeting, Science in Society. There will be seminars with writing tips, networking lunches, and a "science cabaret" featuring what promises to be <a href="http://en.wikipedia.org/wiki/Tom_Lehrer">Lehrer-esque</a> entertainment. <br />This year, the 500 science writers attending this meeting are going to be driving right into a story. See, when I was driving into Baltimore I was following the directions on the hotel website. Unfortunately, police had cordoned off one of my turn streets, so I had to drive around in circles for a while until I could figure out how to get to where I needed to go. I happened to notice white smoke emanating from manholes in the vicinity of the roadblock. <br />It turns out that two manhole covers popped open near one of the busiest intersections in the city, possibly due to a leak in a natural gas main. I'm lucky I got here way past rush hour. Reports <a href="http://www.baltimoresun.com/news/traffic/bal-leak1026,0,2276363.story?coll=bal-home-headlines">here</a> and <a href="http://www.examiner.com/a-364538%7EFirefighters_block_of_parts_of_downtown_Baltimore_due_to_gas_leak.html">here</a> say that the Maryland Dept. of the Environment found low levels of natural gas using handheld meters. For an 88 page pdf discussing U.S. Department of Energy-sponsored development of a state-of-the-art natural gas detector, <a href="http://www.osti.gov/bridge/servlets/purl/840957-dB876y/native/840957.pdf">click here</a>.<br />I'm too tired right now to do any back of the napkin math to figure out how much gas pressure would have to have built up to pop a manhole cover. Any takers?<br />Anyway, no one in <a href="http://www.tremontsuitehotels.com/">the hotel where I'm staying</a> knows what's going on, but maybe by tomorrow something will be in the news. I guarantee someone at this meeting's going to make a story out of it.Carmenhttp://www.blogger.com/profile/10983408726835595496noreply@blogger.com1