tag:blogger.com,1999:blog-34741245489769387002024-03-16T02:16:42.716-05:00Not the Labgood science, bad science, and how chemistry can make the world awesomevinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.comBlogger56125tag:blogger.com,1999:blog-3474124548976938700.post-36016479054048978392017-03-02T09:30:00.000-06:002017-03-02T09:30:08.037-06:00Mental Health Dialogue: 2017 Edition (part 2)<i>Note: this post is a response in a dialogue between Chemjobber and I on grad school and its effects on mental health. Yesterday's post can be found <a href="http://chemjobber.blogspot.com/2017/03/revisiting-again-graduate-school-and.html">here</a>.</i><br />
<br />
Dear Chemjobber:<br />
<br />
I had to do a double take at the calendar when you mentioned we were due for a refresh of this conversation on mental health in graduate school. But, somehow, lo and behold<span style="font-family: "arial" , sans-serif; font-size: 11.0pt;">—</span>it's 2017.<br />
<br />
For me, things have been mostly good. My grad school projects ended up coming out of seeming oscillation into something resembling a stable thesis (bio updated to "Vinylogous <i>was</i> a graduate student..."). Add that on to a bunch of "life" events, and that's my 2015-2016.<br />
<br />
Graduate school can be (and was) stressful, but so is the world beyond, I guess. For all the faults of our pressure cooker academia, it can be a source of insulation or distraction from alternate stresses (<i>e.g.</i> job market uncertainty, figuring out how healthcare works when you're not on an assistantship, dealing with the consequences of everyone you know aging, <i>etc.</i>). And some of those grad school stresses, it seems, do carry over, too.<br />
<br />
All in all, I <i>might </i>do it again if I had to go back. But let's talk.<br />
<br />
<h3>
The state of things</h3>
<div>
<br /></div>
You <a href="http://chemjobber.blogspot.com/2017/03/revisiting-again-graduate-school-and.html">asked</a> how the field has progressed:<br />
<blockquote class="tr_bq">
<b>How are we doing?</b> I think academia might be doing better than two years ago about these issues, but I'm not sure. What do you think?</blockquote>
Has the mountain been nudged? As you might guess from that, I'm not really sure that much has changed, on a grand scale, in chemistry graduate education <i>itself</i> in the last four years. <br />
<br />
I don't think individual departments are likely do so much without concerted pressure. Take for instance, the clamors for safety reform around Patrick Harran's tragically negligent supervision of Sheri Sangji. In 2014, prior to the resolution of the corresponding court case, departments were pretending to care more about safety<span style="font-family: "arial" , sans-serif; font-size: 11.0pt;">—</span>getting professors and students more actively involved in formulating solutions, giving lip service to "task force" initiatives, <i>etc.</i><br />
<i><br /></i>
But of course, when <a href="http://www.sciencemag.org/careers/2014/07/landmark-patrick-harran-case-ends-inconclusively">Harran was able to escape a guilty plea</a> and pay less than two weeks' salary as a token gesture to a burn center, departments realized that they weren't going to be held responsible, and they quietly dropped the matter. (Maybe not all departments, granted.)<br />
<br />
Mental health is going to be similar. I don't see a clear path going forward that would encourage change. There's a massive collective action problem that still persists. And it's even trickier than chemical safety<span style="font-family: "arial" , sans-serif; font-size: 11.0pt;">—</span>there's more vagueness, less accountability, fewer particularized harms.<br />
<br />
What have I seen? I haven't noticed much <i>systemic </i>change on the side of departments or PIs themselves. I did see a few <i>individual </i>PIs get mellower and more understanding<span style="font-family: "arial" , sans-serif; font-size: 11.0pt;">—</span>but over the course of five years, that can happen anyway.<br />
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I also did see someone announce on social media very recently that they were leaving graduate school, and in particular, they said their advisor's management syle was abusive. I don't know that you would be as likely to see that said publicly 5-10 years ago.<br />
<br />
I've also noticed a few people announce their decisions to leave grad school for other options (career changes or MS-level chemistry jobs). Reassuringly, the reception to those people on social media from peers, family, and friends has been very supportive. So if there is judgment, it is largely silent judgment. For what it's worth, I think this is important<span style="font-family: "arial" , sans-serif; font-size: 11.0pt;">—</span>the broader recognition that change is OK, the grad school system is flawed and exhausting, and everyone's got their own path to pursue.<br />
<br />
Mark that down as "somewhat optimistic."<br />
<br />
<h3>
Blaming the screen</h3>
<div>
<br /></div>
<div>
You <a href="http://chemjobber.blogspot.com/2017/03/revisiting-again-graduate-school-and.html">asked</a> how modern distractions might impact the daily grind:</div>
<blockquote class="tr_bq">
<b>Distractions:</b> Do you think our modern times are responsible for some of the mental health difficulties that graduate students face? I don't think I was a paragon of mindfulness or presence in graduate school, but I think today's graduate student faces an array of distractions that are an order of magnitude larger than anything I faced. [. . .] I wonder if it’s something that contributes to deadline-related stress and stress that we might feel in graduate school? How did you deal with it towards the end of your time in graduate school?</blockquote>
This is a really interesting point. It's definitely a concern in grad school<span style="font-family: "arial" , sans-serif; font-size: 11.0pt;">—</span>some PIs go so far as to explicitly dictate in their group manual that there is to be no social media access during the day, among other approaches.<br />
<br />
Truthfully, the instant gratification of the small miracle screens we carry around does make things harder. I often found it hard to get through close reading of long articles without impulsively pulling up Twitter every couple paragraphs.<br />
<br />
But I wonder if these distractions are supply-side or demand-side (I suppose I mean<span style="font-family: "arial" , sans-serif; font-size: 11.0pt;">—</span>do today's sources and devices <i>create</i> distraction or merely serve as an <i>outlet </i>for distraction?)<br />
<br />
For perspective, I've often tried to remedy my own distractedness by locking away my phone, or simply self-imposing a no-phone rule. Usually, though, after a while I find myself getting lost in other thoughts, snapping out of that to realize I've been mechanically skimming paragraphs. I remember having that same daydreaming-while-reading experience before I had a cell phone. (Maybe humans haven't really evolved to sit and read long texts).<br />
<br />
So I'm not <i>totally </i>convinced that technology is a huge amplifier of distractedness. It <i>might </i>be. But maybe it's just a particularly visible outlet that highlights how easily distracted we are. I think it's mostly just convenient and comforting to reassure ourselves that we'd be so much more productive without today's distractions.<br />
<br />
(I'm also generally skeptical of the borderline anti-millennial "back in my day..." wistful sentiments that seem to get tossed around in some spheres about the moral and work-ethic superiority of all adults north of 40).<br />
<br />
As for how I've personally managed to conquer distractions? I haven't. Still a struggle. And definitely still a source of stress in my current position, as it was in grad school (to me, it seems that other people are much more adept at quickly digesting information, retaining it, and finishing things on deadline. Maybe they aren't--maybe that's related to the whole problem of being unable to objectively compare oneself to others--but it does feel that way).<br />
<br />
That being said: to minimize the distraction of <i>minutiae </i>(<i>i.e.</i> all those pesky details in lab that are immediately important for today's experiment but undoubtedly distracting in terms of being able to think creatively or long-term), I think it was really helpful to (1) minimize weekends in the lab (even if your weekdays get busier; and (2) go on long drive on the highway a lot--several hours in the car without anything to do but think can be more productive than one might think.<br />
<br />
<h3>
The elusiveness of objective foresight </h3>
<div>
<br /></div>
<div>
You <a href="http://chemjobber.blogspot.com/2017/03/revisiting-again-graduate-school-and.html">asked</a> how we should be looking at the decision to leave grad school:</div>
<blockquote class="tr_bq">
<b>The “I Quit” Series:</b> [. . .] I learned so much. I wasn’t surprised at how much people didn’t like graduate school (I think the people who really enjoy it are relatively rare), but I was surprised at how happy people were to have left. I haven’t made a solid count, but of the people who wrote in, most of them answered the question “Are you happy you left?” with a resounding “yes.” [. . .] I wish I had some way of forcing graduate students to confront the question of “should I leave?” with some kind of rational test. [. . .] What do you think? Are we looking at this wrong? Should we be encouraging people to stay no matter what? (Do graduate students need more ‘grit and determination’?)</blockquote>
Anecdotally, at least, I think more people who leave grad school are<span style="font-family: "arial" , sans-serif; font-size: 11.0pt;">—</span>if you ask them a year down the road--happy to have done so than are unhappy.<br />
<br />
I saw more instances of this in the last few years than I expected. There were, interestingly, a spectrum of reasons-to-leave (ranging from voluntary to not) but also a spectrum of PI reactions (including one who was both understanding and supportive, and another who made his student's life as miserable as conveniently possible). But they're all (seemingly) happier now.<br />
<br />
I think we can (as a community) probably emphatically agree at this point that (1) grad school is not everything; (2) too many people go to grad school, and you need to <i>really</i> want it; (3) no one knows going in quite what they're getting into; and (4) it's OK to leave grad school if it's not what you want to do.<br />
<br />
I think we've also (as a community) had great discussions of alternatives and career options.<br />
<br />
I think, moreover, that we (as a community) have increasingly brought up the stresses and downsides of grad school—the nebulousness, the power dynamics, the understated role of serendipity in success and failure, the disconnectedness.<br />
<br />
I've also talked about the above to a lot of students who were either considering applying to grad school or who were visiting on recruiting weekends.<br />
<br />
But I don't think a single one of them took my advice. (This relates to your desire for a rational self-imposed test).<br />
<br />
It's a little puzzling. Given broader exposure to grad school problems, shouldn't fewer people be going to grad school? (Maybe there are—I don't have a handle on the exact numbers, but my impression is that the ranks of scientific PhD students are as full as ever).<br />
<br />
My impression is that as humans we all suffer from profoundly terrible objective foresight. ("Maybe it'll be different for me," we think. It usually isn't, of course). And that's part of the grad-school-mental-health problem. The only people who might realistically make a substantial change (grad students themselves, acting en masse) are only in the system for a few years, and those there for longer (PIs and administration) have little to gain from changing anything.<br />
<br />
Some structural changes in grad school might change this. Take <a href="http://www.sciencemag.org/careers/2016/09/implications-graduate-student-unionization">grad student unionization</a>, for instance. That, of course, is controversial, and it's far from obvious that it would fix this problem. (One common criticism is that it would turn the grad student/advisor relationship from cooperative to adversarial; but I think one has to be somewhat naive to think it's that simple, or that there aren't many adversarial relationships already).<br />
<br />
<h3>
Let's get political</h3>
<div>
So far (in this and prior dialogues), we've largely focused on: (1) graduate programs themselves; (2) the internal struggles of graduate students; or (3) finding support outside graduate school. I don't think we've much considered the role of some <i>really</i> external concerns—namely, current events and politics. And grad student participation in politics.</div>
<br />
First, there's no reason that someone can't be politically involved or politically active and not also be a fantastic scientist. That should go without saying, but "politically active" often conjures up images of incivility and frothing at the mouth, but I think that's a stereotype used to deride those with the gumption to care about things that aren't just silica gel and transition metals.<br />
<br />
Second, we're in an interesting time where there's a push for scientists to get more involved in politics (see, <i>e.g.</i>, the still-contentious <a href="http://www.npr.org/sections/thetwo-way/2017/02/23/515584634/should-scientists-march-u-s-researchers-still-debating-pros-and-cons">March for Science</a>, or Prof. Michael Eisen's <a href="http://www.nature.com/news/geneticist-launches-bid-for-us-senate-1.21381">announced bid for Senate</a>).<br />
<br />
<b>But why does it matter?</b><br />
<br />
Grad students are enormously focused on narrow things. Even when focused broadly on a scientific sense, they tend to pour tons of energy into science. And as previously discussed, if they take the time to have an outside interest (say, soccer or politics) it's derided. But, of course, we all live in a broader world that organic chemistry plays only a minuscule role in. Sometimes there are graduate students and professors who are active in political advocacy and social justice. But from experience, this often (and unfortunately) elicits mockery from co-workers.<br />
<br />
Political apathy, of course, is a luxury for the privileged who don't stand to have much taken away from them. (This class includes professors, who as much as they might gripe about funding, tend to have relatively secure jobs at largely tolerant institutions with typically diverse populations).<br />
<br />
This here is only a qualitative observation, of course. But fields like law and medicine have graduate experiences with difficult study and long hours, like chemistry grad school. But in either, you tend to see more devotion to external, broad, society-level causes. (That's probably somewhat related to the nature of the work itself, of course). And there's stresses on mental health there, too, but I think they're largely different in kind. I do wonder if increased encouragement or acceptance of grad student political involvement (let's call it "<i>public policy</i> involvement" for those who sneeze at the word "political") might help foster a feeling of empowerment, or at least attenuate the nihilistic jadedness that you can smell when you walk some chemistry department halls.<br />
<br />
It's difficult to clearly articulate the reasons for graduate student political involvement, I guess. But I do wonder if it would be a good thing (maybe as an extension of it being a good thing for grad students to have outside interests <i>in general</i>). What are your thoughts, Chemjobber? I'm interested in your take on whether graduate students would benefit by being more active in this area (isn't that in the spirit of "Broader Impacts?").<br />
<br />
I also wonder about political involvement by professors. There's some prominent examples of quite conservative or libertarian chemistry professors, for instance, and I've always wondered the effects, if any, on their students (I hope there's very little)—especially when I see a Tweet that's arguably misogynistic or racist. These professors often, nonetheless, have fairly gender-balanced or racially-diverse groups. I wonder if that ever spills over... do students feel they aren't getting a fair shake when their politics don't align with their PI? Or are we good enough at compartmentalizing that we can separate that sphere from the work sphere, and just get our work done without it mattering? (I hope the latter).<br />
<br />
<b>And have you seen the news lately?</b><br />
<br />
I also do wonder about how current events will shape the grad school experience going forward (and by extension, the stresses involved). Namely:<br />
<br />
<b>Healthcare "reform"</b>. A lot of grad students are on their parents' healthcare or a university insurance plan, but not all. But with the climate in Washington, it's conceivable to see coverage for mental health services shrink.<br />
<br />
<b>Funding cuts</b>. A look at the <a href="http://www.sciencemag.org/news/2017/02/trump-s-2018-budget-will-squeeze-civilian-science-agencies">planned 2018 budget</a> reveals a $31 billion cut to the NIH, along with multi-billion-dollar cuts to the NSF and DOE's Office of Science. I can't see this having a positive effect on graduate student life.<br />
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<b>The public and science</b>. This isn't entirely new, of course, but the public seems to have a growing <a href="https://www.washingtonpost.com/posteverything/wp/2015/01/30/even-in-2015-the-public-doesnt-trust-scientists/?utm_term=.7ac85f36bb4e">distrust for experts</a>. Along with a political climate that seems to be gripped by a strong anti-intellectual movement, I wonder how decreased public faith in scientists and academics will shake out, and perhaps if universities will see even less support, requiring higher pressure on pools of students to produce work. (Related, perhaps, to funding cuts).<br />
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<b>Wage and hiring freezes</b>. Of course, there was the <a href="http://www.the-scientist.com/?articles.view/articleNo/47800/title/US-Postdocs-Grapple-with-Salary-Changes/">postdoc salary debacle</a> and the <a href="https://www.whitehouse.gov/the-press-office/2017/01/23/presidential-memorandum-regarding-hiring-freeze">federal hiring freeze</a>. Neither are good, on their face, for postdocs (and misfortune often trickles downhill). Are we seeing more difficult career ladders for grad students?<br />
<br />
<b>Immigration and the Trump administration</b>. This one is particularly worrisome. I had tons of great foreign colleagues in graduate school. Many of those people are having trouble finding jobs. Or they're dealing with an increasingly loud and vicious public discourse <a href="http://www.slate.com/blogs/the_slatest/2017/01/31/reuters_ipsos_muslim_ban_poll_finds_support_for_order.html">demonizing immigrants or demonizing Muslims</a>. In essence, a graduate student who is foreign or Muslim is being subjected to all the normal mental health stresses of grad school but with the added ingredient of broad-scale xenophobia. (It's worth pointing out that in the recent <a href="http://cdn.ca9.uscourts.gov/datastore/opinions/2017/02/09/17-35105.pdf">9th Circuit Court of Appeals decision</a> refusing to stay a preliminary injunction against the administration's <i>de facto </i>Muslim ban, the plight of foreign graduate students and professors played a central role in demonstrating the damage done by the order).<br />
<br />
Anyway, not to leave this on a sour note, but I wonder what other recent or upcoming events might signal good or bad times ahead for graduate students and postdocs. (Or maybe nothing will really change at all).<br />
<br />
<br />
<i>Regards,</i><br />
<i><br /></i>
<i>Vinylogous</i><br />
<br />
<br />vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com35tag:blogger.com,1999:blog-3474124548976938700.post-5253256913906655052015-01-09T08:00:00.000-06:002015-01-09T08:02:25.054-06:00Revisiting grad school and mental health with Chemjobber<i>Note to readers: this post is a response in a dialogue between <a href="http://chemjobber.blogspot.com/">Chemjobber</a> and I on grad school and its effects on mental health. Yesterday's post can be found <a href="http://chemjobber.blogspot.com/2015/01/revisiting-graduate-school-and-mental.html">here</a>.</i><br>
<i><br></i>
Dear Chemjobber:<br>
<br>
It has indeed been awhile since the last mental health dialogue. Since then, I've gained additional perspective from inside grad school, and it is invaluable to hear your view from "the other side." Hopefully some of the observations and recommendations below will be of interest to you and perhaps to readers.<br>
<br>
Last time we talked about this topic, I was significantly earlier on in my grad school career. Since then, I've had battles: dealing with failed multi-month projects, going through intense candidacy preparations, attending to seemingly overwhelming (at the time) departmental milestone requirements, wondering if every experiment that worked was just me <a href="http://en.wikipedia.org/wiki/Impostor_syndrome">fooling myself</a>, adjusting to being several states away from family and my SO, and wondering if my PI knew enough to steer my career in a productive direction.<br>
<br>
Early on, it was easy to get discouraged. Now, it's still easy to get discouraged. That's research, I guess. Part of my struggles entailed coming to terms with the fact that I did not want the job I originally came to grad school for: academia. Moreover, I saw college and high school friends rocket past and start exceptionally successful careers in other discplines, and I have seen other people I regarded as lazy or duplicitous get showered in accolades in their fields. That kind of thing--comparing yourself to people in different career paths--is rough. And when you've sunk 8 years into your university education, it makes changing career trajectories stressful and confusing.<br>
<br>
More than once, due to a culmination of these things, I came to the brink of leaving the grad program. As it happens, I didn't. More on that a little later.<br>
<br>
<b>Defining Mental Health</b><br>
<b><br></b>
In the last two years (and maybe it's just confirmation bias, or increased vigilance on my part due to our earlier dialogue), mental health has received a lot of press (particularly in regards to crime and rationalization of gun violence).<br>
<br>
I think that makes the subject a bit taboo--as if admitting to problems is akin to saying you're an unstable risk.<br>
<br>
Before I write further, I want to articulate what is meant.<br>
<br>
Having a problem with mental health doesn't <i>have </i>to mean severe mental illness. It is a strain on emotional and/or cognitive well-being. It doesn't have to mean severe depression. It can--and that's common--and it's okay.<br>
<br>
This is the best way I've heard it phrased: <i>every single person on Earth has some degree of mental health issues</i>. And so it pays to have empathy.<br>
<br>
For fear of feeling weak or being stigmatized--or simply due to denial, or thinking that the situation isn't serious enough, or that care is too expensive--many people don't get help for mental health problems. And, again: "problems" can range from crippling depression to simply feeling overwhelmed with expectations at work. Either way, it behooves one to be introspective and take advantage of help that is available, as wellness is infinitely more important than pride.<br>
<br>
<b>Has Grad School Changed?</b><br>
<b><br></b>
You asked about change in the attitudes and policies of professors in grad school: are more (younger) professors opening up about the mental health/stress needs of students? Is "work/life balance" more of a serious consideration and less of a joke? Or is it status quo?<br>
<br>
This is one of those questions that it's hard to address in any more than an anecdotal manner. I <i>want </i>the answer to be "yes--new professors are generally more socially and emotionally in tune and respect their students' time and needs". I think that to some degree that is the case, but it's very, <i>very </i>group-dependent. Many (relatively newer) PIs that I've seen don't religiously track hours and do encourage students to have outside hobbies. But since being a PI is still stressful, science academic culture is still a place of forced machismo, and research grant funding is still scarce, I also see many new PIs work their students much harder than average (while being groomed to do so by more senior faculty).<br>
<br>
Here's my rule-of-thumb diagnostic that can be applied to PIs: what do they think (and how do they respond) when a student has no interest in going into academia? It's a rather simplistic way of viewing it, but many of worst professors in this regard are the ones who view anything other than an academic position as failure. Other PIs (often when both young and not purely synthetic-oriented) accept that academic positions are a minority and that life is a balance of priorities and different students have different needs. This latter category is, I hope, becoming more common.<br>
<br>
Hopefully dialogues such as these (and the accompanying discussions we saw last time) at least serve as consciousness raising to spur dialogue between students themselves and between PIs and their labs.<br>
<br>
<b>Behavioral Pitfalls and Mental Health and Dealing with It</b><br>
<b><br></b>
The last two years have given me some time to reflect and also observe--and it seems that certain combinations of behaviors and attitudes are especially bad, mental health-wise, in the context of grad school. But there's also ways to deal with them. For instance:<br>
<br>
<i>Avoid burnout: </i>Some people are prone to starting projects fervently, working on them vigorously for long hours. That kind of work ethic--an almost obsession--can be immensely productive in the short run, but people who do this also tend to burn out really quickly. In jobs where projects switch frequently (maybe graphic design, or consulting, for instance) this might be sustainable.<br>
<br>
Grad school, however, requires a slower burn. Long hours are expected--but they have to be tempered. What's the key, then? I think you have to set in for the long haul and learn what your limits are. Find the burn rate at which you're energized but not drained.<br>
<br>
Of course, that's easier said than done. But as far as I can tell, the people most prone to burnout have a tough time adjusting mentally to graduate school.<br>
<br>
On a related note, <i>make sure to have some hobbies. </i>People without hobbies adjust more poorly to stress. Do things, read things, create things, eat things, etc. Learn a language or something.<br>
<br>
All too often people lose their hobbies and interests in grad school. That's easy to do. I've experienced it--I used to play quite a bit of music at what (I think) was a decently proficient level. That's all but stopped. I used to write a lot--and read a lot, too. The consuming nature of grad school, however, tends to leave your evenings consumed by reading literature, napping on the couch, or just generally decompressing. Or running columns (although--honestly--rarely is a column so important that you have to run it at 6 pm; if you do that frequently, chances are that you're just running away from having to do something else in your spare time that might make you an interesting person).<br>
<br>
So hobbies take effort. But so does exercise, and building relationships, and preparing nontoxic food, but they're worth it, and very important.<br>
<br>
If your labmates or PI ridicule you for having serious outside hobbies (such as coaching a sport, leading church discussion groups, running, brewing beer), then don't work with those people. Seriously. They're vultures.<br>
<i><br></i>
<i>External validation: </i>Not even kidding here--and maybe this is a sad reality--but getting published <i>as quickly as possible</i>, even as a minor author--is immensely helpful for buffering one's mental health. All it is is your name typed neatly into a PDF, but it's also a way to say "I was here. I did something. It's in PubMed now, so it's real."<br>
<br>
Again, easier said than done. But it's something to consider if you're prone to impostor syndrome: what's the best path to publication? Do you have a plan?<br>
<br>
If you're on a project that just isn't working (and hasn't been working for a long time), get another project with a more sure route to publication.<br>
<br>
<i>Have an exit strategy: </i>This might be the <b>biggest </b>contributor to mental health issues in people I know. And I think it's part of why the average path to PhD, as was mentioned in the previous post, is over 6 years. There's no clear indicator of what's "good enough" to graduate. And maybe because of a combination of impostor syndrome, a loss of direction, and thinking "well, everyone takes 6 years", many people just wait until late in their career to look towards the next step.<br>
<br>
I've seen several PIs whose philosophy is that when a student has secured their next position (postdoc, job, etc), he/she will facilitate their graduation as soon as possible. That seems like the best way to do it.<br>
<br>
Not every group is like that, though--and hence many people spend their time in a morass of career uncertainty. If you're ever had a full bladder during a seminar with a particularly long-winded presenter, it's the same idea. It's not the pressure, but the temporal uncertainty of the ending that is most discomforting.<br>
<br>
From my own personal experience, then, the biggest way to deal with the mental stress of grad school is this: <i>decide what variables you can change and where exactly you are taking yourself</i>. For me, this included pulling the plug on a high risk project, and more importantly, it also meant explicitly articulating an exit plan and reaching an understanding on this and my career goal with my PI.<br>
<br>
And it was an immense relief.<br>
<br>
Having a semi-defined end in sight and mind is invaluable (and something I've always envied of those in MBA, JD, DVM, or MD programs, even though those are more stressful in other ways).<br>
<b><br></b>
<b>The Grass Isn't Necessarily Greener</b><br>
<b><br></b>
Chemjobber--looking back on what you said about stress in industry (and about the outside world not being a panacea for mental health tribulations) also highlights something that is unhealthy among those of us in grad school.<br>
<br>
We tend to compare our situation to industry or to other fields (engineering, computer science, pharmacy, law). Usually that descends into "look at the benefits that X has", "look at the few hours that Y works", and "look how much Z gets paid".<br>
<br>
I think what we ignore is how politics driven nearly every career, scientific or not, academic or not, is. We assume that academia is the worst, because we came into academia with illusions of its nobility and vision, and then the curtain was pulled back.<br>
<br>
But my feeling is that the reality is this: it's rare, nowadays, for young professionals <i>not </i>to work extended hours. Maybe 80 hours a week isn't common, and maybe a lot of fields get more Saturdays. But my own parents worked Saturdays and 60+ hour weeks in their twenties--and they are in a business field. My feeling is that part of any professional's early career is learning how to maximize their productivity, deal with time management, and establish their value in the workforce. In grad school, we just do that for much less money.<br>
<br>
That's not the view I had two years ago, admittedly--at the time, I thought 60 hours a week was almost inhumane. That's changed somewhat. <br>
<br>
I write this as a large swath of the US is experiencing a spat of cold temperature (far below freezing, with high winds). I write it from an apartment that, even as a student, I can afford to keep heated, as I use a broadband internet collection to play music in the background. My tap water will not give me parasites. I will not likely be shot tomorrow--in fact, I might eat Chipotle. Some of the food in my fridge will likely expire before I can eat it, and that won't be a big deal for me, financially. I can put gas in my car and travel across several states to see family several times a year.<br>
<br>
The point is this: I am very thankful for what I do have, even if I'm working more hours than I would ideally like to, and if I go in on Saturdays. There's a lot of problems with grad school--power imbalances, careerism, politics--but it's not as bad as we sometimes make it out to be. Dwelling on the negatives, rather than changing what you can and accepting what you can't, is detrimental to mental health.<br>
<br>
Restated: the grass on the other side isn't necessarily as green as it looks, and the grass on this side isn't as brown.<br>
<br>
<b>Just Say "No" to Grad School</b><br>
<b><br></b>
Despite the coping strategies that I have and that I've seen people use, grad school <i>can </i>be too much. And that's okay--everyone's got different expectations and life goals. It simply doesn't make sense to stay in grad school if it's all a downhill slump.<br>
<br>
So that raises what I think is an important question (and one you, Chemjobber, mentioned in your post)--one that I think is worth wrapping up with. Actually, it's two questions:<br>
<br>
<i>How do you make a decision to leave or not leave grad school? </i>and <i>Should I go to grad school in the first place?</i><br>
<i><br></i>
They're related.<br>
<br>
I mentioned a second question--<i>Should I go to grad school in the first place? </i>I'll consider that one first.<br>
<br>
I don't think grad school is for everyone. I don't think grad school is for everyone <i>smart</i>, either. I don't think it's some pinnacle of achievement that puts PhD-holders on an intellectual plane above BS-holders. And I think going to grad school can be an incredibly unwise decision--and it shouldn't be undertaken lightly.<br>
<br>
As the posts and comments in the <a href="http://chemjobber.blogspot.com/2013/01/is-graduate-school-in-chemistry-bad-for.html">last mental health dialogue</a> made clear, <b>grad school can be very mentally and emotionally taxing</b>, And it is especially hard on those who are prone to burnout or mental health issues, which I suspect tend to be amplified in the academic environment (even in lower-hour groups). Be <i>very </i>sure.<br>
<br>
There are lots of bad reasons for going to grad school: not knowing what else to do, ego, thinking it's the path for smart people, not wanting a boss, thinking it's a land of total freedom, wanting to be called "Dr" (PhDs are NOT "real" doctors, and real doctors think it's very adorable when they assume they are), thinking it will be the path to increased riches, etc.<br>
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There are good reasons to go to grad school, of course, but one needs to be exceptionally sure of these. It's <i>half a decade</i>--at least--until the end. That's a lot of opportunity cost--and lost salary. It's sacrificing your twenties on the altar of science.<br>
<br>
As for the other question--<i>How does one know when to quit?</i> I've seen a lot of people who would be happier quitting grad school--but mostly, they don't. They don't out of pride, or inertia, or wanting the title, or being afraid of what others will think. Those aren't good reasons, but they are powerful ones. I've also seen people who think they would be happier quitting but are still driven for the job that the PhD will enable--it's probably worth it for them to stay in, due to the payoff in the long term.<br>
<br>
There's a concept in business decision-making known as "sunk costs". Put plainly, sunk costs have been incurred and thus can't change. In rational economic thinking, you shouldn't consider sunk costs in a decision--they're in the past, and only future costs/benefits--those you can change--are relevant from an objective decision-making standpoint.<br>
<br>
Behavioral economics suggests that people <i>do</i>--quite irrationally--weigh sunk costs. I had a community band director once who exemplified this. He paid quite a sum for a particular musical score. We hated it. He didn't care for it, either. But we played it every few months because he felt that he had "paid good money for it" and "didn't want it to go to waste."<br>
<br>
The same is true of grad students. There's a pervasive thought--"I've already put in 2 years, so it would be a waste of time to quit now." (Or however many years). But time already invested is a sunk cost. It doesn't matter how much time you've put in if you're not going to get anything out of the degree.<br>
<br>
Only three factors should matter when deciding whether to quit grad school:<br>
<br>
<ol>
<li>Am I happy right now? (Am I mentally healthy? Are there variables I can change about my current situation to make myself happier?)</li>
<li>What is the future benefit of me getting this degree <i>in comparison to not getting it? </i>(is it necessary for your career? Is it limiting?) </li>
<li>What am I missing out on by following through with grad school? (This is known as "opportunity cost" and includes the salary you could collect at a different job, time spent with friends, family, and your SO, traveling while young and unencumbered, etc). </li>
</ol>
<br>
If the answers to those aren't positive, there's no reason to stay.<br>
<br>
Quitting grad school is a really taboo subject--maybe even more so than mental health or the fact that academia is pretty rubbish at drug discovery. Why don't we talk about it more? Grad school should not be the only priority in one's life--and it's perfectly OK for it not to be the highest priority (although certain PIs may disagree).<br>
<br>
In the end, it shouldn't matter what colleagues think about whether one quits or not. What matters are the three questions above.<br>
<br>
I asked myself these recently. I was highly stressed, had seen a project burn, and had thought deeply about my life priorities. I didn't see myself as a good scientist, but as someone who could be a mediocre-to-decent pharmacy tech pretending to be a scientist. I was ready to pack up and leave and to take my chances on another career. I had my quitting speech rehearsed and had started the motions. I had strongly implied to several people that this was a sure thing.<br>
<br>
But I thought about it. I considered the factors above--thought about what I could change about my situation to make it work. I talked with some third parties both in and out of my desired career path. And I realized I needed the degree and the experience for what I wanted to do. I talked frankly with my PI, and he/she was supportive (surprisingly so) and understanding of my priorities and needs. And so I made the choice to stay on board, making the changes I needed to in order to be happy and productive.<br>
<br>
I hope it was the right decision. Maybe in 2 more years we can revisit this topic again and see.<br>
<br>
<br>
<i>To wrap up: thanks, Chemjobber, for the opportunity to revisit this topic. I felt our last dialogue on this was valuable and appreciated the insight from the numerous scientists who weighed in. Thanks for your perspective, and I hope you stay well. </i><br>
<i><br></i>
<i>Regards,</i><br>
<i><br></i>
<i>Vinylogous</i><br>
<br>
<br>vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com70tag:blogger.com,1999:blog-3474124548976938700.post-69765920350164477252015-01-06T05:30:00.000-06:002015-01-06T05:30:00.763-06:00Minty fresh terpenoids <div>
With the holidays concluding (and stocks of candy canes dwindling) it's natural to ask: what's the difference between spearmint, peppermint, and wintergreen flavorings? </div>
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Beyond the differences in their biological origin, various people have (not surprisingly) analyzed the constituents of the essential oils of each. </div>
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<b>Peppermint oil</b> (<i>Mentha </i>× <i>piperita L., </i>a cross between watermint, <i>Mentha aquatica</i>, and spearmint, <i>Mentha spicata</i>) has <a href="http://www.ncbi.nlm.nih.gov/pubmed/24965379">seasonal</a> and <a href="http://www.ncbi.nlm.nih.gov/pubmed/25493616">regional</a> <a href="http://www.ncbi.nlm.nih.gov/pubmed/22417540">variation</a>, but it is primarily a <a href="http://www.ncbi.nlm.nih.gov/pubmed/19768994">mixture</a> of menthol (>30%) and menthone (>15%, sometimes >30%). Also present are a <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0114767">large diversity of additional compounds</a>, including menthyl acetate, eucalyptol, limonene, beta-pinene, beta-caryophyllene, <i>trans</i>-carane, pulegone, (+)-carvone, and neomenthol. Some of these components (pulegone and menthofuran, for instance), are undesirable from flavor or toxicity standpoints, and have been the subject of <a href="http://www.ncbi.nlm.nih.gov/pubmed/21963983">metabolic engineering</a>. A sampling:</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh33qekWIYb89spkGxYl7DlrS9v-KXyaYAGSPu1AbArkWCEdYpZF0TTaLiCuEeTf3nEDITiurae3wmvtH0SeFwtG8rpwgEYKV5OVF_yV4HVaF8WBnFp0mNsvLN0g0svBqJSmGs-0Tf4VxA/s1600/peppermint.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh33qekWIYb89spkGxYl7DlrS9v-KXyaYAGSPu1AbArkWCEdYpZF0TTaLiCuEeTf3nEDITiurae3wmvtH0SeFwtG8rpwgEYKV5OVF_yV4HVaF8WBnFp0mNsvLN0g0svBqJSmGs-0Tf4VxA/s1600/peppermint.png" height="170" width="400" /></a></div>
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<b>Spearmint</b> comes from the essential oil of <i>Mentha spicata </i>and differs markedly from peppermint oil mostly in the relatively low abundance of menthol (<1%); it's <a href="https://books.google.com/books?id=BYPPEjWMOOQC&pg=PA406&lpg=PA406&dq=myrcene+spearmint&source=bl&ots=jv32qW53-y&sig=X3vUn0yvG_cdCqaV7BR7PflrJS0&hl=en&sa=X&ei=sLeoVPzLGsqLyATDkYGoAw&ved=0CCUQ6AEwAQ#v=onepage&q=myrcene%20spearmint&f=false">still</a> a <a href="http://www.sciencedirect.com/science/article/pii/S0926669008002355">complex</a> <a href="http://www.ncbi.nlm.nih.gov/pubmed/20942459">mixture</a>. The primary flavor component in this case is <i>R</i>-carvone (>50-75%). Limonene is more prominent than in peppermint. Other components include eucalyptol, <i>trans-</i>carveol, dihydrocarveol, caryophyllene, beta-bourbonene, linalool, beta-pinene, and germacrene D. </div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhRamo5QXX_o_vygYuu4_F1NDK_fuVNHfV7GYG9c7EuHJFabFkWp01V1uBa5QH8X7xq9iY1h7qqPj7JkMYXOgWns0k7l0DjaGhuIYoqK_0UPKn2nkkF4JIZcaC5aQPari3Q-a0lt2_IOic/s1600/spearmint.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhRamo5QXX_o_vygYuu4_F1NDK_fuVNHfV7GYG9c7EuHJFabFkWp01V1uBa5QH8X7xq9iY1h7qqPj7JkMYXOgWns0k7l0DjaGhuIYoqK_0UPKn2nkkF4JIZcaC5aQPari3Q-a0lt2_IOic/s1600/spearmint.png" height="192" width="400" /></a></div>
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<b>Wintergreen </b>(essential oil commonly from <i>Gaultheria procumbens</i>) is arguably <a href="http://www.scribd.com/doc/8726619/Analysis-of-Wintergreen-Oil">simpler</a> than either peppermint or spearmint and has a greater variety of sources. The chief flavor component here is methyl salicylate (a whopping ~98%), although one also finds limonene, myrcene, cadinene, carene, and pinene (alpha-pinene, in contrast to the predominantly beta-pinene in peppermint/spearmint).</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiO_Dzso0UME-s2RRfEpX9VO2ZFa8tKxV6DYdvkR32y-oMziTpwTAFWOccbgqRIPAUIhxY5ewoNGtau8Q-mn1ooZ2ClLCYjCrKbaqhh3MXdti0ERlBtkEkX6vwYBZV7NwBt0QZ_QBqsB_E/s1600/wintergreen.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiO_Dzso0UME-s2RRfEpX9VO2ZFa8tKxV6DYdvkR32y-oMziTpwTAFWOccbgqRIPAUIhxY5ewoNGtau8Q-mn1ooZ2ClLCYjCrKbaqhh3MXdti0ERlBtkEkX6vwYBZV7NwBt0QZ_QBqsB_E/s1600/wintergreen.png" height="90" width="400" /></a></div>
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For a really nice graphic of chemical compounds as flavor components in herbs and spices in general, see <a href="http://www.compoundchem.com/2014/03/13/chemical-compounds-in-herbs-spices/">this post at Compound Interest</a>. </div>
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All in all, terpenes are nice.</div>
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vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com35tag:blogger.com,1999:blog-3474124548976938700.post-27553729293588294072013-07-24T07:00:00.000-05:002013-07-24T07:00:00.584-05:00Sixteen ColumnsVittorio over at Labsolutely has a very clever and amusing post up <a href="http://www.labsolutely.org/2013/07/21/x-men-school-for-gifted-chemists/">re-imagining the X-Men as chemists</a>.<br />
<br />
So what other media genres share cross-over with our field?<br />
<br />
The modern art form deemed the "<a href="https://en.wikipedia.org/wiki/Chick_flick">chick flick</a>" shares key features with tactics used to recruit students into graduate school in chemistry. Namely: (1) hopelessly romantic view of the content; (2) focus on idolizing the celebrities of the subfield (<i>e.g. </i>Tom Hanks, Phil Baran); and (3) careful shielding of the subject from reality of life/lab. And of course, both chick flicks and science place an emphasis on diaries.<br />
<br />
In a salute to both, here are some chick flicks in the context of science:*<br />
<br />
<ol>
<li>How to Lose a Grant in 10 Days</li>
<li>Unemployed Going on 30</li>
<li>The Proposal</li>
<li>Never Been Published</li>
<li>27 Postdocs</li>
<li>What's Reproducibility Got to Do with It</li>
<li>The Devil Wears PPE</li>
<li>Sixteen Columns</li>
<li>My Best Friend's Defense</li>
<li>What PIs Want</li>
<li>Save the Last Authorship</li>
<li>Bridget Jones's Lab Notebook</li>
<li>When Harry Met Sally at an ACS Regional Meeting</li>
<li>The Lab Notebook</li>
<li>Out of Academia</li>
<li>Sleepless in Grant Season</li>
<li>The English Postdoc</li>
<li>Gloves Actually</li>
<li>How Stella Got Her Glassware Back</li>
<li>10 Things I Hate About U...niversities</li>
<li>Pride & PNAS</li>
<li>Crazy, Stupid, Reaction Mechanisms</li>
<li>Peggy Sue Got Funded</li>
<li>P.S. I Love the Combiflash</li>
<li>Flashcolumn</li>
</ol>
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<span style="font-size: x-small;">* Note: these are in no particular order; the author claims no expertship on relative merits of chick flicks.</span><br />
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<br />vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com17tag:blogger.com,1999:blog-3474124548976938700.post-42743225116292765152013-07-11T00:08:00.000-05:002013-07-11T00:08:09.953-05:00Why Steve Strauss should stop hiring English majors and hire some scientists insteadRecently, a few people I know shared <a href="http://www.huffingtonpost.com/steve-strauss/hiring-english-majors_b_3484409.html">this column</a> on Facebook. Written by Steve Strauss, a lawyer/author and self-described "small business expert", the short piece from the Huffington Post makes the case that English majors are pretty much the bee's knees. Strauss prefers to hire English majors for a variety of roles, as he explains:<br />
<blockquote class="tr_bq">
I love English majors. I love how smart they are. I love their intellectual curiosity. And I love their bold choice for a major. Most of all, I love to hire them. </blockquote>
<blockquote class="tr_bq">
A <a href="http://www.huffingtonpost.com/steve-strauss/www.nytimes.com/2013/06/21/opinion/brooks-the-humanist-vocation.html?src=me&_r=0">recent article</a> by the great David Brooks in the New York Times about the changing nature of the Humanities in higher education just reinforced why, when given my druthers, English majors are my employee of choice. </blockquote>
<blockquote class="tr_bq">
And the reason is not that I am a writer; I more consider myself an entrepreneur than anything else. I run a small business and the people I hire do a variety of tasks -- SEO, project management, social media, and so forth. </blockquote>
<blockquote class="tr_bq">
For my money (literally and figuratively), for my needs, and I suggest the needs of most small businesses, English majors are easily the top choice when it comes to getting the type of teammate who can make us all better, as they say in basketball.</blockquote>
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Strauss goes on specify some key traits apparently endemic to the English major population. These are: (1) English majors are smart and creative independent thinkers, more so than business majors; (2) English majors are bolder risk-takers than others; (3) English majors are always better writers; and (4) English majors are easy to work with.</div>
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I suspect many scientists will disagree. I take issue with the broadness of Strauss's assertions--though he never claims to have broadly surveyed skillsets of humanities scholars, his descriptors read like mere feel-good fluff. Yes, there are English majors who have those characteristics, and many English majors are successful. But "rigor" and "difficult assignments" are not essential traits of the undergraduate English experience. While English may <i>allow </i>deep thinking, it doesn't absolutely require it, and it's certainly easier to skate through an English degree than, say, one in chemical physics or organic chemistry.<br />
<br />
You see more chemists who also know literature than you see literary analysts who know molecular orbital theory. But isn't that just because science is more <i>specialized</i>? Well, yes and no. Individual fields of science certainly have their own jargon, methodology, and bodies of knowledge. But the scientific process is fairly universal, and you see people switch fields in their BS/PhD and PhD/postdoc transitions.<br />
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That all sounds harsh, of course, and borders on the increasingly-prevalent-but-misguided attitude of "cut the humanities, boost only employable fields". So to clarify: I like the humanities. I really do. I've always enjoyed literature and music (both production and consumption), and I think their study is vital for making a person more culturally aware and well-rounded. I have opinions on writers and composers. I was one of <i>those</i> people who didn't whine about general-education requirements interfering with "real" coursework. But assigning top general employability status to English majors overlooks a key group of students who, when successful, possess all the abovementioned skills <i>and more</i>: science majors.<br />
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<b>The case for hiring science majors</b><br />
<b><br /></b>
As previously mentioned, Strauss touted the creativity of English majors and their ability to think analytically. Creativity is essential to good science as well; skilled researchers tend to be creative people who see alternate ways to solve problems. Moreover, scientists find solutions that <i>work</i>, based on reality and reproducibility<i>. </i>This clarification is important, because "analysis" means very different things in scientific and non-scientific circles. However, scientists are quite good at two things: (1) finding information; and (2) evaluating information.<br />
<br />
Strauss also claims English majors are superior risk-takers. But scientists are too. They have to be. Good research is always at the edge of knowledge--which means it might not work. Bench time might be wasted. A six-year PhD might produce no results and lead to no job. Ideas might get defunded and banished to obscurity. Going to grad school is a tremendous risk. So is working for an untenured professor, or starting a brand-new project. So the advantage here again goes to scientists. Additionally, scientific risk-taking is grounded in reality--helpful for businesses.<br />
<br />
What other employable traits do scientists tend to have?<b> Work ethic</b>: long hours are the norm and determination over long periods of time (ca. 5 years) is required. <b>Versatility</b>: the scientific method is employable between variant research areas but also to management and business decisions. <b>Technical skills</b>: this probably goes without saying, but intimate knowledge of scientific theory and technique isn't easily gleaned from Google. Even in non-bench roles, this can be quite important. <b>Teamwork</b>: whereas writing English papers is a solitary venture, lab research is done in groups, and collaboration between students and labs on the experiment or project scale is commonplace. <b>Objectivity</b>: whereas the humanities stress the voice and identity of the individual (subjectivity), science emphasizes minimization of bias. This is useful in risk assessment, evaluation, project design, etc.<br />
<br />
All in all, I think science majors sound pretty employable.<br />
<br />
<b>What we can learn from our English-wrangling colleagues</b><br />
<br />
The claim about English majors being superior writers is also worth examining. Do English majors write? Yes. Do they write a lot? Most of them. Do they write well? The good ones write <i>academic papers</i> well, but an increased vocabulary and flowery verbiage doesn't mean <i>good communication</i>. Of course, many English majors are good communicators, but the degree doesn't guarantee that. And not having an English degree doesn't mean you can't write just as well as someone who has one.<br />
<br />
It's worth noting that significant differences exist between scientific/technical and academic (non-scientific) writing. In another life, I worked closely with undergraduate writing tutors. Most were English majors, and as a lot they were very intelligent. But all of them were horrid at actually helping science students improve their communication skills. The result was a continuous stream of frustrated chemistry students with half-mangled lab reports. The writing process is fundamentally different across the humanities/science divide, which makes me skeptical that the garden-variety English major would be good at writing in a technical or scientific context (where content is highly specific, highly technical, and verbal economy is vital). Some are good at it, but it's not because of Chaucer.<br />
<br />
That being said, scientists themselves are very commonly <i>awful </i>writers. Those who deny this or think it's not important are simply either ignorant or delusional. Then again, scientists are perhaps more likely to be blunt and direct, which has its appeal. Regardless, it's probably good for budding scientists to take all the writing experience they can get and to pay attention not only to the facts of what they write but the organization and presentation. Clear communication makes ideas easier to sell, cuts down on wasted time, and improves work efficiency. The ability to write well (more than just <i>JACS </i>communications) can be a huge selling-point when building an employment skillset, as it extends to grants, business proposals, technical reports, and intellectual property claims. <br />
<br />
<b>A final anecdote</b>.<br />
<br />
A friend of mine switched from pre-med to business during undergrad and found himself in a business database systems class. The class entailed a team-based project wherein each group of students needed to create a database system for a local business. Several of the born-and-bred business majors insisted that the class was probably the most difficult in the university. Having taken two years of pre-med coursework, my friend pointed out the difficulty and rigor in the hard sciences, especially in independent research. <i>Oh, no way</i>, the business majors insisted, <i>scientific research is just following recipes</i>.<br />
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The piece is short, so it's worth reading. Do also peruse the comment section, which is rife with people praising Strauss's words and/or correcting each others' grammar/diction. </div>
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vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com27tag:blogger.com,1999:blog-3474124548976938700.post-44386700071402865062013-06-25T07:00:00.000-05:002013-06-25T07:00:00.891-05:00Stop using that word: AccordanceConsider "accordance". It's a sleek, shiny word. But it's terribly misused in scientific manuscripts.<br />
<br />
To pick on just one example, take the following text from a <a href="http://pubs.acs.org/doi/abs/10.1021/ja4031193">recent publication</a> by <a href="http://www.kelleher.northwestern.edu/">Neil Kelleher's group</a> at Northwestern (bold emphasis mine):<br />
<blockquote class="tr_bq">
<b>Our observations were in accordance with a previous study</b> on nostocyclopeptide, where certain amino acids in the peptide sequence were found essential for the spontaneous macrocyclization of the peptidyl aldehyde intermediate into a cyclic imine.</blockquote>
And another example from <a href="http://pubs.acs.org/doi/full/10.1021/ja4012468">a total synthesis</a> of daptomycin by Xuechen Li:<br />
<blockquote class="tr_bq">
The spectrum was in full accordance with those in the literature.</blockquote>
Not quite right.<br />
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"Accord" implies <a href="http://www.merriam-webster.com/dictionary/accord">agreement</a>. It's what writers usually <i>mean</i> when they use "accordance". For instance:<br />
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His dismal personal life was<b> in accord </b>with his excellent progress in total synthesis.</blockquote>
"Accordance", in contrast, implied obedience. It refers to <a href="http://www.merriam-webster.com/dictionary/accordance">compliance with a rule</a>.<br />
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My one day of vacation per year is <b>in accordance </b>with group policy.</blockquote>
Examples of the correct use of "accordance" are actually hard to find. Consider <a href="http://pubs.acs.org/doi/full/10.1021/ja312222k">this paper</a> by <a href="http://www.chem.wisc.edu/~osirc/">Robert West at Wisconsin</a>. An excerpt (bold emphasis mine):<br />
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<b>In accordance with Bent’s rule</b>, the increased R–O bond polarities of permethylated species lead to increased oxygen hybrid s-character and R–O–R bending angles in both ethers and siloxanes.</blockquote>
That one is arguably correct.<br /><br />The difficulty is probably that "in accord with" doesn't flow quite smoothly. Perhaps a better option would be simply to say "in agreement with". Either way, reviewers probably won't catch it.<br />
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This has been a public service announcement.vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com11tag:blogger.com,1999:blog-3474124548976938700.post-14905436809682045042013-06-20T07:00:00.000-05:002013-06-20T07:00:00.767-05:00Carbenes: turns out, nature has them, tooEnzymes are like nature's little <a href="http://en.wikipedia.org/wiki/Glovebox">gloveboxes</a>. It's really quite interesting what kind of chemistries are possible in aqueous, biological conditions just by manipulation of the local electronic and steric environment by the structure of enzymatic active sites.<br />
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Take <a href="http://en.wikipedia.org/wiki/Carbene">carbenes</a>. Everybody likes a carbene--it's a lone pair on carbon, but it's formally neutral, and it does interesting reactions like alkene insertion (cyclopropanation), C-H insertion, rearrangements, and the like.<br />
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One of the more interesting aspects of carbenes is their variable reactivity. They can exist in a singlet (depicted as lone-pair) or triplet (depicted as diradical) form. Depending on their electronic environment, they can react as nucleophiles (aided by a high-lying HOMO) or electrophiles (encouraged by lowering the LUMO). Their reactions can be stereospecific through concerted pathways (singlet carbenes) or non-stereospecific through stepwise mechanisms (triplet carbenes). All of this is tuned, not surprisingly, through the electronic/steric environment around the carbon in question.<br />
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Carbenes are typically highly reactive and short-lived, though examples of persistent carbenes are now well-known. <i>N</i>-heterocyclic carbenes (NHCs) make a prime example. The electron-rich di-adamantyl NHC shown above, for instance, <a href="http://pubs.acs.org/doi/abs/10.1021/ja00001a054">was described in 1991</a> and can be crystallized (it melts, by the way, at 240 degrees Celsius).<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhczUpvzTUJ8ttu1-W_SMtqIKm3vc1ZOYm-Dc3aT0Rcv7dPK7KznXyrDkn__BpCDUFSVT1aJvNPbP0pBM6VjvsMMytyRch0ZMLVQP4RHhLJYhT99MpXi03W0AnlkN06B08cUwgHg1wFu8/s1600/grubbs.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhczUpvzTUJ8ttu1-W_SMtqIKm3vc1ZOYm-Dc3aT0Rcv7dPK7KznXyrDkn__BpCDUFSVT1aJvNPbP0pBM6VjvsMMytyRch0ZMLVQP4RHhLJYhT99MpXi03W0AnlkN06B08cUwgHg1wFu8/s200/grubbs.png" width="181" /></a></div>
Note the electronic nature of the carbene: the carbon is flanked by two nitrogens, each bearing lone pairs capable of donating electron density into the carbene's <i>p </i>orbital. This acts to stabilize the singlet state and imbues NHCs with admirable properties as metal ligands (electron rich sigma donors which bond quite strongly to metal centers) The most famous of these is probably <a href="http://www.blogger.com/"><span id="goog_1185297749"></span>Grubbs' second-generation catalyst<span id="goog_1185297750"></span></a>, which bears an NHC in lieu of one of the phosphine ligands of the first-generation counterpart. Besides <a href="http://en.wikipedia.org/wiki/Olefin_metathesis">olefin metathesis</a>, though, persistent carbenes (as NHCs) are quite useful ligands for tricky C-C cross-couplings. Specifically, the <a href="http://onlinelibrary.wiley.com/doi/10.1002/ejoc.201000359/pdf">so-called Pd-PEPPSI complexes</a> are useful for coupling of <i>tetrahedral</i> carbon centers to each other.<br />
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It turns out that nature utilizes carbenes as well. Take a look at vitamin B1--also known as thiamin. It's an essential coenzyme which, as it turns out, we can't make and must obtain in our diet. There's several forms consisting of various decorations, usually of the hydroxyl moiety. One of these is <a href="http://en.wikipedia.org/wiki/Thiamin_diphosphate">thiamin diphosphate</a> (ThDP), which, if you didn't guess, is thiamin with diphosphate attached (it also goes by the name thiamin pyrophosphate, or TPP, which is definitely not confusing at all). ThDP is a coenzyme for <a href="http://en.wikipedia.org/wiki/Pyruvate_decarboxylase">pyruvate decarboxylate</a> and <a href="http://en.wikipedia.org/wiki/Pyruvate_oxidase">pyruvate oxidase</a>, among <a href="http://www.teed.uni-stuttgart.de/cgi-bin/new_THDP/index.pl">other</a> enzymes.<br />
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If you look at thiamine, there's a place--right between that sulfur and its neighborly nitrogen--that seems like a nice candidate for a carbene. There's been a debate in the literature; that carbon must be deprotonated for catalytic activity, and it hasn't been clear whether the associated enzymatic reaction proceeds via a carbanion or the <a href="http://www.sciencemag.org/content/276/5314/942">short-lived carbene</a>. A recent report in <i>Nature Chemical Biology</i> <a href="http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.1275.html">provides evidence for the latter</a>. The authors examined thiamin diphosphate with the enzyme pyruvate oxidase (from bacterial origins). Phosphate was employed as a mimic of the substrate (pyruvate) that would bind similarly but not form a covalent adduct--this was to see if substrate binding might correspond with the formation of a carbene.<br />
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Via <a href="http://en.wikipedia.org/wiki/Circular_dichroism#Application_to_biological_molecules">circular dichroism</a> (CD), and <a href="http://en.wikipedia.org/wiki/X-ray_crystallography">X-ray diffraction</a>, the authors give evidence that although the coenzyme is <i>C</i>-protonated in its resting state, binding of phosphate results in accumulation of either the carbanion/carbene form. This is narrowed down to the carbene chiefly through analysis of the XRD structure. Not only was the electron density consistent, but the bond lengths and angles were similar to synthetic thiazolium carbenes previously reported. The authors mention similar results upon <a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2012.08513.x/abstract">analysis of the ThDP/cyclohexane-1,2-dione hydrolase complex</a>.<br />
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Essentially, under physiologically relevant equilibrium conditions, the thiamine/enzyme complex can <i>accumulate </i>a carbene. In water. That's quite cool.vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com30tag:blogger.com,1999:blog-3474124548976938700.post-78599494875257864982013-05-22T07:30:00.000-05:002013-05-22T07:30:00.725-05:00Academic salaries: some numbers and graphsThe topic of academic salaries came up recently and I figured I'd look a little further. Where does chemistry stand? After all, jobs are scarce--how do academic positions pay compared to other disciplines?<br />
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Lots of resources exist for salary issues that are much more data-thorough, so take the following numbers with a grain of salt. For more in-depth info, a few resources include<a href="http://www.higheredjobs.com/salary/"> HigherEdJobs</a>, <a href="http://chronicle.com/article/Faculty-Salaries-Vary-by/127073">The Chronicle of Higher Education</a>, or a <a href="http://lmgtfy.com/?q=academia+salaries+by+discipline">web search</a>.<br />
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I took a (somewhat) random single institution (<a href="http://en.wikipedia.org/wiki/Bowling_Green_State_University">Bowling Green State University</a>, Ohio) of medium size (ca. 15,000 undergraduates) that also offers graduate degrees (in <a href="http://www.bgsu.edu/departments/chem/graduate.html">chemistry</a>, an M.S. in chemistry and a Ph.D in photochemical sciences are available). Ohio was chosen as an example state simply because of the ready availability of data.<br />
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Salary information (for a few years back) is available for all Ohio's higher ed institutions through the <a href="http://www.buckeyeinstitute.org/higher-ed">Buckeye Institute</a>. I grabbed the 2010 info for the university and present below the averages for four standard academic ranks (lecturer/instructor, assistant professor, associate professor, and full professor) across 14 broad but somewhat arbitrarily chosen disciplines. Standard deviations aren't included and sample sizes were small in some cases, so <i>caveat emptor</i> and all that. (<i>NB</i>: click any chart for a larger view)<br />
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First, a graph of the disciplines ranked by associate professor salaries. It's quite interesting to me that chemistry is near the top--ahead of biology but also physics and geology. Moreover, associate professor salaries in chemistry rank a little short of computer science (by about $7,000) but <i>above</i> economics (by about $8,000). As would probably be expected, two business disciplines (management and accounting/M&IS) are way ahead. I don't know if that's endemic to the particular school or a general trend. Regardless (and probably again to no one's surprise), it looks like chemistry and the other sciences are pretty far ahead of the humanities by as much as business-related fields are ahead of science.<br />
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Ranking by full professor puts chemistry more in the middle of the pack:<br />
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Quite interestingly, though, are the salaries for assistant professor positions (typically the first 3-6 years of an academic appointment). Here the distribution is almost bimodal, with chemistry falling in a group ranging from about $50,000 to $66,000. Then there's a $24,000 jump to the business disciplines and computer science, which compensate assistant professors on average from $89,000 up to a whopping $119,000! (For the math-challenged organic chemists, that's about <b>double</b> the chemistry salary for the first five years).<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhmbvlPNNBxBqhX8REDIIE6DjpNESGrLX1z5LHhZ397uqAIZdWdqQsMke6f1dCrzvolYTR_cPMp8_st__4yaCNVi5TaMxcuuYXP6IUrarI4WlsOtPBemu_BtdAJjPU_DAb6-cURrVCF9RU/s1600/assistant-salary.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="235" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhmbvlPNNBxBqhX8REDIIE6DjpNESGrLX1z5LHhZ397uqAIZdWdqQsMke6f1dCrzvolYTR_cPMp8_st__4yaCNVi5TaMxcuuYXP6IUrarI4WlsOtPBemu_BtdAJjPU_DAb6-cURrVCF9RU/s400/assistant-salary.png" width="400" /></a></div>
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Why the giant divide? Market demand certainly plays a large role. Folks with graduate-level business and computer science skills are very, very employable, and generally aren't in markets plagued by the oversupply that science (and especially the humanities) face.<br />
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Lastly, check out the ranked salaries for instructors/lecturers. These are the teaching-only positions; for some disciplines this doesn't require a PhD. (For chemistry, I've seen very few lecturers <i>without </i>PhDs; many have postdoc or industrial experience).<br />
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Management here has the highest salary by far, but that's incidentally an <i>n = </i>1 type scenario (there's only one lecturer in the management department, and they appear have an 'executive' position). Here the business gap disappears; average salaries range from $38,000 to $52,000. Interestingly, computer science ranks in at $61,000, which is probably indicative of its <i>very </i>high employability--you have to pay someone a lot to draw them away from an attractive industry job.<br />
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For fans of seeing-it-all, here's a ranked-by-associate graph including all four ranks.<br />
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Lastly, here's the average salaries for most of the public university chemistry departments in that particular state (Ohio) [note--data was not easily harvestable for Ohio University, Shawnee State, Central State, or Youngstown State].<br />
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This itself is somewhat interesting, as there's a wide distribution (assistant ranges from an average of $55,000 to $78,000; associate from $70,000 to $97,000; full professor from $101,000 to $131,000). Moreover, salary averages don't appear to correlate to institutional prestige (<i>cf</i>. Ohio State and University of Akron, for instance) nor to cost-of-living.<br />
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The ordering of schools even changes by faculty rank--Cleveland State tops out the assistant professor category, but Bowling Green wins for associate professor and University of Toledo for full professor. The only consistent element, it seems, is that Kent State pays the lowest for chemistry professors, across the board, of all the state schools shown.<br />
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Again, take all this data with a grain of salt; I just think it's interesting stuff.vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com25tag:blogger.com,1999:blog-3474124548976938700.post-16447858910675781292013-04-27T20:45:00.001-05:002013-04-28T12:24:44.783-05:00The Office and the labJust as the <a href="http://justlikecooking.blogspot.com/2013/04/chemmoviecarnival-closing-credits.html">#ChemMovieCarnival drew to a close</a>, chemistry made another appearance on national television!<br />
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In the most recent episode of <i>The Office </i>(a mockumentary about a paper company; it's usually hit-or-miss but still funnier than the British version*)<i>, </i>the branch manager, Andy Bernard, was cast in a chemical safety video ("HRPDC Chemical Handling Protocol") in an attempt to break into an acting career.<br />
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The on-screen lab was pretty clearly a molecular biology or chemical biology space -- you can see microscopes, centrifuges, Pipetmans,** a cold-room, 96-well plates, and plenty of buffers; additionally, the glassware is largely Erlenmeyers, graduated cylinders, and volumetric flasks.<br />
<br />
Unlike most featured lab spaces on TV (we're looking at <i>you</i>, NCIS and CSI...), it looks like the producers used an <i>actual lab. </i>If not an actual lab, it's a very good replica (as evidenced by the abundant bench clutter).<br />
<br />
For the sake of the chemical community, I present a graphical abstract below.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg99uEsmi63Yz_AYbrLbI-AQJCqVc5Yl408GkuWXCYQ0dxHDf0lsduoczXi_L1zSzC3WjrHzV0cPLtT87LNsVziRuzGNy2wAhCVVwt78X0UdQnCgxK1QqDiOtqMpN5p-mTn0oun90oPeOY/s1600/office-1.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="223" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg99uEsmi63Yz_AYbrLbI-AQJCqVc5Yl408GkuWXCYQ0dxHDf0lsduoczXi_L1zSzC3WjrHzV0cPLtT87LNsVziRuzGNy2wAhCVVwt78X0UdQnCgxK1QqDiOtqMpN5p-mTn0oun90oPeOY/s400/office-1.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Drying rack contains an appropriate mix of glassware.</td></tr>
</tbody></table>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgdmt9g7QONthER2E9KgIT8cJGJ1H4kworzbNfmh-mq9QHYFhIWaq0U7Qi07GInmjLyQgEJ8igkY8Og2Mpzs6m3Akb4WGl1eFKZ1A5aqgO4_FGaijXXIW5ab75Spc7GNzsvS2k-_aVUCSY/s1600/office-2.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="223" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgdmt9g7QONthER2E9KgIT8cJGJ1H4kworzbNfmh-mq9QHYFhIWaq0U7Qi07GInmjLyQgEJ8igkY8Og2Mpzs6m3Akb4WGl1eFKZ1A5aqgO4_FGaijXXIW5ab75Spc7GNzsvS2k-_aVUCSY/s400/office-2.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption">What lab would be complete without an egregious safety violation? <br />
(note the presence of snacks in the lower left corner<span style="font-size: x-small; text-align: start;">)</span></td></tr>
</tbody></table>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiCqI44-EDCobVwRUc2XFKWYXXJA4gVMAI5mjgsdjBkMJIdGVMojq0klR9h9oa9JjekW67g2PCq_Koh6OUhclRiggAhyio6AoguQmCZJD3XiDD0edmTOHYUNiV42WVPnUD1Qapv1Vg6Szc/s1600/office-3.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiCqI44-EDCobVwRUc2XFKWYXXJA4gVMAI5mjgsdjBkMJIdGVMojq0klR9h9oa9JjekW67g2PCq_Koh6OUhclRiggAhyio6AoguQmCZJD3XiDD0edmTOHYUNiV42WVPnUD1Qapv1Vg6Szc/s400/office-3.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Benchtop clutter looks about right.</td></tr>
</tbody></table>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijOlqka4VaLzTVAgslAeob2s1ufl8_LNoPNYavisM58Yw49dQbbGDTe2OTgVmCscUq_F0uH9QKHjkKZyjOWnEFyOP2A3CRnBgHUedVnFludWZtlNHRSu5TZZR0BcancLtiXITOboLmxYo/s1600/office-4.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="221" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijOlqka4VaLzTVAgslAeob2s1ufl8_LNoPNYavisM58Yw49dQbbGDTe2OTgVmCscUq_F0uH9QKHjkKZyjOWnEFyOP2A3CRnBgHUedVnFludWZtlNHRSu5TZZR0BcancLtiXITOboLmxYo/s400/office-4.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Note the scientist in the far background using proper PPE.</td></tr>
</tbody></table>
<div class="separator" style="clear: both; text-align: center;">
</div>
\<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj5YfOJ9FSnbODSpNkytNY6Y3NxgFYdb_dT6HpMbW9xsSjTVsqcxqICCsJhmTjHGAUbr47gFk6HRQiNfUOiH0GYjxWbmtYY_ijW6amNhtiKR3XxVEjA__Svl80SA-yVV-4nM6kN9Acsv0o/s1600/office-5a.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="221" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj5YfOJ9FSnbODSpNkytNY6Y3NxgFYdb_dT6HpMbW9xsSjTVsqcxqICCsJhmTjHGAUbr47gFk6HRQiNfUOiH0GYjxWbmtYY_ijW6amNhtiKR3XxVEjA__Svl80SA-yVV-4nM6kN9Acsv0o/s400/office-5a.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Demonstration of eyewash station use, plus screaming.</td></tr>
</tbody></table>
Note that undergraduates usually have the same aversion to the eyewash station that Andy Bernard does.<br />
<br />
And my favorite exchange of dialogue:<br />
<br />
<blockquote class="tr_bq">
Director 1: Okay, stop. Why are you smiling?<br />
Andy: I just made a character choice to be a scientist who really likes what he does and enjoys his job.<br />
Director 2: Okay, well, maybe no smiling on this one.</blockquote>
<br />
<br />
<span style="font-size: x-small;">* Note: some people get really upset when you say this to them. Try it!</span><br />
<span style="font-size: x-small;">** I love me some Pipetmans.</span>vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com8tag:blogger.com,1999:blog-3474124548976938700.post-22163655801654487812013-04-24T21:21:00.001-05:002013-04-24T21:21:51.031-05:00Chemical Fun from 1921What's more fun than historical documents? Historical <i>chemistry </i>documents! From one such document: the following tongue-in-cheek paragraph appeared in the April edition of the briefly-published and mostly-otherwise-serious <a href="http://www.library.illinois.edu/imay/">quarterly departmental (U of I) magazine</a> <i>The Illinois Chemist </i><b>1921</b>, <i>5</i>(3), 12.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiN03PDYZyzaDV-J2YakY-fNo1jsKR2aZqpajJb1Ad0oYqnDfxznInrBtmihkcQrWvM8jZZikL_kGdCP4g22XO40KKO_6-7q70yet89hTkvK1GMA5loBmqdCn8WSH0Rx9gmEjLE9TNysJw/s1600/chemicalFun.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="148" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiN03PDYZyzaDV-J2YakY-fNo1jsKR2aZqpajJb1Ad0oYqnDfxznInrBtmihkcQrWvM8jZZikL_kGdCP4g22XO40KKO_6-7q70yet89hTkvK1GMA5loBmqdCn8WSH0Rx9gmEjLE9TNysJw/s400/chemicalFun.jpg" width="400" /></a></div>
<br />
The text (written out):<br />
<br />
<blockquote class="tr_bq">
CHEMICAL FUN. Procedure (to be followed with extreme carelessness): Select several choice cut medium sized hydrogen ions from a bottle and scour until thoroughly clean. Wipe and dry carefully. Avoid handling. Lay aside. Now soak a few large chunks of metallic sodium in a beaker of distilled water and allow to stand quietly. In the meantime be collecting a pailful of cathode rays. Filter these, using suction. Beat them to a froth with two and three-quarters pounds of green radium (the red variety is highly unsuitable for this experiment). Now stir in the hydrogen ions, one at a time. Drain the sodium and put it in above mixture. Grind up with T. N. T. and put in a mortar and add all at once. Thus the mixture will become catalyzed. -- Voodoo, M. I. T.</blockquote>
<br />
Chemical fun, indeed. Sounds like a job for <a href="http://blog-syn.blogspot.com/">Blog Syn</a>!<br />
<blockquote class="tr_bq">
</blockquote>
vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com6tag:blogger.com,1999:blog-3474124548976938700.post-22732678476569556302013-04-18T22:53:00.003-05:002013-04-18T22:53:35.998-05:00#ChemMovieCarnival: Chocolate and chemical academiaIt's time for the <a href="http://justlikecooking.blogspot.com/2013/04/chemistry-at-movies-blog-carnival.html">#ChemMovieCarnival</a>, as organized by See Arr Oh (who posted <a href="http://justlikecooking.blogspot.com/2013/04/chemmoviecarnival-aaaand-action.html">this first day round-up</a>). So far we've seen chemistry featured in <a href="http://cenblog.org/newscripts/2013/04/chemmoviecarnival-dramatic-acid-base-chemistry-in-fight-club/">Fight Club</a>, <a href="http://www.thecollapsedwavefunction.com/2013/04/bad-science-ironman-2.html">Iron Man 2</a>, <a href="http://chemjobber.blogspot.com/2013/04/chemmoviecarnival-great-escape-or.html">The Great Escape</a>, <a href="http://cenblog.org/just-another-electron-pusher/2013/04/chemmoviecarnival-the-absent-minded-professor/">The Absent Minded Professor</a>, <a href="http://behindnmrlines.blogspot.co.uk/2013/04/chemistry-at-movies.html">G.I. Joe</a>, <a href="http://chemjobber.blogspot.com/2013/04/sarah-cady-on-chemmoviecarnival-real.html">Real Genius</a>, and <a href="http://www.labsolutely.org/2013/04/17/lets-macgyver-it/">MacGyver</a>, among others.<br />
<br />
Some of the above examples highlight some pretty bad movie science. I thought I'd share a movie clip that was on the other end of the spectrum!<br />
<br />
Everyone's familiar with Willy Wonka and the Chocolate Factory--the 1971 musical film starring the immortal Gene Wilder. The film's protagonist is Charlie Bucket, a child from a poor family whose genuine heart leads him to success where several other spoiled/privileged children fail. Early on, we're shown Charlie's education, including the following chemistry demonstration. The clip is a <i>little </i>modified from the original at the end (it was the only one I could find!).<br />
<br />
<iframe allowfullscreen="" frameborder="0" height="315" src="http://www.youtube.com/embed/Zh6EXnZ-Yjg" width="560"></iframe><br />
<br />
It's a remarkably accurate portrayal of life in chemical academia. After all, all the hallmarks are there:<br />
<br />
<ul>
<li>Disregard for proper PPE/lab safety.</li>
<li>Intellectual snobbery/faculty egotism.</li>
<li>Over-eager undergrads who don't know what they're doing.</li>
<li>Secrecy and irreproducibility.</li>
</ul>
<div>
<br /></div>
<div>
Just like life in the lab! (Of course, <i>Pure Imagination </i>is perhaps more apt to describe the pragmatism of many projects).</div>
vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com8tag:blogger.com,1999:blog-3474124548976938700.post-23545384922052446652013-04-18T07:00:00.000-05:002013-04-18T07:00:00.095-05:00Carrots, chlorine, and chemophobia<div class="tr_bq">
On a recent lunchtime "survey of the literature" (<i>i.e. </i>Facebook break) I noticed that an old classmate posted the following paragraph (it's not new--but I hadn't seen it before):</div>
<br />
<blockquote>
<div style="text-align: justify;">
“DANGER TO YOUR FAMILY!!</div>
<br />
<div style="text-align: justify;">
From the Department of Life Education:</div>
<br />
<div style="text-align: justify;">
Baby Carrots:</div>
<br />
<div style="text-align: justify;">
The following is information from a farmer who grows and packages carrots for IGA, METRO, LOBLAWS, etc.</div>
<br />
<div style="text-align: justify;">
The small cocktail (baby) carrots you buy in small plastic bags are made using the larger crooked or deformed carrots which are put through a machine which cuts and shapes them into cocktail carrots – most people probably know this already.</div>
<br />
<div style="text-align: justify;">
What you may not know and should know is the following:</div>
<br />
<div style="text-align: justify;">
Once the carrots are cut and shaped into cocktail carrots they are dipped in a solution of water and chlorine in order to preserve them (this is the same chlorine used in your pool).</div>
<br />
<div style="text-align: justify;">
Since they do not have their skin or natural protective covering, they give them a higher dose of chlorine.</div>
<br />
<div style="text-align: justify;">
You will notice that once you keep these carrots in your refrigerator for a few days, a white covering will form on the carrots. This is the chlorine which resurfaces. At what cost do we put our health at risk to have esthetically pleasing vegetables?</div>
<br />
<div style="text-align: justify;">
Chlorine is a very well-known carcinogen, which causes Cancer. I thought this was worth passing on. Pass it on to as many people as possible in hopes of informing them where these carrots come from and how they are processed.</div>
<br />
<div style="text-align: justify;">
I used to buy those baby carrots for vegetable dips. I know that I will never buy them again!!!!”</div>
</blockquote>
<br />
<div>
First, it should be noted that the person who shared the post works in a biomedical profession and <i>probably </i>should know better. Second, this looks like a classic chemophobic recipe: (1) take familiar concept; (2) point out chemical; (3) extol nastiness of chemical, real or imaginary; (4) panic.<br />
<br />
It should be pointed out, of course, that the "warning" is alarmist and exaggerated. Most fruits/veggies are rinsed in water containing low-ppm chlorine -- levels comparable to drinking water -- not in a highly-chlorinated solution as implied. Chlorine is an antimicrobial protectant in thse cases. Moreover, the white residue is, obviously to chemists, not chlorine 'resurfacing' (???) but simply dehydrated carrot. And something that needs mention: <i><b>there's no evidence that chlorine is a carcinogen</b> </i>(see <a href="http://www.cancerwa.asn.au/resources/cancermyths/chlorine-cancer-myth">here</a> and <a href="http://toxnet.nlm.nih.gov/cpdb/chempages/CHLORINE.html">here</a> for instance)<i> </i>(You wouldn't want to go on a date with pure chlorine, of course, but not because of a cancer danger).<br />
<br />
The chemophobia doesn't surprise me, though, since "chlorine" sounds nasty.<br />
<br />
I am surprised, however, by some of the responses on the internet. They're unusually fact-based! In fact, in the first two pages of Google search results for "baby carrots chlorine", only a few support the myth. But let's look at the chemophobic minority first:<br />
<br />
<b>The chemophobes</b><br />
<b><br /></b>
Angela Garrison, a writer at alternative health site <i>The Alternative Daily</i>, <a href="http://www.thealternativedaily.com/why-baby-carrots-are-killing-you/">gave this warning about the carrots</a> (also posted at <a href="http://www.riseearth.com/2012/10/why-baby-carrots-are-killing-you.html">RiseEarth</a>) in 2012. She largely parrots the viral bite above, adding some nonsense about baby carrots being ground-up regular carrots (they're sliced, but certainly not ground, and it would be pretty impressive if manufacturers could reconstitute the texture like that from carrot paste). Additionally, the title ("Why Baby Carrots are Killing You") is <i>perhaps </i>more dramatic than warranted. She alleges that the chlorine bath gives them their orange color (and has never apparently heard of <a href="http://en.wikipedia.org/wiki/Carotene">carotene</a>). It's worth reading the article (which is characteristically factless); but I have to include this excerpt which does a smashing good job of confusing chlorine with chloroform and delightfully ignores both citation and any discussion of dosage:<br />
<br />
<blockquote class="tr_bq">
As defined by the EPA, Chlorine is a pesticide. Its purpose is to kill living organisms. So it would make sense that when you ingest chlorine, it kills some parts of our body like the healthy bacteria in your gut and intestinal flora for instance. Chlorine is a highly toxic, yellow-green gas most heavily used in chemical agents like household cleaners and can be found in the air near industrial areas especially around paper processing plants. Exposure to Chlorine has been linked to health problems such as sore throat, coughing, eye and skin irritation, rapid breathing, narrowing of the bronchi, wheezing, blue coloring of the skin, accumulation of fluid in the lungs, pain in the lung region, severe eye and skin burns, lung collapse, a type of asthma known as Reactive Airways Dysfunction Syndrome (RADS).<br />
<br />
Chlorine is also added to the public water supply. So not only are you drinking it, but you are absorbing it through the largest organ in your body, your skin. In fact, 2/3 of human absorption of chlorine is from inhaling the steam in the form of chloroform and fast absorption through your open pores in the warm shower or bath. The inhalation of chloroform is a suspected cause of asthma and bronchitis, especially in children… which has increased 300% in the last two decades. Other health risks associated with chloroform is cancer, potential reproductive damage, birth defects, dizziness, fatigue, headache, liver and kidney damage. Chloroform is also found in the air and in food, like baby carrots.</blockquote>
While no one is encouraging anyone to go breathe the stuff, that's a bit much.<br />
<br />
Another unsuprisingly chemophobic source is <a href="http://articles.mercola.com/sites/articles/archive/2009/07/28/Chlorine-in-Your-Baby-Carrots.aspx">Mercola.com</a> (website for <a href="http://en.wikipedia.org/wiki/Joseph_Mercola">prominent snake-oil salesman Joseph Mercola</a>). Mercola starts (in 2009) by insisting that chlorine is a carcinogen (spoiler: it's not), delves into a litany of other nasty roles chlorine and chlorinated byproducts can play, and ends by recommending chlorine-free carrots. Total Health magazine <a href="http://totalhealthmagazine.com/articles/diet/chlorine-a-face-lift-for-your-carrots.html">seems to largely echo</a> (almost plagiarize) these claims.<br />
<br />
The chemophobia has to have been taken fairly seriously by many--indeed, Bolthouse Farms created an entire website (<a href="http://truthaboutbabycarrots.com/">truthaboutbabycarrots.com</a>) to respond to the claims. But surprisingly, <i>the above three examples were the only two immediate negative results</i> in my two-page Google foray.<br />
<br />
<b>The non-chemophobes</b><br />
<b><br /></b>
Interesting, the majority of responses to the chlorine-carrot allegations are non-chemophobic (and largely come from non-scientists!). Journalist Bart Van Bockstaele at Digital Journal (2008) posts <a href="http://digitaljournal.com/article/260034">a response</a> that includes a discussion of the confusion around the 'chlorine' nomenclature whilst dismissing all health concerns and properly pointing out that science hasn't shown chlorine to be carcinogenic anyway. (Note that some of the text is pretty similar to that found on the somewhat odd website <a href="http://www.carrotmuseum.co.uk/babycarrot.html#chlorine">World Carrot Museum</a>).<br />
<br />
At FarmProgress (2013), editor Jennifer Vincent <a href="http://farmprogress.com/blogs-stop-black-balling-baby-carrots-5045">admonishes those spreading misinformation</a>, pointing out the public health efficacy of chlorinated water and describing how she corrected someone else who was spreading the carrot scare.<br />
<br />
Joel Mackey of Z6Mag (2013) gives <a href="http://z6mag.com/featured/baby-carrots-chlorine-does-a-viral-message-reveal-the-truth-yes-and-no-1617970.html">a somewhat disorganized response</a>, but two items stand out: (1) he contacted the companies and investigated the matter himself; and (2) there's some neat Google trends graphs that show that searches for 'baby carrots chlorine' increased going into 2013.<br />
<br />
Lisa Leake of the whole-foods effort <a href="http://www.100daysofrealfood.com/about/">100 Days of Real Food</a> (which <i>sounds </i>like it should be brimming with chemophobia) has <a href="http://www.100daysofrealfood.com/2012/12/11/the-truth-about-baby-carrots/">a nice, accessible response</a> in which she (1) made a point of looking up the relevant information and not just trusting 3rd party information; and (2) explained some of the layperson chemical misconceptions in the carrot-chlorine scare.<br />
<br />
Other, shorter responses include those by <a href="http://www.drweil.com/drw/u/QAA400972/Baby-Carrots-Bad-for-You.html">Dr. Andrew Weill</a>, <a href="http://www.waterandhealth.org/white-film-baby-carrots-myth-fact/">Linda Golodner of the Water Quality & Health Council</a> (she points out the health-protective benefits of low levels of chlorine in water!), <a href="http://eatprayfarm.com/archives/1225">Megan Loberg of Eat, Pray, Farm</a> (who points out that even 'organic' producers use chemicals to wash carrots), and <a href="http://news.consumerreports.org/health/2009/04/baby-carrots-treated-with-chlorine.html">Consumer Reports</a>, <a href="http://momsagainstcooties.com/baby-carrot-urban-myth-debunked-processing-with-chlorinated-water-protects-health-and-helps-prevent-foodborne-illness/">Moms Against Cooties</a>.<br />
<br />
And of course, anti-hoax websites such as <a href="http://www.snopes.com/food/tainted/carrots.asp">Snopes</a> and <a href="http://wafflesatnoon.com/2012/12/05/are-baby-carrots-dangerous/">wafflesatnoon</a> dismiss the claims (Snopes is itself a little chemically misleading, implying that neat chlorine is used to treat the carrots).<br />
<br />
<b>Overall, </b>the responses are encouragingly NOT chemophobic in general. That's a relief to see, I think: engagement by the non-chemical community is probably more convincing to the general public than engagement by chemists (whether we like it or not).<br />
<br />
<br />
<br />
<br />
<br /></div>
vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com4tag:blogger.com,1999:blog-3474124548976938700.post-6173329184305150322013-04-04T20:08:00.000-05:002013-04-04T20:08:00.448-05:00Analytical chemistry and the dinner tableI saw this headline recently on NPR: "<a href="http://www.npr.org/blogs/thesalt/2013/03/26/175377244/food-fraud-database-lets-us-all-play-detective">Food Fraud Database Lets Us All Play Detective</a>." From the description, I expected some degree of chemophobia (habit):<br />
<blockquote class="tr_bq">
Spices colored with carcinogens? Milk that "never saw a cow"? A free global database opens the door on the many ways that people adulterate [food]</blockquote>
Though I expected the carcinogen to be simply "chemicals" or something, it turned out to be the (indeed carcinogenic) <a href="http://en.wikipedia.org/wiki/Sudan_I">Sudan dyes</a>. In fact, NPR avoided chemophobia on this one!<br />
<br />
The article is worth checking out -- it's a brief read, and it points to a really interesting resource: the <a href="http://www.foodfraud.org/">USP Food Fraud Database</a>. I'm not going to delve much into what the database is, since the NPR highlight already did that. But it's worth pointing out a feature I found interesting (and perhaps contrary to my experience with the food world, where anecdotal claims are usually key)--the database lists food items (ingredients), what the adulterant was, and <i>the method of detection</i> (PCR, Raman, NMR, etc.). Moreover, the scholarly or other reference in question is listed, for those interested in further clickthroughs. Makes for a nice highlight of how analytical chemistry techniques are used in real-world applications--and how particularly techniques are uniquely suited for different classes of analytes.<br />
<br />
But now I'm going to be burning some time searching all the ingredients in my kitchen.<br />
<br />vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com4tag:blogger.com,1999:blog-3474124548976938700.post-1238192457930553882013-04-01T07:00:00.000-05:002013-04-01T07:00:06.587-05:00Total synthesis funding declared top national priorityWASHINGTON -- Among recent changes to the federal budget was <a href="http://www.youtube.com/watch?v=oHg5SJYRHA0">a joint announcement by the White House and the Congressional Budget Office</a> (CBO) that along with postmodernist literature critique and intermediate basketweaving, natural product total synthesis has been declared a "top funding priority" for the nation.<br />
<br />
The news of the funding priority shift Monday morning came as welcome news to thousands of synthetic chemists in academia, who had worried in recent years that federal belt-tightening might divert funds away from their activities.<br />
<br />
Although the funding measures have been laid out in detail in a <a href="http://www.youtube.com/watch?v=oHg5SJYRHA0">6000-page document</a> readily accessible on the CBO website, several government officials gave public statements early on Monday to clarify the scope and magnitude of the announcement.<br />
<br />
From the White House's press room, President Barack Obama spoke to reporters. "I consider this my most important contribution to the nation's interest so far," he said, stepping away from his prepared script and wiping a hint of a tear from his eye as he addressed the cameras earnestly. "For too long, our federal government has prioritized translational and applied research. And while contributions to medicine and energy are somewhat important, or something, I guess, we've too long neglected the biggest questions in science that will keep our country great. For example, there are so many alkaloid and polyketides that have been isolated from sea sponges that we just don't <i>know </i>the absolute stereochemical configuration of. And a few of these have some sort of cytotoxic activity or something at millimolar concentrations," the President added.<br />
<br />
Cries of "USA! USA!" could be heard from several reporters in the audience who were briefly overtaken with emotion.<br />
<br />
NIH director Francis S. Collins <a href="http://www.youtube.com/watch?v=oHg5SJYRHA0">issued a statement</a> later in the day on behalf of the National Institute of Health. "We are allied with the President on this strategic historic decision," the report reads. "While some might object to the fact that the NIH has completely defunded cancer research, antibiotic research, and genetics projects, we caution the public that the money invested in total synthesis will reap much richer rewards for the scientific community and the public. For instance, one of the total syntheses might contribute a valuable synthetic method that can be used in a different total synthesis from the same lab group."<br />
<br />
The NSF did not issue a statement but a source within the organization pointed out that all NSF predoctoral fellowships this year were awarded to students studying total synthesis.<br />
<br />
Despite the billions of dollars of refocused funding, not everyone is happy with the move. The American Physics Society <a href="http://www.youtube.com/watch?v=oHg5SJYRHA0">issued a formal letter of protest</a> against the measures, which are estimated to result in the closure of 99.5% of physics labs across the country. Said the report: "What's a carbon?"<br />
<br />
Surprising to many was an announcement by the Pentagon that drastic military funding cuts would be made to support the total synthesis effort. US Defense Secretary Chuck Hagel <a href="http://www.youtube.com/watch?v=oHg5SJYRHA0">addressed troops worldwide</a> via a televised message. "Um, yeah, so, guys, we appreciate your hard work and whatnot, but you can all go home. We're cancelling all this 'war' business, honestly. It's a money sink." In one video of an Army base in Afghanistan, soldiers were seen reacting to the news with elation. Hagel continued: "And let's be honest. Enlarging the postdoc pool is the true route to national security."<br />
<br />
In other news, job prospects for chemists look to be increasingly encouraging. In 2013 alone, twelve of the fifteen largest pharmaceutical companies have launched massive hiring campaigns, resulting in nearly complete employment among recent PhD graduates.<br />
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vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com6tag:blogger.com,1999:blog-3474124548976938700.post-6341616243584122482013-03-28T07:00:00.000-05:002013-03-28T07:00:03.021-05:00Stipends: A waste of funding?A little while ago the subject of teaching assignments came up among some colleagues (as it is wont to do). Specifically, we were discussing which PIs had habits of sticking their students on repeated teaching assignments and which PIs didn't have their students teach unless they <i>really </i>wanted to.<br />
<br />
I was a little surprised that one of the very well-funded synthesis groups here had an abundance of TAs. One of the students (him/herself a TA) explained it thus: "We don't like to waste money on paying people." The point was that they viewed grant money as primarily for supplies and fancy instrumentation. For instance, they'd shelled out quite a bit of cash recently for some fancy chromatography and microscopy equipment.<br />
<br />
It was an interesting perspective, and I'm not sure what to think of the philosophy.<br />
<br />
I've seen PIs before who tended to put students on TA quite frequently -- for their entire PhD, in many cases. But those have typically been groups with little-to-no funding, where available grant money wouldn't even cover a meager grad student stipend.<br />
<br />
I've also seen well-funded PIs who limit their students to two semesters of teaching (or whatever the departmental requirement happened to be), regardless of external fellowships available to the individuals in their lab. In those cases, a large portion of the available grant money is devoted to stipend/tuition expenses.<br />
<br />
So a lab that has plenty of cash that it needs to burn and decides to burn it by buying valuable (but not <i>essential</i>) upgrades--that's different.<br />
<br />
It might be a subdiscipline thing. I suspect that "hard" synthesis groups -- methodology and total synthesis -- tend to rely more on a TA culture (perhaps the funding situation is less predictable here?). In contrast, most biologically-oriented organic groups seem to find the funding (from training grants and other sources) to keep their lab RA-based. Additionally, some grants have specifications.<br />
<br />
Even so--can personnel costs be considered a "waste"? The word I would suggest is "investment." But it might be because I think a well-trained, happy chemist with decent instrumentation/supplies is more valuable than a slightly nicer MPLC.vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com4tag:blogger.com,1999:blog-3474124548976938700.post-23213848152654191352013-03-18T21:06:00.000-05:002013-03-18T23:07:54.955-05:00Singers and musicians, apocryphal quotes, and chemistsRecently, I saw the following quote get shared widely among my acquaintances on a particular social media outlet:<br />
<blockquote class="tr_bq">
Singers and Musicians are some of the most driven, courageous people on the face of the earth. They deal with more day-to-day rejection in one year than most people do in a lifetime. Every day, they face the financial challenge of living a freelance lifestyle, the disrespect of people who think they should get real jobs, and their own fear that they’ll never work again. Every day, they have to ignore the possibility that the vision they have dedicated their lives to is a pipe dream. With every note, they stretch themselves, emotionally and physically, risking criticism and judgment. With every passing year, many of them watch as the other people their age achieve the predictable milestones of normal life - the car, the family, the house, the nest egg. Why? Because musicians and singers are willing to give their entire lives to a moment - to that melody, that lyric, that chord, or that interpretation that will stir the audience’s soul. Singers and Musicians are beings who have tasted life’s nectar in that crystal moment when they poured out their creative spirit and touched another’s heart. In that instant, they were as close to magic, God, and perfection as anyone could ever be. And in their own hearts, they know that to dedicate oneself to that moment is worth a thousand lifetimes.<br />
<i>-David Ackert, LA Times</i></blockquote>
<div>
I kind of hate to reproduce it--not because it's pandering and indulgent*, necessarily, but because <i>I can't find the original source</i>, and as a scientist, that bothers me. It's attributed to David Ackert of the LA Times. No one seems to mention that the LA Times website doesn't even <i>mention</i> a David Ackert, much less this quote. So the authenticity/origin is dubious (that doesn't seem to matter to those who push it along). </div>
<div>
<br /></div>
<div>
A quick search of the <a href="http://www.tumblr.com/tagged/david%20ackert">internet</a> reveals several modifications of the quote, wherein people have substituted 'actors' and 'artists' for 'singers and musicians'. So, I figured: why not 'chemists'? (We do use instruments). Let's try.</div>
<blockquote class="tr_bq">
[Chemists] are some of the most driven, courageous people on the face of the earth. They deal with more day-to-day rejection in one [group meeting] than most people do in a lifetime. Every day, they face the financial challenge of living a [STEM] lifestyle, the disrespect of people who think they should get real jobs, and their own fear that they’ll never work again. Every day, they have to ignore the possibility that the vision they have dedicated their lives to is a pipe dream. With every [column], they stretch themselves, emotionally and physically, risking criticism and judgment. With every passing year, many of them watch as the other people their age achieve the predictable milestones of normal life - the car, the family, the house, the nest egg. Why? Because [chemists] are willing to give their entire lives to a [synthesis] - to that [ring], that [stereocenter], that [functional group], or that [weird perfluorinated tail] that will [get them into <i>JACS</i>, or <i>Org. Lett.</i>, or heck, <i>Tet. Lett</i>., it's gonna get ignored anyway]. [Chemists] are beings who have tasted life’s nectar in that crystal moment when they poured out their [organic layer by mistake] and [broke] another’s [favorite sep. funnel]. In that instant, they were as close to [unemployment] as anyone could ever be. And in their own hearts, they know that to dedicate oneself to that moment is worth a thousand lifetimes [...PSYCH! Hahahahahahaahahaah. Heh.].<br />
<i>-David Ackert, LA Times</i></blockquote>
<div>
Seems to fit.<br />
<br />
<i>Update: 11:05 PM</i>. Re: source of original, for those interested (thanks to Chemjobber for the legwork). According to David Ackert:<br />
<blockquote class="twitter-tweet">
@<a href="https://twitter.com/gravelpot">gravelpot</a> I wrote the piece 15 years ago- it originally appeared in Backstage West. Don't think it ever appeared in LA Times.<br />
— David Ackert (@DavidAckert) <a href="https://twitter.com/DavidAckert/status/295982077931814912">January 28, 2013</a></blockquote>
<script async="" charset="utf-8" src="//platform.twitter.com/widgets.js"></script>
</div>
<div>
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<span style="font-size: x-small;">* Caveat: I've done a lot of music stuff myself; I'm not hating on musicians here. Just saying.</span></div>
vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com10tag:blogger.com,1999:blog-3474124548976938700.post-84873689107856112482013-03-04T22:11:00.001-06:002013-03-04T22:11:28.353-06:00JACS comment section? Back to the future<div class="tr_bq">
It's been a very interesting couple of weeks in the realm of <a href="http://blog-syn.blogspot.com/">Blog Syn</a> (the beginning of <a href="http://blog-syn.blogspot.com/2013/03/blog-syn-003a-secret-ingredient.html">Blog Syn #003A</a> has a roundup for anyone who hasn't been following). People across a number of blogs have noted the importance (or at the very least, usefulness) of chemists participating in social media and rapid web communication (indeed, <a href="http://openflask.blogspot.com/">even Phil Baran's lab has started a blog</a>, despite <a href="http://openflask.blogspot.com/2013/02/phils-two-cents-on-blogging.html">hegemonic bias against blogging</a> in the field of organic synthesis). </div>
<br />
How can chemists use social media to the greater benefit? Take, for instance, the first comment in <a href="http://chemjobber.blogspot.com/2013/03/blog-syn-is-water-key-ingredient-see.html">Chemjobber's reply to the IBX+water conclusion</a>. Polychem <a href="http://chemjobber.blogspot.com/2013/03/blog-syn-is-water-key-ingredient-see.html?showComment=1362433918063#c7877946944759375170">says</a> (bold emphasis mine):<br />
<blockquote>
<b>This work makes me think that every paper published on pubs.acs.org deserves its own comment section.</b> I can imagine it being abused, but there may be some good insights by having essentially a wider peer review where you don't have to pay to print your rebuttal.<br />Good job Blog Syn people!</blockquote>
Hmm... a comment section at <i>JACS</i>? Check out <a href="http://pubs.acs.org/doi/abs/10.1021/ja9654995">this 1996 editorial from the journal</a>! For those stuck outside the paywall, an excerpt:<br />
<blockquote class="tr_bq">
There is no question that digital computers have had a large impact on the publication of scientific research. JACS uses computers in the management of the journal data base and in production of the journal. Most manuscripts are now submitted in final form as floppy disks, and e-mail is often used for correspondence with authors and reviewers. Recently, especially with the wide accessibility and usage of the World Wide Web (WWW), interest has turned to electronic publishing, i.e., to the posting of manuscripts on the web rather than, or in addition to, producing a hard copy (print) journal. The advantages of electronic publishing include the faster appearance of a paper at a presumed lower cost than printing (with the attendant possibility of wider distribution) as well as the ability to provide materials, like computer programs, movies, color figures, and large amounts of experimental data, not available in the hard copy. Concerns about electronic publishing include the maintenance of the quality and integrity of the published literature, providing for the long-term archiving of papers, and assuring that financial support is available to carry out the needed peer review and maintenance of the archive. These points are discussed in a booklet available from ACS Publications: <i>Will Science Publishing Perish</i>?</blockquote>
Interesting that the ACS proposed lower cost and wider distribution--I wonder if that worked out that way? The last section of the editorial is also a fun read:<br />
<blockquote class="tr_bq">
<b>JACS Web Page -- An Experiment. </b>The JACS web page (accessible via the ACS publications page at http://pubs.acs.org) displays instructions for authors, links to supporting information, and the table of contents for the latest issue of the journal. As an experiment we will also try out a section for selected correspondence and comments. Readers can submit, by way of a form available on the web page, scientific comments pertaining to recently published JACS papers. Authors will be asked to reply. Posting of comments will not be automatic. Comments for posting will be selected by the editors and they will not be sent out for review. There will be no appeals for comments not selected. Comments will not be published in hard copy or CD versions of the journal nor will they be archived. We hope these comments will generate interesting discussions and help amplify and clarify ideas and results published in JACS papers. They are not meant to discuss priorities or present still unpublished ideas or results. Additions and corrections will still be published in the printed version of JACS. We hope the level of discussion on the JACS page will be significantly higher than the average WWW newsgroup! This experiment will be terminated if the community feels it is not useful (or if it becomes too burdensome for the editors). At this time we cannot accept manuscripts submitted electronically for review; however, we are investigating the possibility of doing this in the future. As stated at the outset, the science publication field is evolving rapidly. The new possibilities are intriguing, but the community will best be served by an orderly evolution that involves the best features of both the print and electronic media.</blockquote>
It's quite revealing to see the difference between scientific publishing just 17 years ago (oh wow, 1996 was 17 years ago??) and now--after all, electronic submission is <i>de rigueur </i>not only for SI but for main text and for correspondence with reviewers.<br />
<br />
More interesting, though: <b>there was a comment section on JACS <i>before </i>the journal even started putting the manuscripts themselves online</b>. Seems like unusually progressive thinking by the ACS!<br />
<br />
But if you go to the <a href="http://pubs.acs.org/journal/jacsat">JACS website</a> now, there's no comment section. What happened to it? A search of editorials from the journal gives no relevant hits and <a href="http://pubs.acs.org/doi/abs/10.1021/ja015113c">a 2002 editorial discussing other web-based aspects of JACS</a> makes no mention of it. Did it die a quick, fiery death?<br />
<br />
Indeed, there's a lot of room for publishers to include the community in scientific discourse. Some do a little: <i>Nature Chemistry</i>, for instance, has a good <a href="http://www.nature.com/nchem/journal/v5/n3/nchem.1549/metrics">metrics section</a> that indexes blogs (but no comment section). The ACS journals don't have comments, nor do Taylor & Francis, the RSC journals, Elsevier, or PNAS.<br />
<br />
Does <i>anyone </i>do comments?<br />
<br />
Yes! Take a look at PLoS One (<a href="http://www.plosone.org/article/comments/info%3Adoi%2F10.1371%2Fjournal.pone.0056935">example article</a>): they have comment section built in to a very slick web interface.<br />
<br />
It'll be interesting to see how the face of scientific communication changes over the next few years.<br />
<br />vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com10tag:blogger.com,1999:blog-3474124548976938700.post-52219072072555904132013-02-24T18:10:00.001-06:002013-02-24T18:10:34.862-06:00Reading assignments, vol. 11<h3>
Communication of science</h3>
<ul>
<li>Fans of ChemDraw and Pierre Morieux (who isn't??) should note that <a href="http://chemjobber.blogspot.com/2013/02/the-chemdraw-wizard-is-back.html">he has a second video</a>.</li>
<li>Science writing guru Khalil Cassimally provides <a href="http://blogs.scientificamerican.com/incubator/2013/02/13/35-mostly-different-guidelines-for-science-writers/">a roundup of some useful tips for science writers</a>.</li>
<li>How accessible is your science? At Duke University, a genetics professor has proposed <a href="http://www.insidehighered.com/news/2013/02/22/duke-proposes-mandatory-short-video-pitch-accompany-dissertations">asking grad students to prepare a short video aimed at non-specialists to accompany their dissertations</a>. This is a good idea, I would think; it makes science more accessible but also makes scientists work on (oft-neglected) soft skills.</li>
<li>This satirical piece at The Pessimist (affiliated with Despair, Inc) about '<a href="http://thepessimist.com/2013/02/13/how-to-work-like-a-writer/">How to Work Like a Writer</a>' was an enjoyable, quick read. The article gives a link to a Computerworld blog post about PowerPoint describing <a href="http://www.computerworld.com/s/article/9236645/Give_killer_presentations_Think_like_a_writer">how to harness tactics used in writing to make presentations more effective</a>. Though it's written for a technology/computer audience, it's worth taking to heart if you're a scientist, too.</li>
</ul>
<br />
<h3>
Peer review and publication</h3>
<ul>
<li>Neuroskeptic writes about the perhaps-sensical, perhaps-counterintuitive situation of stats quality in journals. It seems that high-impact journals (e.g. Science and especially Nature) are <a href="http://blogs.discovermagazine.com/neuroskeptic/?p=3565">more likely than many low-impact journals to have insufficient statistical analysis</a>. This may not be surprising, given the incentive for those journals to publish hyped-up work. Is there a similar trend in chemistry? I suspect that many medium-tier journals provide more solid experimental characterization and writeup than some of the flashier ones.</li>
<li>Scientists unsatisfied with the <i>status quo </i>of journal publishing practices will find this development interesting. <a href="http://blogs.discovermagazine.com/gnxp/?p=20175">Biologist Michael Eisen has declared that he will publicly post each paper from his lab</a> <i>prior to journal submission </i>for pre-publication, community-oriented peer review. It's a refreshing idea--hopefully others will follow suit.</li>
<li>Derek Lowe <a href="http://pipeline.corante.com/archives/2013/02/22/what_if_the_journal_disappears.php">points to the disappearance</a> of the electronic-only open-access publication <i>Journal of Advances in Developmental Research. </i>Although he notes the relative unimportance of that particular journal, he brings up some points that open-access advocates should pay close attention to: predatory publishing and digital preservation. On a related note, Kevin Bonham writes about <a href="http://scienceblogs.com/webeasties/2013/02/12/peerj-the-science-journal-we-need-and-deserve/">the premiere of a new prominent online-only journal, PeerJ</a>.</li>
<li>The story of the recent Xi Yan plagariasm endeavor (and the journal's lackluster, non-punitive response) <a href="http://justlikecooking.blogspot.com/2013/02/was-justice-served.html">has been written about with proper consternation</a> by See Arr Oh. This kind of case is amazing, as it's the kind of thing routinely warned against in undergraduate writing courses and in orientation lectures at grad programs. Despite this, the plagiarists quite often win (for another plagiarist who 'won', check out <a href="http://artsbeat.blogs.nytimes.com/2013/02/12/plagiarism-pays-jonah-lehrer-gets-20000-for-speech/">Jonah Lehrer</a>). For those with a spare half-hour, check out the Chemjobber/See Arr Oh <a href="http://justlikecooking.blogspot.com/2013/02/podcast-cj-and-sao-talk-plagiarism.html">podcast about plagiarism and peer review</a>. Also, the comments section at the relevant In the Pipeline posting contains <a href="http://pipeline.corante.com/archives/2013/02/19/the_wages_of_copypasting.php">a discussion of the ethics of paper submission and whose fault plagiarism is</a> (one commenter seems to think it lies with editors/reviewers and <i>not </i> professors).</li>
<li>In the last two weeks, two more entries came out at Blog Syn (<a href="http://blog-syn.blogspot.com/2013/02/blog-syn-002-pd-catalyzed-c-3-selective.html">a Pd-catalyzed site-selective C-H olefination</a> and <a href="http://blog-syn.blogspot.com/2013/02/blog-syn-003-benzylic-oxidation-of_18.html">an IBX-mediated benzylic oxidation</a>). Give them a read--and submit your comments if you have suggestions or questions! Blog Syn is supposed to be a discussion-oriented endeavor (and the further updated to Blog Syn #003 illustrate that, I think). On another note, despite broad support (including from more than one <a href="https://twitter.com/TehshikYoon/status/292072648731676672">big-name prof</a>), Blog Syn does have its critics. See particularly the comments section at In The Pipeline, which is <a href="http://pipeline.corante.com/archives/2013/02/19/more_from_blog_syn.php">brimming with vitriol</a> (so much that Derek Lowe jumped in to defend Blog Syn).</li>
<li>Science librarian Bonnie Swoger discusses <a href="http://blogs.scientificamerican.com/information-culture/2013/02/13/providing-context-for-the-metrics-used-to-evaluate-the-scientific-literature/">common metrics of scientific publishing</a>, such as<i> </i>h-index and impact factor, citing the importance of context in any comparisons. </li>
</ul>
<br />
<h3>
The job market</h3>
<div>
<ul>
<li>Don't miss Chemjobber's <a href="http://chemjobber.blogspot.com/2013/02/reddit-chemistry-jobs-faq-part-1.html">Reddit Chemistry Jobs FAQ Part 1</a>, which focuses on non-traditional jobs for chemists. As someone with a non-traditional career in mind, I found the post worthwhile and I second the recommendation of Dr. Lisa Balbes's <a href="http://www.amazon.com/Nontraditional-Careers-Chemists-Formulas-Chemistry/dp/0195183673">non-traditional careers book</a>. I found <a href="http://cenblog.org/just-another-electron-pusher/2011/08/you-want-to-do-what-explaining-your-nontraditional-career-to-the-world/">this post from the ancient literature</a> (2011) relevant.</li>
<li>Glen Ernst <a href="http://cenblog.org/just-another-electron-pusher/2013/02/i-know-enough-with-the-bad-news-already/">discusses the surplus of scientists in the job market</a>. Accompanying his post is a graph clearly showing the recent (last ten years') trend wherein postdoctoral assignments have pulled ahead of jobs for new PhD graduates.</li>
</ul>
</div>
<br />
<h3>
Research highlights</h3>
<ul>
<li>Orac of Respectful Insolence makes a pointed criticism of anti-pharma, pro-alternative-medicine types by pointing out <a href="http://scienceblogs.com/insolence/2013/02/20/a-brief-fable-about-a-pharmaceutical-company-for-the-benefit-of-believers-in-alternative-medicine/">the aspects of alt-med hero Stanislaw Burzynski's work that would enrage his followers if Merck had done it</a>.</li>
<li>At Forbes, Steven Salzberg points out <a href="http://www.forbes.com/sites/stevensalzberg/2013/02/18/naturopathic-shenanigans-in-the-maryland-legislature/">some upcoming legislation in Maryland</a> that's being pushed by naturopaths seeking to equate 'alternative medicine' with evidence-based practices.</li>
<li>Check out the always-interesting Alex Wild's public service announcement about the correct orientation of <a href="http://blogs.scientificamerican.com/compound-eye/2013/02/21/most-zombie-ant-photographs-are-upside-down/">zombie ant fungus pictures</a>. And the accompanying pictures, which are certainly cooler than anything you'll see in lab this week.</li>
<li>I'm not well-versed in nutrition research, much of which gets criticized by scientists, but this piece by Scientific American intern Marissa Fessenden regarding the complicated mixtures of chemicals in food is certainly interesting. The proposal is that <a href="http://blogs.scientificamerican.com/observations/2013/02/22/food-delivers-a-cocktail-of-hormone-like-signals-to-body/">the complicated biochemistry of food may cause hormone-like signalling, which could lead to downstream effects</a>. Chemophobes will be surprised to learn that food contains chemicals, of course.</li>
<li>Those interested in chemophobia will find interesting this piece at Fire in the Mind which looks at the folks who oppose fluoridation of water. The phenomenon he describes--<a href="http://blogs.discovermagazine.com/fire-in-the-mind/?p=90">harnessing the "truthiness" of scientific studies while ignoring the real data/conclusions</a>--is obviously not limited to fluoridation. The piece is an extension of Keith Kloor's post about how <a href="http://blogs.discovermagazine.com/collideascape/2013/02/21/why-facts-dont-matter/">how many people simply dismiss facts</a>.</li>
<li>DNLee makes the case that <a href="http://blogs.scientificamerican.com/urban-scientist/2013/02/23/sci4all-making-science-allies-essential-to-promoting-stem/">a crucial way to improve STEM education is via of STEM-supportive parents and community members</a>.</li>
<li>I found two posts by Derek Lowe particularly interesting this/last week. The first was about <a href="http://pipeline.corante.com/archives/2013/02/11/phrma_and_why_people_dislike_the_drug_industry.php">the pharmaceutical industry and public perception</a>--the point was that the industry doesn't need to care if people like it, as they'll still take medication. This suggests that those looking to change policies and practicis of the industry should do so by focusing on regulation and legislators, not on company-oriented protest. The second piece cast a skeptical light on an NIH claim that<a href="http://pipeline.corante.com/archives/2013/02/12/do_we_really_know_the_cause_for_over_4500_diseases.php"> the causes of 4,500 diseases have been identified by research</a>.</li>
<li>It may be encouraging to science-minded folks that <a href="http://scienceblogs.com/evolutionblog/2013/02/21/creation-museum-attendance-decreasing/">attendance at the Creation Museum is decreasing</a>.</li>
<li>At The Pump Handle there's a short piece about <a href="http://scienceblogs.com/thepumphandle/2013/02/18/trust-chromium-and-the-epa/">conflicts of interest, the EPA, and chromium</a>.</li>
<li>Keith Kloor writes about <a href="http://blogs.discovermagazine.com/collideascape/?p=10301">the tendency of the 'Freethinker' movement to shut down debate</a> by dismissing religion as non-important. He maintains this as a problem of the 'New Atheist' movement--and I agree--since empirically, brute force never seems to be a particularly good method of conversion.</li>
<li>Chad Orzel has a brief commentary on <a href="http://scienceblogs.com/principles/2013/02/14/physics-vs-chemistry-nobody-does-research-on-newtonian-mechanics/">the academic cultural differences</a> on who-teaches-what vs who-uses-what in physics and chemistry.</li>
<li>Protein folding is important. NMR is important. So check out this writeup (and the <a href="http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.1181.html">original article</a>) of a study in which <a href="http://blogs.discovermagazine.com/80beats/?p=42917">temperature-controlled NMR spectroscopy was used to visualize protein folding</a> (specifically, the folding of <a href="http://www.ncbi.nlm.nih.gov/pubmed/15359276">a DNA-binding protein</a> from <i>Enterococcus faecalis</i>, a bacterium you will probably care a lot more about if you're hospitalized).</li>
<li>Microbiology grad student K.D. Shives shares <a href="http://www.insidehighered.com/blogs/gradhacker/how-cope-when-work-follows-you-home">two opposite strategies for dealing with work-life balance</a> in science grad school.</li>
</ul>
vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com5tag:blogger.com,1999:blog-3474124548976938700.post-86323229759846815242013-02-14T07:00:00.000-06:002013-02-14T07:00:10.747-06:00A rose by any other IUPAC name...Today is Valentine's Day, and what's more quintessentially appropriate than roses? If you're enjoying the scent of flowers today, you have <i><b>chemicals </b></i>(*gasp*) to thank!<br />
<br />
Here's a few of those chemicals found naturally in the scent of various rose cultivars:<br />
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGhKr_fDMIVqQVIvr_H6R6-CMYdqWasOB4K-vMPoYVGIhWhv1Y-mf4KBp1spVW9O42bcqsoW_4lArY8TRb0EJirgEkCj_WppSsFK4BKvJAa9Uqe5hzTovs9nP2tqbWHiJwYOQ6nUC_gnI/s1600/rose-scents2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGhKr_fDMIVqQVIvr_H6R6-CMYdqWasOB4K-vMPoYVGIhWhv1Y-mf4KBp1spVW9O42bcqsoW_4lArY8TRb0EJirgEkCj_WppSsFK4BKvJAa9Uqe5hzTovs9nP2tqbWHiJwYOQ6nUC_gnI/s400/rose-scents2.png" width="395" /></a></div>
<br />
Enjoy your terpenes, everyone!<br />
<br />
<span style="font-size: x-small;"><b>References</b> (further reading for the brave)</span><br />
<span style="font-size: x-small;"><ol>
<li>Flament, I., Debonneville, C., and Furrer, A. (1993). Volatile constituents of roses: Characterization of cultivars based on the headspace analysis of living flower emissions. In <i>Bioactive Volatile Compounds from Plants</i>, R. Teranishi, R.G. Buttery, and H. Sugisawa, eds (Washington, DC: American Chemical Society), pp. 269–281. DOI: <a href="http://pubs.acs.org/doi/abs/10.1021/bk-1993-0525.ch019">10.1021/bk-1993-0525.ch019</a></li>
<li>Charles S. Sell. (2003). <a href="http://books.google.com/?id=rIoXXL7OGCoC&pg=PA256">A fragrant introduction to terpenoid chemistry</a>. Cambridge: RSC, Royal Society of Chemistry. pp. 256–257. ISBN 978-0-85404-681-2.</li>
</ol>
</span>vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com5tag:blogger.com,1999:blog-3474124548976938700.post-60552245356385567502013-02-12T07:00:00.000-06:002013-02-12T07:00:11.159-06:00Stop using that word: FacileCertain words tend to catch on in the scientific literature, such as "novel", which <a href="http://nsaunders.wordpress.com/2010/10/30/findings-increasingly-novel-scientists-say/">increased exponentially in usage starting in the 1980s</a>. One of those catchy words is one that I previously* used like candy: <b>facile</b>.<br />
<br />
Chemists like to describe reactions as "facile." By that, they usually mean easily-performed, smooth, or simple. You know, not much fuss involved. And indeed, that's one of the definitions (from the <a href="http://www.oed.com/view/Entry/67455">OED</a>):<br />
<blockquote class="tr_bq">
<i>adj. </i>(<b>1</b>) <b>a</b>. That can be achieved with little effort; straightforward, easy. In later used freq. in disparaging sense: contemptibly easy. <b>b</b>. Of instructions, a device, etc.: easy to understand or make use of; simple. <b>c</b>. Of a course of action, a method, etc.: presenting few difficulties.</blockquote>
That is the original, historical meaning. Another (more modern) definition carries a different implication (from the <a href="http://english.oxforddictionaries.com/definition/facile">Oxford Pocket Dictionary</a>):<br />
<blockquote class="tr_bq">
<i>adj. </i>(<b>1</b>) ignoring the true complexities of an issue; superficial; or (<b>2</b>) (of a person) having a superficial or simplistic knowledge or approach</blockquote>
And if you type "facile" into Google, you get this immediately:<br />
<blockquote class="tr_bq">
<i>adj</i>. (esp. of a theory or argument) Appearing neat and comprehensive only by ignoring the true complexities of an issue; superficial</blockquote>
<div>
Essentially, "facile" in modern usage (last century or so) has a negative connotation. And take a look at the synonyms for facile (<a href="http://english.oxforddictionaries.com/view/th/e/t_en_gb0005396">Oxford again</a>):<br />
<blockquote class="tr_bq">
simplistic, superficial, oversimple, oversimplified, schematic, black and white; shallow, pat, glib, slick, jejune, naive</blockquote>
It's interesting to note that <a href="http://en.wiktionary.org/wiki/facile">wiktionary</a> has a chemistry-specific entry for "facile":<br />
<blockquote class="tr_bq">
(chemistry) Of a reaction or other process, taking place readily.</blockquote>
Of course, language is defined by usage, so maybe I'm being picky here. But why not describe procedures as "straightforward", "robust", "easily performed", or any number of other, less ambiguous descriptors? (My intuition says those terms sound too common/"blue-collar" to many academics)<br />
<br />
When did "facile" catch on? Well, from a crude <a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=facile">PubMed search</a>, it looks like the late 1990s was the tipping point (incidentally, PubMed makes it way easier than SciFinder to get data on this kind of thing. Sorry, CAS). Additionally, most of these references are (not surprisingly) from synthetic organic chemistry papers. See also <a href="http://www.worldwidewords.org/topicalwords/tw-fac1.htm">this description of the two meanings of the word</a> and their historical context.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhpesYBvcHkZb_p8kN6VPdKn5IhR7kY0SXn97UnJQQPy-t5oU9B8okNOa-QKUAbfgVIZuZnhoBaVJWPL_Xe46y9CU2KEmuZI9lopH2kFCF86_Y6rTpD8eLk309j5RTjYorqfUE_4Y9B7qk/s1600/facile.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="265" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhpesYBvcHkZb_p8kN6VPdKn5IhR7kY0SXn97UnJQQPy-t5oU9B8okNOa-QKUAbfgVIZuZnhoBaVJWPL_Xe46y9CU2KEmuZI9lopH2kFCF86_Y6rTpD8eLk309j5RTjYorqfUE_4Y9B7qk/s400/facile.png" width="400" /></a></div>
The shrouded meaning of facile adds overlooked complication when authors start to invent words (after all, organic chemists are wont to derivatize things). There's <a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=nonfacile">a handful of examples</a> from the literature that use "nonfacile" (which isn't even a word; go ahead, check the <a href="http://www.oed.com/">OED</a> or <a href="http://www.merriam-webster.com/">Merriam-Webster</a>).<br />
<br />
Take this example from an otherwise-good trifluoroborate-preparation paper (Lennox, A.J.J., Lloyd-Jones, G.C. <i>Angew. Chem. Int. Ed. </i><b>2012</b>, <i>51</i>(37), 9385-9388. doi: <a href="http://onlinelibrary.wiley.com/doi/10.1002/anie.201203930/full">10.1002/anie.201203930</a>):<br />
<blockquote class="tr_bq">
Replacing MeOH with diethyl ether led to co-precipitation of <b>2a</b> with other potassium salts (KF/RCO<sub>2</sub>K etc.), thus making isolation of pure <b>2a</b> nonfacile. Switching to MeCN kept trifluoroborate <b>2a</b> in solution, but an excess of carboxylic acid (e.g. acetic or <i>ortho</i>-iodobenzoic acid) was still required (Scheme 2).</blockquote>
So if "facile" means "contemptibly easy" or "appearing neat and comprehensive only by ignoring the true complexities of an issue", what does "nonfacile" mean? Was isolation of <b>2a</b> not <i>contemptibly </i>easy (just acceptably easy?). Did isolation merely <i>appear </i>difficult while really, under the surface, it was simple?<br />
<br />
Stop using that word.<br />
<br />
<span style="font-size: x-small;">* <i>i.e.</i> before a reviewer pointed out the proper definition.</span></div>
vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com11tag:blogger.com,1999:blog-3474124548976938700.post-57125650021937610972013-02-10T16:58:00.004-06:002013-02-10T17:00:01.995-06:00Reading assignments, vol. 10Here's the link roundup for the week:<br />
<br />
<h3>
Science communication</h3>
<ul>
<li>The Open Notebook, a science-journalism-focused site <a href="http://www.theopennotebook.com/about/">described</a> as a "non-profit organization that provides unique tools and resources to help science journalists at all experience levels hone their craft", is introducing a series of short videos featuring prominent science writers giving advice. First up is the esteemed Deborah Blum. Watch the <a href="http://www.theopennotebook.com/2013/02/05/single-best-advice-deborah-blum/">video</a>: the point she makes about <a href="http://www.theopennotebook.com/2013/02/05/single-best-advice-deborah-blum/">being able to distill things down to a sentence</a> is a good one. It extends beyond journalism, too--can you sum up your one-hour research seminar in a sentence? How about your journal club article?</li>
<li>Physics professor and blogger Chad Orzel has <a href="http://scienceblogs.com/principles/2013/02/05/science-online-advice-long-term-blogging/">some recommendations about science blogging</a>. First and foremost: enjoy it.</li>
<li>Illustrator Glendon Mellow points out <a href="http://www.forbes.com/sites/emilywillingham/2013/02/08/can-nerd-nodes-reach-resistors-of-scientific-consensus/">some ineffective or just plain bad uses of imagery in pro-vaccination science communication</a>. He uses this as a case study of why science communicators need to be mindful of the images they use and why using illustrations/photos can be beneficial to reaching an audience.</li>
<li>Maryn McKenna brings some results from ScienceOnline to the internet, discussing <a href="http://www.wired.com/wiredscience/2013/02/scio13-genre/">what science writers can learn from genre novels</a>.</li>
</ul>
<h3>
Denialism, chemophobia, and fraud</h3>
<ul>
<li><a href="http://notthelab.blogspot.com/2013/02/reading-assignments-vol-9.html">Last week I included a link</a> to a <a href="http://www.nytimes.com/2013/02/03/magazine/the-boy-with-a-thorn-in-his-joints.html?_r=0">chemophobic, medically-related New York Times piece</a> accompanied by a <a href="http://cultureofchemistry.fieldofscience.com/2013/02/chemophobia-boy-with-thorn-in-his-joints.html">commentary/analysis</a> by Michelle Francl at The Culture of Chemistry. This week, Francl has taken her argument to Slate magazine with <a href="http://www.slate.com/articles/health_and_science/medical_examiner/2013/02/curing_chemophobia_don_t_buy_the_alternative_medicine_in_the_boy_with_a.html">an excellent, pointed piece</a>. The second page, especially, contains an effective argument against blind naturophilia.</li>
<li>At Forbes, Emily Willingham <a href="http://www.forbes.com/sites/emilywillingham/2013/02/08/can-nerd-nodes-reach-resistors-of-scientific-consensus/">provides recommendations for fighting denialism</a> via a social-networking, almost grassroots approach. She also recommends not calling denialism "denialism". I think her points are good, and I would suspect they are empirically more effective than a Dawkins-style mind-clubbing.</li>
<li>Derek Lowe points out a frightening example of <a href="http://pipeline.corante.com/archives/2013/02/07/how_to_enhance_your_online_reputation_sure.php">a post at Retraction Watch being taken down after a fraudulent DMCA notice was filed against the blog</a>. This kind of thing is a threat to scientific integrity and is illustrative of how 'reputation companies' and others can stifle important communication.</li>
</ul>
<h3>
Chemical education & academia</h3>
<div>
<ul>
<li>Glen Ernst <a href="http://cenblog.org/just-another-electron-pusher/2013/02/the-10k-ba-is-it-possible-in-chemistry/">writes skeptically of the concept of a "10K BA"</a> (<i>i.e.</i> radically cheap, cost-effective degree) in the context of undergraduate chemical education. It's hard to imagine being able to support effective lab facilities for that amount.</li>
<li>Educators: Don't miss grad-student and educational specialist Michael Evans' thoughtful and thorough <a href="http://graphiteworks.wordpress.com/2013/02/10/chemical-education-roundup-2-9-13/">chemical education roundup</a>.</li>
<li>At Fragments of Truth, we find <a href="http://fragments-of-truth.blogspot.com/2013/02/professor-hands-out-erase-undesirable.html">a tongue-in-cheek 'story' proposing "erase undesirable data" coupons</a> in order to accelerate PhD student publication and graduation.</li>
<li>Kate Clancy and Chris Chambers provide <a href="http://www.guardian.co.uk/science/blog/2013/feb/08/pseudoscience-stereotyping-gender-inequality-science">a response to "pseudoscience and stereotyping" in regards to how to increase involvement of girls in science</a>. At Brain Flapping, Dean Burnett provides a parody of stereotypes with <a href="http://www.guardian.co.uk/science/brain-flapping/2013/feb/06/boys-and-science-maintaining-gender-divide">some amusing "recommendations" for making boys more interested in science</a>.</li>
<li>From C&EN comes news that <a href="http://cen.acs.org/articles/91/i6/National-Science-Foundation-Director-Steps.html">the director of the NSF, Subra Suresh, has stepped down</a> to accept a job as the president of Carnegie Mellon University.</li>
</ul>
<h3>
Public policy</h3>
</div>
<div>
<ul>
<li>The abundance of over-used or inappropriatedly-used antibiotics in agriculture is an important topic for public health. This <a href="http://www.wired.com/wiredscience/2013/02/narms-adufa-2011/">brief piece in Wired, with accompanying infographics</a>, shows that the problem is indeed bad. Some highlights: 80% of antibiotic use in the US is for livestock; also, <i>Salmonella</i> isolates from poultry are increasingly showing multidrug resistance. The piece also questions the efficacy of the FDA's policy of "voluntary" antibiotic regulation/reporting.</li>
<li>Scot Huler points out that North Carolina's new leader of the Department of Environmental and Natural Resources is a climate-change denier <a href="http://blogs.scientificamerican.com/plugged-in/2013/02/08/still-bringing-the-science-crazy-in-nc/">who considers oil to be a renewable resource</a>. </li>
<li>A little feature by Colorado State University explores <a href="http://www.today.colostate.edu/story.aspx?id=7961">the role one faculty member, an expert in plant-pathogen intereactions, is playing in biosecurity and public policy</a>. It's a cool example to illustrate the importance of "beyond-the-lab" science impact.</li>
<li>The American Institute of Physics (AIP) provides <a href="http://www.aip.org/fyi/2013/026.html">a summary of a the first House Science Committee meeting of this Congressional term</a>. It seems favorable; topics of discussion included how to increase numbers in STEM education (including improving K-12 STEM education), how to maintain R&D tax credits for businesses, and how to improve immigration policies to retain international STEM graduates. The chemistry job market was absent.</li>
</ul>
</div>
<h3>
Other</h3>
<ul>
<li>B.R.S.M. points out <a href="http://brsmblog.com/?p=1902">an interesting paper that is decidedly not gluten-free</a>.</li>
<li>At ChemBark, Paul (and commenters) <a href="http://blog.chembark.com/2013/02/07/a-highly-cited-paper/">point out some highly-cited chemistry papers</a>, comparing the Sanger sequencing paper to KCN's entire career. There's a 1.4:1 ratio of citations in that case, which isn't really fair: Sanger sequencing is at least one or two orders of magnitude more important than KCN's career.</li>
<li>Chemjobber describes <a href="http://chemjobber.blogspot.com/2013/02/process-wednesday-direct-benzylation-on.html">a (somewhat) large-scale industrial use of C-H activation</a>. This area of chemistry is the basis of many high-profile academic groups, so it's nice to see examples adopted in what some would call the 'real world'. </li>
<li>See Arr Oh <a href="http://justlikecooking.blogspot.com/2013/02/slow-down-bob.html">scribes an open letter homage</a> to R.B. Woodward. Also included is a link to open-access PDFs of R.B. Woodward's <a href="http://dspace.mit.edu/handle/1721.1/12465">doctoral</a> (and <a href="http://dspace.mit.edu/handle/1721.1/10875">bachelor's</a>) theses from MIT. It's really quite fascinating to be able to see how the nature of chemical writing has (and hasn't) changed since 1937. My favorite sentence so far: "When the reaction was complete, the dark brown oil was washed several times with water dried over a small amount of anhydrous sodium sulphate and distilled in a gigh vacuum" (sic). </li>
<li>Derek Lowe discusses <a href="http://pipeline.corante.com/archives/2013/02/06/trouble_hiring_whom_exactly.php">a recent HR-geared report on pharma employment</a>. A heavy implication of the report is that management is having a difficult time finding qualified employees, which Derek disagrees with.</li>
<li>This <a href="http://www.newyorker.com/reporting/2013/02/11/130211fa_fact_keefe">New Yorker profile of Amy Bishop</a>--the scientist who shot six of her colleagues in a faculty meeting--is a long, long read, but it's well-done and illustrates the complexities of what the media (and others) tend to simplify as either a problem with the pressures of academia or purely a case of poor mental health.</li>
<li>Ewan Birney of The Guardian brings us <a href="http://www.guardian.co.uk/science/2013/feb/10/scientists-emotions-highs-lows">a set of short vignettes about the role emotions play in science</a>. It's interesting to read and be mindful of, especially given public perception of scientists (as well as scientist perception of scientists).</li>
<li>This Scientific American blogpost by Samuel Arbesman discusses a new metric for <a href="http://www.wired.com/wiredscience/2013/02/finding-bang-for-your-buck-in-the-world-of-open-access/">determining the ideal impact-to-cost ratio</a> when selecting an open-access journal.</li>
<li>I liked <a href="http://blogs.discovermagazine.com/crux/?p=2756">this story at The Crux</a> (Discover Magazine) about <a href="http://blogs.discovermagazine.com/crux/?p=2756">the role of microbes in shaping biodiversity</a>.</li>
<li>Cassandra Willyard (The Last Word on Nothing) writes about <a href="http://www.lastwordonnothing.com/2013/02/05/sleep-aids/">a classical music album in the 1960s that was produced as an advertisement for a sleep aid</a>. The album's liner notes include the chemical structure for the drug.</li>
</ul>
vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com2tag:blogger.com,1999:blog-3474124548976938700.post-8814930402499697182013-02-06T07:00:00.000-06:002013-02-06T09:48:25.918-06:00Wanna buy some tetrahedral centers?Chemists: Devise syntheses for the following molecules in enantiopure form, starting from affordable, commercially available precursors.* Oh, and make sure your routes are <b>three steps or fewer</b>.<br />
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEixrJ9lTQoIfv2hzV8AC1lgvSxvymrIFexpnzXmBH1P8ZJvcrxKMMBsTW6FqgCqH5OXWn04ZvC2EpiLSXU0x8g3GnfREfA_nuYld2XTiuTBtZmnALjrwVYxH5OWQMgINByxj_KZY48a_bM/s1600/ctd-tm.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="367" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEixrJ9lTQoIfv2hzV8AC1lgvSxvymrIFexpnzXmBH1P8ZJvcrxKMMBsTW6FqgCqH5OXWn04ZvC2EpiLSXU0x8g3GnfREfA_nuYld2XTiuTBtZmnALjrwVYxH5OWQMgINByxj_KZY48a_bM/s400/ctd-tm.png" width="400" /></a></div>
<br />
As conventional total syntheses, of course, that would be a tall order, and each molecule would take a substantial amount of time and effort. But in <a href="http://www.nature.com/nchem/journal/vaop/ncurrent/full/nchem.1549.html">an interesting new paper</a> (behind paywall at <i>Nature Chemistry</i>) by Paul Hergenrother's group at the University of Illinois at Urbana-Champaign, the authors do just that, as well as preparing numerous other, equally complex molecules. The effort introduces a new variant on <a href="http://en.wikipedia.org/wiki/Divergent_synthesis">diversity-oriented synthesis</a> (DOS) which the authors coin "<a href="http://www.scs.illinois.edu/~phgroup/research4.html">Complexity to Diversity</a>"--or CtD.<br />
<br />
<h3>
Complexity to Diversity</h3>
<br />
What CtD entails is this: the authors take stereochemically defined, readily available natural products (here from three classes of biosynthetic small molecules) and perform skeletal transformations on them, using the complexity (chirality and ring structure) present in the molecules to create new compounds that have unusually high numbers of stereocenters and structural sophistication. Moreoever, the compounds are produced in <i>very </i>few steps (from one to about five, averaging three), meaning that regardless of individual stepwise yield, any of the materials may be obtained in quantities sufficient for biological testing or (importantly to chemists) full analytical characterization (check out the SI; there's a lot of NMR data and even a crystal structure!). (This, of course, stands in stark contrast to total synthesis approaches, wherein 3 mg may be the sum total available at the end and making more means gallons of tears and sweat).<br />
<br />
At first, the idea of using <i>natural products </i>(typically thought up as targets) as starting materials may sound odd, but (1) that's how nature does it; and (2) semi-synthesis from easily-procured natural materials is a common strategy, the most common example being paclitaxel. One note, in case this wasn't clear: the authors aren't proposing this as an <i>alternative </i>to traditional total synthesis; rather, it's a <b>forward </b>approach designed to generate a library of novel compounds.<br />
<br />
The authors employed three starting materials readily available on multigram scales: gibberellic acid (pronounced like "jib", not "gib"), adrenosterone, and quinine. These each represent a major class of biosynthetic natural products: terpenes, steroids, and alkaloids, respectively. Of course, each of these compounds have been the subject of <a href="http://www2.lsdiv.harvard.edu/labs/evans/pdf/smnr_2004_Scheerer_Jonathan.pdf">total</a> synthesis <a href="http://www.scs.illinois.edu/denmark/presentations/2005/gm-2005-06_07.pdf">efforts</a> (indeed, quinine is covered in KCN's <a href="http://www.amazon.com/Classics-Total-Synthesis-II-Strategies/dp/3527306846">Classics in Total Synthesis Vol. II</a>, while adrenosterone pops up in Carreira's <a href="http://www.amazon.com/Classics-Stereoselective-Synthesis-Erick-Carreira/dp/3527299661">Classics in Stereoselective Synthesis</a>).<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjQphbjr27S-jbmvDPnBU-8s1AL0UpF4hiOWtziHYS7pqPPdObnr_z2AbMgjyrESpBh2b6GSnIAcoZIFwr8qTun3lVWu9oUp6jwUl5uHOajNSd14cwLX68fKWg1OCrbrZ4z-H3ZuW9BHwM/s1600/ctd-sm.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="142" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjQphbjr27S-jbmvDPnBU-8s1AL0UpF4hiOWtziHYS7pqPPdObnr_z2AbMgjyrESpBh2b6GSnIAcoZIFwr8qTun3lVWu9oUp6jwUl5uHOajNSd14cwLX68fKWg1OCrbrZ4z-H3ZuW9BHwM/s400/ctd-sm.png" width="400" /></a></div>
<br />
The key was the use of structurally transformative reactions (<i>i.e</i>. ring distortions, as in the title of the paper). Take the following example: adrenosterone was submitted to sodium azide and sulfuric acid, giving an interesting tandem ring-expansion (<a href="http://organicreactions.org/index.php/Schmidt_reaction_(summary)">Schmidt reaction</a>) and ring-cleavage. This product (already non-trivially different from adrenosterone in terms of both ring structure and functional group presence) was subjected to a <a href="http://en.wikipedia.org/wiki/Luche_reduction">Luche reduction</a> of the unsaturated ketone, giving stereoselectively an alcohol which was then <a href="http://en.wikipedia.org/wiki/Acetylation">acetylated</a>.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiM9AxPJzISFrEZy7AGgrjDlorE5UKQ9yG-ehhIhhUfk0XTA7eix66PSZf0w0VKVXDbinHzqFDfMjvvymW8DbUn-rLqz4PmEsuUXmDb1EFBQ54RR34pAoU_E9j9HRFltr_w1TbigIbbObE/s1600/adreno1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="248" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiM9AxPJzISFrEZy7AGgrjDlorE5UKQ9yG-ehhIhhUfk0XTA7eix66PSZf0w0VKVXDbinHzqFDfMjvvymW8DbUn-rLqz4PmEsuUXmDb1EFBQ54RR34pAoU_E9j9HRFltr_w1TbigIbbObE/s400/adreno1.png" width="400" /></a></div>
<br />
Another example (this one from gibberellic acid): an initial treatment of gibberellic acid with aqueous base resulted in allylic rearrangement of the lactone to give the trisubstituted alkene. The carboxylic acid moiety was then subjected to amidation and a subsequent dual-purpose treatment with <i>in situ</i>-generated trifluoroperacetic acid, resulting in two stereoselective epoxidations and opening of one of the epoxides via a <a href="http://en.wikipedia.org/wiki/Wagner%E2%80%93Meerwein_rearrangement">Wagner-Meerwein rearrangement</a>.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgOpJp46r7KHKU3bUlYYEvhucK__lETHa6i3pDPCWZIC6-PPVcha9HzSX94NmEoRIJ589hacSBHxgJFGPJh-TTdFEc4F2I0ebjzTGzewi3a4DJBk1KUbrXcRWvOImQTy9UTLUh_HHBBgmw/s1600/gib1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="288" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgOpJp46r7KHKU3bUlYYEvhucK__lETHa6i3pDPCWZIC6-PPVcha9HzSX94NmEoRIJ589hacSBHxgJFGPJh-TTdFEc4F2I0ebjzTGzewi3a4DJBk1KUbrXcRWvOImQTy9UTLUh_HHBBgmw/s400/gib1.png" width="400" /></a></div>
<br />
A third example (of course, with quinine). In a (to me) pretty neat first step, an acid-catalyzed elimination (described as <a href="http://en.wikipedia.org/wiki/Hofmann_elimination">similar to a Hofmann</a>) followed by a <a href="http://en.wikipedia.org/wiki/Carboxybenzyl">carboxybenzyl <i>N</i>-protection step</a> gives a rearranged ring system that has lost one of two fused rings but produced a ketone (via the enol tautomer). The ketone is then subjected to <a href="http://en.wikipedia.org/wiki/Petasis_reagent">Petasis methylenation</a> (aka Diet <a href="http://en.wikipedia.org/wiki/Tebbe_reagent">Tebbe</a>), setting it up for a nice <a href="http://en.wikipedia.org/wiki/Ring-closing_metathesis">Grubbs-catalyzed RCM</a> ring closure to afford the <i>cis</i>-decalin (sort of) moiety.<br />
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<br />
There's lots more examples than that in the paper. In fact, from those three starting compounds, the authors managed to generate a decent-sized proof-of-concept library (a cool feature of the web interface of the journal is that <a href="http://www.nature.com/nchem/journal/vaop/ncurrent/compound/nchem.1549_ci.html">a list of all the compounds in the paper is available here</a>, complete with easily accessed ChemDraw files and PubChem links. There are <b>169 </b>molecules listed. The SI is <i>big</i>. Granted, all the combichem types and HTS folks will dismiss that as a very <i>small </i>library, but it covers a much wider area of chemical space than a typical HTS collection, as the authors point out--I'll get to this shortly).<i> </i><br />
<i><br /></i>
<h3>
</h3>
<h3>
The birth of the CtD</h3>
<br />
The concept of CtD is interesting, as it has its roots in two areas of organic chemistry which haven't been in vogue recently: <a href="http://en.wikipedia.org/wiki/Divergent_synthesis">diversity-oriented synthesis</a> (as mentioned before), and <a href="http://en.wikipedia.org/wiki/Enantioselective_synthesis#Chiral_pool_synthesis">chiral pool synthesis</a>.<br />
<br />
<b>Diversity-oriented synthesis</b> (which is conceptually <a href="http://pubs.rsc.org/en/Content/ArticleLanding/2008/OB/b719372f">similar to combinatorial chemistry but differs in its emphasis of skeletal diversity over substituent diversity</a>) received a lot of attention when it was first championed by <a href="http://www.broadinstitute.org/chembio/lab_schreiber/home.php">Stuart Schreiber</a>, but industry hasn't adopted it as a strategy (though Schreiber and other proponents haven't given up on the concept; check out <a href="http://pubs.acs.org/doi/abs/10.1021/ml200244k">this article for an anti-malarial 'hit' generated by DOS</a> in 2011). Derek Lowe has <a href="http://pipeline.corante.com/archives/2009/01/20/diversityoriented_synthesis_oriented_the_right_way.php">written about it</a> several times, with <a href="http://pipeline.corante.com/archives/2010/11/11/and_one_was_just_right.php">appropriate reservations</a> (incidentally, I'm a little amazed at how much chemist-rage Schreiber seems to induce in Derek's comment sections).<br />
<br />
Incidentally, Hergenrother was a postdoc for Stuart Schreiber around 1999-2001, making him part of a group of several Schreiber alumni who utilize and extend DOS methodology (including <a href="http://www.mskcc.org/research/lab/derek-tan">Derek Tan</a> at Sloan-Kettering and <a href="http://www-spring.ch.cam.ac.uk/drs/drs.shtml">David Spring</a> at Cambridge).<br />
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<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgX0sWm8hrY4B73RgX6K3dFZnLQa_XfpGcbKfgJA0NKc-CbhJLYEHJ2gUYLcmS6e9vZImwPg4nxxHBfLjB5IuQucoxRQwYOvQiEH_FKqDCPyB-F8qqPspU_srFpPBrsyuLmSNOT9ZAybWY/s1600/glucose.png" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="89" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgX0sWm8hrY4B73RgX6K3dFZnLQa_XfpGcbKfgJA0NKc-CbhJLYEHJ2gUYLcmS6e9vZImwPg4nxxHBfLjB5IuQucoxRQwYOvQiEH_FKqDCPyB-F8qqPspU_srFpPBrsyuLmSNOT9ZAybWY/s200/glucose.png" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Chiral and inexpensive.</td></tr>
</tbody></table>
<b>Chiral pool synthesis </b>(aka chiral template synthesis), on the other hand, is simply using readily available chiral starting materials to build complex targets (sometimes called first-generation asymmetric synthesis). For instance, common "chirons" (<i>i.e.</i> chiral <a href="http://en.wikipedia.org/wiki/Synthon">synthons</a>) include amino acids and carbohydrates. Nowadays, this method has been somewhat largely supplanted by chiral auxiliaries and chiral catalysis (sometimes called second- and third-generation approaches) because of their broader scope and other advantages--you don't need a completely new starting material for the other enantiomer, for one, and the chiral reagent can be used in very, very small (hence reduced-cost) amounts if it's a catalyst.<br />
<br />
So CtD seems to be a child of these two methods. Its birth was also likely motivated by biomedically-driven motives: <a href="http://www.chemistry.illinois.edu/faculty/Paul_Hergenrother.html">Hergenrother's group</a> is very involved in high-throughput screening (HTS) efforts for anticancer and antibacterial purposes. I mentioned that DOS gets a bad rap partially because it is an "academic exercise" without use in real industry; I noticed that Hergenrother has (non-CtD) licensing agreements with two companies (<a href="http://eon.businesswire.com/news/eon/20130107006862/en/lung-cancer/pancreatic-cancer/cancer-metabolism">StemPar Sciences</a> and startup <a href="http://www.businesswire.com/news/home/20120127005824/en/startup-University-Illinois-Vanquish-Oncology-Develop-Personalized">Vanquish Oncology</a>). It'll be revealing to see if CtD spills over into any industrial connections.<br />
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<h3>
Natural product-like compound libraries</h3>
<br />
So why bother? Aren't there screening libraries out there? Aren't some of these libraries huge? Isn't combinatorial chemistry well-established? Can't you get, like, six thousand billion compounds and count on one being the magic winner?<br />
<div>
<br />
Well, the authors conducted a significant cheminformatic analysis of screening collections and marketed drugs in order to support their strategy. They noted <a href="http://pubs.acs.org/doi/abs/10.1021/jm200504p">a recent survey article from </a><i><a href="http://pubs.acs.org/doi/abs/10.1021/jm200504p">J. Med. Chem</a>.</i>:<br />
<blockquote class="tr_bq">
A recent study examined eight structural parameters (molecular weight, ClogP, polar surface area, rotatable bonds, hydrogen-bond donors and acceptors, and complexity and fraction of sp3-hybridized carbons (Fsp3)) of compounds synthesized by medicinal chemists over the past 50 years, and then compared them to marketed drugs</blockquote>
The point was this: <b>the properties of screening collections don't generally match up well to marketed drugs</b>, and in certain sub-categories of drugs (say, antibiotics) the mismatch is worse than for others (say, kinase inhibitors). Hence, HTS efforts using these collections are putatively destined for higher-than-expected inefficiency.<br />
<br />
In analyzing the results of CtD, Hergenrother <i>et al.</i> chose to focus particularly on proportion of tetrahedral (vs. planar) carbons (Fsp3) and ClogP, comparing the CtD library to the <a href="http://www.chembridge.com/index.php">ChemBridge</a> 150,000-compound collection. See <a href="http://www.nature.com/nchem/journal/vaop/ncurrent/fig_tab/nchem.1549_F5.html">Figure 5</a> of the article (reproduced partially below) for the analysis, presented in shiny, colorful graphs. They demonstrate a clear difference between commercial libraries and the CtD compounds on three metrics: stereocenters, tetrahedral content (representing complexity), and ClogP.<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjqu7g-BXKNpv96cS9sx4KiwvERzdjtBgxqbyyCrKC5-GUv7Ux4u2H435xoIScdQEPZ5K-nzpwI1nSFFPeTVyJdjWh_lA1I0086UYusruxe7xKFSLovxmx8OR1OBEshtQbUswpnGJyNC6s/s1600/chemoinformatic.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="202" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjqu7g-BXKNpv96cS9sx4KiwvERzdjtBgxqbyyCrKC5-GUv7Ux4u2H435xoIScdQEPZ5K-nzpwI1nSFFPeTVyJdjWh_lA1I0086UYusruxe7xKFSLovxmx8OR1OBEshtQbUswpnGJyNC6s/s400/chemoinformatic.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Example of chemoinformatic analysis from paper, differentiating ChemBridge<br />
library (red) from novel CtD library (blue). Click the image for a larger (<i>i.e</i>.<br />
readable) version. <b>Source</b>: part of <a href="http://www.nature.com/nchem/journal/vaop/ncurrent/fig_tab/nchem.1549_F5.html">Figure 5 from the article</a> (Nature).</td></tr>
</tbody></table>
<br />
Additionally, a matrix is shown with <a href="http://en.wikipedia.org/wiki/Jaccard_index#Tanimoto_Similarity_and_Distance">Tanimoto similarity coefficients</a> (essentially a geometry-based metric of 'similarity') that indicates substantial geometrical diversification even within groups derived from a common precursor. I'm not 100% convinced on how well Tanimoto scores predict <i>useful </i>diversity (for instance, a compound and its enantiomer would have a coefficient of 1.0 for complete similarity, and so would brominated and fluorinated versions of each other**). Still, it's an interesting metric! Note: a Tanimoto matrix of all 169 compounds is in the SI, if you like that kind of thing.<br />
<br />
To sum that up: the group argues that they've created a library that is more 'drug-like' (and/or natural-product-like) than traditional (read: flat and boring) screening collections. Seems reasonable, but I wish there were more chemoinformatic analysis included.</div>
<div>
<br /></div>
<div>
<h3>
It's tricky (potential pitfalls)</h3>
<br />
The synthetic chemist in me likes this paper a lot: after all, who doesn't like a healthy dose of wedges and dashes in as few steps as possible? However, I've got a few questions. Some potential limitations:</div>
<div>
<br /></div>
<div>
<b>Derivatization</b>. Med chem efforts tend to involve lots of taking a compound and slightly modifying it a bunch of times followed by screening of the derivatives (this is why med chem articles are pretty much the <i>most boring thing in the world to read</i>). I worry that leads generated in this way would be difficult to conduct derivization studies on. The authors do address this:<br />
<blockquote class="tr_bq">
To demonstrate that traditional derivatization strategies can be applied even to these highly complex compounds that contain an array of chemical moieties, small libraries were synthesized based on 12 of the 49 compounds. As shown in <a href="http://www.nature.com/nchem/journal/vaop/ncurrent/full/nchem.1549.html#supplementary-information">Supplementary Fig. S4</a>, small collections of imides, N-benzylated amides, aryl amides, amides, lactones, secondary and tertiary alcohols, epoxides, triazoles, ureas and sulfonamides were created readily from these 12 small molecules, and in this manner an additional 119 highly complex compounds were synthesized.</blockquote>
Still, with the strategies employed here, it's very easy to envision only being able to functionalize a small area of a given molecule--and it's also feasible that the functionalizable area would be distant from the actual pharmacophore.<br />
<br />
<b>Throughput</b>. Though the output here is good, the reactivity on complex materials is often, well, rather unpredictable. Accordingly, thorough purification and characterization is needed at each step. That rather limits the high-throughput aspect of an approach like this, especially compared to combi-chem and DOS approaches that use highly predictable pathways that can be automated. After all, the idea is to generate a <i>library</i>. Numbers-wise, it's like comparing your bookshelf to your university library (although, if your university library has three million slightly different copies of Twilight but your bookshelf has Dostoevsky, Hugo, Hemingway, Shakespeare, and Poe, numbers might not matter).<br />
<br />
<b>Scope/compound selection</b>. The authors do place some guidelines for selecting CtD compounds and reactions near the end of the paper. Still, when compared to simple, achiral starting materials, the selection of multigram-available, affordable natural products with appropriate orthogonality of functional groups seems scant. It could very well be that the good CtD compounds get taken very quickly, leaving few useful options. A lot of that depends on availability of natural products, of course--but is industry really isolating and/or making enough of these for this purpose? The authors address this, somewhat, giving a list of some suggested natural products. But it's a short list.<br />
<br />
<b>Does CtD walk the walk? </b>It's interesting to see that no biological screening was reported. As one of the goals of this kind of research is to expand the scope of chemical space covered in screening collections, and by doing so, to improve screening efforts, it will be important to see if that benefit comes to fruition. The chemoinformatic analysis in the paper suggests these compounds to be more natural product-like/more drug-like--will that come to anything, practically? I hope it does. But there's a big gamble here that because complexity is <i>correlated </i>with many drugs (e.g. antibiotics), it'll be <i>causative</i> too.<br />
<br />
(End of gloom-rant).</div>
<div>
<br /></div>
<div>
I do think this kind of project would be an excellent training exercise for early graduate students. Routes are short, the chemist would get exposed to a variety of reactions, structural elucidation skills would get quickly strengthened, and the results could very easily be contributed to screening libraries, potentially leading to leads for biologically-driven studies.<br />
<br />
One last thought: this work has the potential to annoy a lot of people (perhaps for bad reasons). I can see total synthesis chemists getting annoyed at the economy of steps; I can see med chemists getting annoyed at the lack of trigonal carbons and flat rings; I can see methodology or process chemists getting annoyed at the lack of optimization (since yields here aren't important); and I can see chemical biologists being confused as to whether this is or isn't just a rehash of DOS.<br />
<br />
But I think it's a cool paper.<br />
<br /></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgveHys-qZOcYW2W83LJeAyCNkQU-6DPv1DOG4xu58hKUOuc2kwkPdMhgiN7HlDgvxu4uawWJg4UKq00h7y8CoctQJ5JiLB09aik0OkUg_ElP5JMh5As_nO8a3MS9AmvKNHFkRO8xJ_uo/s1600/medchem.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="121" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgveHys-qZOcYW2W83LJeAyCNkQU-6DPv1DOG4xu58hKUOuc2kwkPdMhgiN7HlDgvxu4uawWJg4UKq00h7y8CoctQJ5JiLB09aik0OkUg_ElP5JMh5As_nO8a3MS9AmvKNHFkRO8xJ_uo/s400/medchem.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Comparison of synthetic approaches*** (a) Target-oriented synthesis;<br />
(b) Medicinal chemistry/lead optimization; (c) Diversity-oriented synthesis.</td></tr>
</tbody></table>
<div>
<br /></div>
<div>
<i><br /></i></div>
<div>
<i>Note: this journal article has also been covered in <a href="http://cen.acs.org/articles/91/i4/Ringing-New-Drug-Candidates.html">C&EN</a> and by <a href="http://chemcascade.wordpress.com/2013/01/28/a-ring-distortion-strategy-to-construct-stereochemically-complex-and-structurally-diverse-compounds-from-natural-products/">Chemistry Cascade</a>.</i><br />
<i><br /></i>
<span style="font-size: x-small;">* Of course, this instruction is disingenuous, given that retrosynthetic analysis is not really feasible here and it's not target-oriented synthesis anyway, but hey. </span><br />
<span style="font-size: x-small;">** I think.</span><br />
<span style="font-size: x-small;">*** Alternate interpretation: total synthesis is not as good as Come On Eileen, med chem is better than but pretty much as boring as Nickelback, and DOS confuses as many people as David Bowie.</span><br />
<span style="font-size: x-small;">**** I'm guilty of using lots of footnotes. Sorry, <a href="http://justlikecooking.blogspot.com/2013/02/friday-fun-title-goes-here.html">See Arr Oh</a>!</span><br />
<span style="font-size: x-small;"><br /></span>
<span style="font-size: x-small;"><i>[Edit: fixed minor typographical errors.]</i></span></div>
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vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com11tag:blogger.com,1999:blog-3474124548976938700.post-42917592214841755072013-02-03T09:00:00.000-06:002013-02-03T15:13:38.495-06:00Reading assignments, vol. 9<br />
<div>
This week's stuff is pretty heavily communication-themed; a lot of that is going around with the ScienceOnline 2013 deal having gone down. Anywhere, here's some general science enjoyment:</div>
<div>
<br /></div>
<h3>
Chemophobia</h3>
<div>
<ul>
<li>Chemophobia has been a major topic of the social-media-dom recently due to the <a href="http://scienceonline.com/scienceonline2013/">ScienceOnline 2013 conference</a>. In particular, Saturday marked the chemophobia-specific portion of the conference (Session 8A), which included <a href="http://cenblog.org/terra-sigillata/2013/02/01/watch-twitter-on-saturday-for-chemophobia/">a contemporaneous Twitter discussion</a> via the hashtag <a href="https://twitter.com/search?q=%23chemophobia&src=hash">#chemophobia</a>. For those who had to work this Saturday (woo, columns, woo) <a href="https://docs.google.com/document/d/1VWQ85ZyfnakQHUOrw6LZ1PbDI5CuAOC6TvRuMW55PXI/edit">the session notes have been posted online</a>, and there's <a href="http://scio13.wikispaces.com/Session+8A">a quite impressive wiki entry</a> containing an abundance of relevant and interesting chemophobia-related links and discussions.</li>
<li>Michelle at The Culture of Chemistry has <a href="http://cultureofchemistry.fieldofscience.com/2013/02/chemophobia-boy-with-thorn-in-his-joints.html">a thoughtful analysis</a> of a recent <a href="http://www.nytimes.com/2013/02/03/magazine/the-boy-with-a-thorn-in-his-joints.html">chemophobia-rife New York Times story</a>; she points to language and how it affects perception of concepts.</li>
<li>Paul at ChemBark shares his tips and proposed strategies for <a href="http://blog.chembark.com/2013/02/01/combatting-chemophobia/">how to combat chemophobia</a>. It's a good read that sums up the origins and dangers of chemophobia pretty well. The recommendations are good, too: ACS should be doing its part (come on, guys!) but graduate students and faculty need to take it upon themselves to do outreach, regardless of the perceived waste of time. (That being said, the hostile intellectual atmosphere and the rough job market make spending any time on outreach seem unappealing to those trying to get as many ninth-author <i>Tet. Lett. </i>papers as possible published before graduating).</li>
<li>Don't miss this latest Chemjobber podcast, wherein he discusses <a href="http://chemjobber.blogspot.com/2013/01/podcast-dr-rebecca-guenard-and.html">chemophobia and chemical communication</a> with freelance writer/chemist Rebecca Guenard. </li>
</ul>
<h3>
Science communication</h3>
<div>
<ul>
<li>See Arr Oh <a href="http://justlikecooking.blogspot.com/2013/02/friday-fun-title-goes-here.html">pokes fun at general features of chemistry blog entries</a>.</li>
<li>I found <a href="http://www.scilogs.com/communication_breakdown/swain-benchpress-program/">this guest post by Frank Swain</a> both insightful and heartening. He writes of his UK-based BenchPress Project, which seeks, among other things, to have volunteer <a href="http://www.scilogs.com/communication_breakdown/swain-benchpress-program/">scientists give guest lectures to journalism students</a>. The goal is to increase science and math (maths) literacy among journalists. I think it's a pretty important effort; even if scientists themselves try to do outreach and writing, journalists have the broadest audience and the means to reach them. Changes in science communication have to come from within both sectors!</li>
<li>David Rubenson argues that despite a growing need for science communication, <a href="http://www.the-scientist.com/?articles.view/articleNo/34196/title/Opinion--Communication-Crisis-in-Research/">the <i>quality </i>of science communication has been in decline</a>. He points to several symptoms (e.g. cluttered slides) and causative agents (e.g. overstretched researchers). I found significant his reference to two Nobelists who published infrequently (also, it reminded me of Daniel Day-Lewis).</li>
<li>Always-interesting and often-controversial, Keith Kloor discusses the relative<a href="http://blogs.discovermagazine.com/collideascape/2013/02/01/whats-more-important-science-literacy-or-news-literacy/"> importance of general science literacy and news literacy</a>. He argues for the importance of the latter (while not neglecting the former); in particular, he calls for news literacy to have a place in education. It shouldn't be an unfamiliar concept to scientists, who (should) be experienced at evaluating credibility of sources.</li>
<li>UIUC anthropologist and science blogger Kate Clancy has an interesting piece (relevant to anyone who uses social media, especially those who write) about the pros and cons of filling out your online presence with your <a href="http://blogs.scientificamerican.com/context-and-variation/2013/01/29/context-and-identity-in-science-writing-scio13id/">real identity</a>.</li>
</ul>
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<h3>
Pseudoscience and denialism</h3>
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<ul>
<li>Notorious TV doctor Dr. Oz has received some negative limelight this week. Derek Lowe, for instance, responds to <a href="http://www.newyorker.com/reporting/2013/02/04/130204fa_fact_specter">a recent New Yorker profile</a> by commenting quite frankly (and accurately) on <a href="http://pipeline.corante.com/archives/2013/01/29/dr_ozs_problem.php">the gross degree of subjectivity and religiosity purveyed by Oz</a>. Lowe is probably preaching to the choir, but he makes a very strong argument by pointing out that the institution of medicine, which is responsible for Oz's success, was decided not a post-modernist, choose-your-own-facts endeavor. Orac is not pleased, not surprisingly, and <a href="http://scienceblogs.com/insolence/2013/01/30/dr-ozs-journey-to-the-dark-side/">criticizes Dr. Oz's recent endorsement of homeopathy</a>. In the vein of homeopathy, <a href="http://www.youtube.com/watch?v=HMGIbOGu8q0">this video is relevant and amusing</a>. Lastly, see this quick list of some<a href="http://www.forbes.com/sites/jeffbercovici/2013/01/28/dr-ozs-five-wackiest-medical-beliefs/"> downright wrong beliefs</a> peddled by the good doctor.</li>
<li>Moving from medicine to sports, read a brief account of some <a href="http://pipeline.corante.com/archives/2013/01/30/scamorama.php">pseudoscientific nonsense from athletes</a>.</li>
<li>Amazingly, the teaching of evolution is still threatened by denialists the world over. It's a big problem in Turkey, for instance, where the Scientific and Technical Research Council of Turkey has <a href="http://scienceblogs.com/gregladen/2013/02/02/evolution-debate-ends-in-turkey/">stopped publishing books that support the theory of evolution</a>. Evolution has <a href="http://www.nature.com/nature/journal/v458/n7236/full/458259a.html">been in Turkey's crosshairs</a> for a while. Meanwhile, here in the United States, we have <a href="http://www.house.mo.gov/billtracking/bills131/biltxt/intro/HB0291I.htm">Missouri House Bill 291</a> (titled the "Missouri Science Standard Act"). Read P.Z. Myers' <a href="http://scienceblogs.com/pharyngula/2013/02/01/whoa-missouriyoure-not-going-to-let-this-one-pass-are-you/">breakdown of the legislation</a> (which is in limbo). The bill is pretty frightening, pretty blantantly pro-creationism, and also terribly hypocritical. Also, Greg Laden points out <a href="http://scienceblogs.com/gregladen/2013/01/30/science-vs-anti-science-updates/">a new anti-science bill in Arizona and the contrasting opposition to an anti-science bill in Montana</a>.</li>
</ul>
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Other</h3>
</div>
<ul>
<li>This week Brandon Findlay has been running a series of posts about <a href="http://chemtips.wordpress.com/tag/columns-week/">column chromatography</a>. It's a good introduction or a good refresher, so give them a read.</li>
<li>Derek Lowe has an<a href="http://pipeline.corante.com/archives/2013/01/28/time_to_refill_your_prescription_for_zxygjfb.php"> interesting take on drug names</a> (and how they've changed!).</li>
<li>Neuroscientist Jessica Carilli <a href="http://jessicacarilli.blogspot.com.au/2013/01/go-to-graduate-school.html">makes the case for grad school</a> in light of recent discussions of the unhealthy aspects of graduate study as well as the abysmal scientific job market.</li>
<li>It's not infrequent to hear people complain about the uselessness of certain research programs, or at least to insist that they're too expensive (if the financial benefits aren't immediately obvious). Pete Etchells <a href="http://blogs.discovermagazine.com/crux/?p=2744">comments on NASA and the Curiosity rover, arguing against these viewpoints </a>and giving some examples of how NASA technology has been repurposed for wide benefit.</li>
<li>Maryn McKenna explores the poultry industry: specifically, how <a href="http://www.wired.com/wiredscience/2013/01/poultry-transparency/">lack of transparency leads to unsustainable antibiotic use</a> practices that contribute to widespread antibiotic resistance.</li>
</ul>
<div>
<i>[Edit: I forgot Brandon Findlay's <a href="http://chemtips.wordpress.com/tag/columns-week/">columns week</a>! Urp!]</i></div>
</div>
vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com6tag:blogger.com,1999:blog-3474124548976938700.post-1239741517975192882013-01-31T07:00:00.000-06:002013-01-31T07:00:09.371-06:00Tips for grad school recruiting weekendsIt's the new year, which means over the next few months everyone who has applied to grad school in chemistry (and other fields... there <i>are </i>other fields, right?) should be receiving responses back from admissions committees. Acceptance letters generally contain salary information, program information, and an invitation to a visit weekend. In chemistry, these visits are almost always paid for by the department. Yep: free trip, food, and drinks. But why?<br />
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There are two ways to look the motivation behind visit weekends. Decide the veracity of either for yourself:</div>
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<b>Rationalization 1:</b> Most good chemistry departments don't want to waste their time and money.* An admitted student in a graduate program is expensive: stipend, research supplies, tuition, etc. are all paid for by the department and/or the student's adviser. So it's in everyone's best interest to make sure students are picking the appropriate school for them. Hosting a visit weekend allows prospective students to meet their possible classmates, their future advisors, and see if the grad program and facilities are appealing to them. That way there's a better chance they are happy where they go, leading to a better chance of graduation.</div>
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<b>Rationalization 2:</b> If you throw free stuff at students who have been paying for school, offer them money, and paint an inordinately sunny picture of your grad program, you'll get more students. The more students you get, the harder you can work students, and it won't matter as much if some leave. Cheap labor! </div>
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Grad school visits can be fun. They differ from med school interviews, vet school interviews, and non-science grad school visitation weekends in one key way: you're already accepted. And the visit doesn't cost you anything financially.** Note the following figure, which illustrates the processes comparatively:<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJ_KsmyRud8A0UwOhE8heBI6k3Nuk1GGfXYub3fDN0Hv7-NAkNQDxvgO2i9S-2pv27ZSFOnD65FFsYmeDGsQF-LpJeOLQ9Bgv8D5c0x5XtvCn3tJYVgnCoxQxyHvnSjdCnzqodEjIdR-o/s1600/flow.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="273" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJ_KsmyRud8A0UwOhE8heBI6k3Nuk1GGfXYub3fDN0Hv7-NAkNQDxvgO2i9S-2pv27ZSFOnD65FFsYmeDGsQF-LpJeOLQ9Bgv8D5c0x5XtvCn3tJYVgnCoxQxyHvnSjdCnzqodEjIdR-o/s400/flow.png" width="400" /></a></div>
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Overall, grad school visits are an important opportunity. Keep in mind a few things:</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWwMid4kSxqibNhOCaMfg_UZZiI4m-DLbK7mrWnKvZgW6xtn9-ntQN15pPIq8alJK5f6cEz07lS7dOuXzKCXq_VGH92AQ_8225Ij7CVJz22JNSw6jKYCDgMlh5UpOeKIQ-xJc21Kwv-XM/s1600/dresscode.png" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="255" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWwMid4kSxqibNhOCaMfg_UZZiI4m-DLbK7mrWnKvZgW6xtn9-ntQN15pPIq8alJK5f6cEz07lS7dOuXzKCXq_VGH92AQ_8225Ij7CVJz22JNSw6jKYCDgMlh5UpOeKIQ-xJc21Kwv-XM/s320/dresscode.png" width="320" /></a></div>
<b>1. It's not an interview</b>. You're not trying to impress the department. They're trying to convince you to make essentially minimum wage, working the equivalent of 1.5 to 2 full-time jobs for probably 6 years with minimal outside social contact or hobbies so that one person in your department can get approximately 5 more papers. Also you'll have to babysit undergrads. If you're going on a visitation weekend (except, I guess, at Scripps, which actually <i>does </i>hold interviews) that means you're <i>in</i>. You're guaranteed a spot. It's <i>their</i> job to impress <i>you</i> and convince you to attend.<br />
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That being said, don't dress like a slob; don't drink too much; don't deliberately offend anyone. Your professional career is beginning, and first impressions are <i>kind </i>of important. But it's not a med school interview or a corporate meeting: in grad school, getting work done is more important than showing off your suit and haircut. So relax and be yourself. Unless you happen to be an arrogant idiot.</div>
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<b>2. Don't talk about yourself very much.</b> Again, you're not trying to impress the admissions committee. You shouldn't be trying to impress any of the students there (they won't be impressed by you, no matter how many fifth-author <i>Chem. Bioorg. Med. Chem. Lett. Eur. J. Int. Ed., Dalton Trans. </i>papers you have)--it serves no point. Make the visit about listening and learning, not about boasting. You can boast after you succeed in chemistry and land a $40k job after ten years of school. Instead, observe the professors. Are they approachable? Arrogant? Distant? Humble? Listen to how the grad students talk. Do <i>they </i>brag? Are they competitive or easy-going? Can any of them talk about something besides chemistry? Are <i>they </i>trying to impress you? And very importantly, pay attention to the other prospective students on the visit. Do they all act like they have something to prove? Are they people you could get along with? Are they bragging about their seventeen fifth-author <i>Chem. Bioorg. Med. Chem Lett. Eur. J. Int. Ed., Dalton Trans. </i>papers? Are they fun to hang out with? (Being fun to hang out with is a legitimate concern; you'll see some of these people a <i>lot</i>).</div>
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<b>3. Find the best and the worst about the program.</b> Generally, admissions committees will carefully select which grad students host prospective students. They'll hand-pick the ones who still have their optimism; may the group that have just passed candidacy exams or who haven't had to TA in a while. Generally 2nd to 3rd year students.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEineURNUQzotWn7HNa39B0TLHLDF2a7V5rTihbVb5HlWLIFb4gxd76catWuczUnnoB13wW_4-8JmRdZIcfQEBmdAIRqJnYPvet2eVxGeKs4bt2AZwPrygrt1V-uNx1WwS1om0cJnh90QjU/s1600/science.png" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="250" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEineURNUQzotWn7HNa39B0TLHLDF2a7V5rTihbVb5HlWLIFb4gxd76catWuczUnnoB13wW_4-8JmRdZIcfQEBmdAIRqJnYPvet2eVxGeKs4bt2AZwPrygrt1V-uNx1WwS1om0cJnh90QjU/s400/science.png" width="400" /></a></div>
It's important to listen to these students: you want to find out about the good parts of the program! But make sure you seek out the embittered, late-stage students as well. You want a spectrum of opinions. Find at least one student who doesn't <i>really </i>want to talk to you. Have a conversation like this:</div>
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<blockquote class="tr_bq">
You: "Hey, seventh-year grad student!" </blockquote>
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Student: "F@#* off." </blockquote>
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You: "Cool! What do you think of Professor Schmorey? His research is so cool! I want to be a PI! Do you like working for him?" </blockquote>
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Student: "F@#* off." </blockquote>
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You: "Awesome! Is teaching <i>really </i>fun or <i>super </i>fun?" </blockquote>
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Student: "F@#* off."</blockquote>
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In short, you need to know what the possibilities are. No department is as rosy as the admissions people want you to think. Ascertain what the emotional arc will be on your grad school journey.<br />
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Also, be wary of how much or how little effort/money the school puts into recruitment. Too much effort: are they desperate for students? Too little effort: do they even care? It's a courtship. Try to distinguish genuine enthusiasm from mere marketing.<br />
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<b>4. Ignore the stipend (but do look at cost of living).</b> Yes, it's cool that they're going to be paying you. At least, it's cool for about four weeks, then it's depressing, because you could be managing a McDonald's and making more money than that, but that would only be a 40 hour work week, you'd get benefits, and hey, you'd get infinity fries if you wanted them.</div>
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Point is: you're not going to get rich in grad school. That's not the point. If a school doesn't pay enough to live off of, that's a problem, but pretty much every school will. Ask grad students about it on your visit weekend. But it's not a good idea to make a "high" stipend an important part of your decision. You'll be poor either way.*** What's more important is choosing a school that will benefit you in the long run.<br />
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Also, don't ask other prospective students if they got additional fellowships or signing bonuses, or brag about yours. You'll either wind up sad or you'll annoy everyone.</div>
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<b>5. Learn about departmental seminars. </b>No one really says this, oddly. I guess I think it's important because I've seen schools with very bad seminars and schools with very good seminars. Seminars (sometimes called colloquiums) are when the department hosts a speaker (usually an academic scientist; occasionally an industrial chemist) who gives 1 or 2 free lectures to the department about their research. Often there's coffee, muffins, cookies, tea, etc. </div>
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Departmental seminars can be very bad for several reasons: sometimes attendance is required; sometimes the material is boring; sometimes the speakers aren't engaging and the PowerPoints are weird and the artwork and data are definitely recycled from 1995, and who uses WordArt anyway? Usually this happens at lower-tier schools, where no money is available to pull in noteworthy scientists and so anyone within a walking radius is invited to lecture. In these cases, seminars can interfere with getting your labwork done, as you don't really gain anything from them.</div>
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But seminars can be very good. Ask current students about this! Some schools have fantastic speakers--Nobel prize winners,**** influential chemists, people whose names you've read or whose work you've learned about. These are great opportunities: you can network (important), you can hear interesting chemistry, and you can broaden your base of knowledge. In short, good invited speakers are an important, underrated factor you should consider in your decision. </div>
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<b>7. Don't make it all about the research. </b>Your undergrad advisor will sit down and look you sternly in the eye. "Make sure you're choosing a school for the <i>science</i>," he'll say (or she'll say). That's what a lot of people will tell you: to make sure the science is something really interesting. That makes sense, doesn't it? It's a research program! You'll be doing research every day! Isn't that important?<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhbJtmqNibRmCSdgnbwbtpdOO4WQYIn9J9zN_S4-FhGhFzHDXpMAaQsc52E2E4tIkCfzg6C28hVo6j2dTPZwoMp8OBmK1g9doNorqKMLyhT2LN1cu_Tmg10PtXClwTIenSoTtLLLI9_UTA/s1600/whip.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="248" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhbJtmqNibRmCSdgnbwbtpdOO4WQYIn9J9zN_S4-FhGhFzHDXpMAaQsc52E2E4tIkCfzg6C28hVo6j2dTPZwoMp8OBmK1g9doNorqKMLyhT2LN1cu_Tmg10PtXClwTIenSoTtLLLI9_UTA/s400/whip.png" width="400" /></a></div>
Yes, it's obviously important. It would be absolute drudgery to be stuck for an indeterminate number of years doing a project you hated -- or worse, were ambivalent about. So it's critical to pick a program that has a couple interesting-sounding research areas. Ask students on your visit weekend about their research: do they seem excited by it? Often it's not the exact research itself but the people involved that make the work exciting--if you have an encouraging research advisor and helpful labmates but a good project you may easily end up more motivated than someone who has their lifelong dream project but a manipulative advisor and bitter labmates.<br />
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You'll probably change what you're interested in during your first semester. Additionally, very, very, very few people end up doing for their career what they do in grad school. Tenure-track positions are rare, and they almost always require one or two postdoc appointments beforehand, and they involve a change in research focus. Plus, many people go into industry or non-traditional careers completely unrelated to their dissertation topic. So don't worry about finding the 100% perfect research fit. It's vital to learn about things other than The Science on your visit. After all, you'll be <i>living </i>there too.</div>
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<b>8. Meet the professors you want to work for. </b>Some people don't think this is very important. But you're committing a <i>lot </i>to the program--more than half a decade. Shouldn't the person who will hold your fate in their hands at least show up to meet you?<br />
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There's a lot of professors who don't go to recruiting weekends, citing busy travel schedules. To an extent, that's understandable. But is the professor you want to work for more interested in promoting him/herself than serving as a mentor to you?<br />
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Meeting professors and groups will also show you that group webpages are deceiving. Some professors who seem crazy good on paper are kind of weird and creepy in real life. Conversely, some folks with lame webpages or research that didn't strike you as appealing are engaging and exciting to talk to.<br />
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<b>9. Don't do homework at the hotel. </b>It's just undergrad. Don't take it so seriously. Use the free coffeemaker! Hang out with other prospective students and current grad students! Seriously: take the opportunity to socialize on the visits, even if you're tired.<br />
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Overall, remember: in the worst case, your visit weekend will mean free food and a free trip. Unless, of course, the university loses the paperwork and doesn't reimburse you for the plane ticket, in which case you paid $600 for a trip to a weird town but didn't get to see anything except NMRs.</div>
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<span style="font-size: x-small;">* Some departments do seem to <i>want</i> to waste money and time, but that's another matter. </span></div>
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<span style="font-size: x-small;">** There are exceptions, of course. Some schools don't have the budget to pay for prospective students to travel. Others only have enough money to pay for gas or meals. Some will make you arrange your own travel.</span></div>
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<span style="font-size: x-small;">*** Obviously, extreme differences -- say $19k vs $25k for the same city -- might be worth considering. </span></div>
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<span style="font-size: x-small;">**** Actually, from experience: Nobel prize winners are, more often than not, <i>terrible </i>speakers. But it's nerd cred to hear them, I guess.</span></div>
vinylogoushttp://www.blogger.com/profile/04278027233887601040noreply@blogger.com24tag:blogger.com,1999:blog-3474124548976938700.post-24430139902714477872013-01-27T07:00:00.000-06:002013-01-27T07:00:04.703-06:00Reading assignments, vol. 8Links and interesting topical stories from the week follow below.<br />
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<h3>
Academia</h3>
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<li>Scientific and writer DNLee of Scientific American gives <a href="http://blogs.scientificamerican.com/urban-scientist/2013/01/24/a-dream-deferred-how-access-to-stem-is-denied-to-many-students-before-they-get-in-the-door-good/">a powerful account of the factors denying good STEM education to many students</a> (namely, those of low socioeconomic status). It's a very important read, as it highlights many issues in science education (and education and science culture in general) that very often get ignored. </li>
<li>At Gene Expression, Razib Khan <a href="http://blogs.discovermagazine.com/gnxp/?p=19833">comments on affirmative action and science</a>. He's largely dismissive of it, saying science doesn't <i>need </i>cultural diversity per se (with a caveat that such diversity is valuable from a <i>social </i>perspective). It's a worthwhile read; only the myopic would be reluctant to admit there is a rather skewed demographic makeup in science relative to the entire population.</li>
<li>Derek Lowe has a commentary on an <i>ACS Med. Chem. Lett.</i> opinion piece regarding <a href="http://pipeline.corante.com/archives/2013/01/22/academias_role_in_drug_discovery.php">the role of academia in drug discovery</a>. It's worth thinking about, especially to those interested in science funding or science policy. The case can really strongly be made that academia can not replace pharma as a productive drug production vehicle, but the decoupling from financial risk means academic labs can push innovations that are potentially high impact but not necessarily profitable.</li>
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Scientific representation and misrepresentation</h3>
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<li>This Sceptical Chymist guest post by PhD student Fabian Carson about <a href="http://blogs.nature.com/thescepticalchymist/2013/01/the-art-of-presenting.html">presentation skills for scientists</a> is very relevant to the current state of chemistry talks (let's face it: most chemistry talks are terrible; even big-name speakers with high impact research can give eye-glazing accounts). The points are concise and <i>should </i>be common knowledge, but presentation skills aren't taught very much and so I'd bet that many scientists don't know this stuff or just don't care. One caveat: Carson recommends Prezi. I heartily encourage you to never, ever, ever touch Prezi. It's garish and terrible. Don't do it. </li>
<li>On a related note, Khalil Cassimally emphasizes the importance of communication to the general public and<a href="http://blogs.scientificamerican.com/incubator/2013/01/23/communicating-science-workshop/"> announces a very exciting-looking science communication workshop for grad students, titled "Communicating Science."</a> The workshop will occur this June in Cambridge, MA, and registration is free!</li>
<li>A couple posts here can be further sub-categorized to "responses to chemophobia":</li>
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<li>Professor Janet Stemwedel uses <a href="http://blogs.scientificamerican.com/doing-good-science/2013/01/25/can-we-combat-chemophobia-with-home-baked-bread/">breadmaking as a vehicle to combat chemophobia</a>. This is a good spin on chemicals and food, and it's particularly relevant given the quite explosively diarrheic chemophobia that tends to emit from the "foodie" community. </li>
<li>See Arr Oh gives his thoughts on <a href="http://justlikecooking.blogspot.com/2013/01/some-thoughts-on-bvo-writeups.html">some current negative media attention on brominated vegetable oil</a>. As with any scary-sounding chemical, BVO has received some arguably warrantless attention from people who think they're health-conscious. </li>
<li>On his blog The Simple Candle, chemistry professor Stephen Prilliman <a href="http://simplecandle.wordpress.com/2013/01/25/21/">encourages reclaiming the word "chemical" from its widespread negative connotations</a>. He presents a Twitter strategy to do so.</li>
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<li>See Arr Oh <a href="http://justlikecooking.blogspot.com/2013/01/wwwtp-medchemcomm-edition.html">also points out to us a very embarassing TOC graphic</a> from <i>MedChemComm</i>.<i> </i></li>
<li>In light of recent instances of scientific fraud and <a href="http://justlikecooking.blogspot.com/2013/01/open-and-shut-case.html">plagiarism</a>, the finding that<a href="http://blogs.scientificamerican.com/the-curious-wavefunction/2013/01/22/study-indicates-that-scientific-fraud-may-have-a-male-bias/"> scientific fraud may have a male bias</a> is interesting and relevant.</li>
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<h3>
Chemistry job market</h3>
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<li>Glen Ernst comments on a 1979 article from C&EN bemoaning <a href="http://cenblog.org/just-another-electron-pusher/2013/01/from-the-archives-a-surplus-of-phds/">an impending surplus of chemistry PhDs exceeding the number of available jobs</a>. As Glen points out, "non-traditional" here meant not being a university professor. Today, the scope of "traditional" careers has broadened, but the employment outlook seems bleaker. Still, it's an interesting insight from the late 70s.</li>
<li>I found <a href="http://chemjobber.blogspot.com/2013/01/interview-pierre-morieux-chemdraw-wizard.html">this interview of ChemDraw wizard</a> (and recently-hired Perkin Elmer employee) Pierre Morieux by <a href="http://chemjobber.blogspot.com/2013/01/interview-pierre-morieux-chemdraw-wizard.html">Chemjobber</a> quite interesting. It's a neat career path, and a cool story of how social media and online networking can land you a job. At the same time, comments imply that some chemists think it is overkill (and perhaps a telltale sign of the job market) that a long PhD and a competitive postdoc do not result in a "traditional" job. (I'd caution that non-"traditional" careers aren't necessarily fallbacks and can be more rewarding than the big-name jobs; I'd also like to point out that many people in many professions change career paths many times!). </li>
<li>At Chemistry World, economist Paula Stephan has some perhaps-controversial, perhaps-obvious (depending who you ask) points on the PhD glut. She<a href="http://www.rsc.org/chemistryworld/2013/01/too-many-scientists"> likens grad school to a pyramid scheme</a>, where the focus of grad school has shifted from producing quality scientists to producing PI-promoting research. She has a series of thoughtful recommendations for improving graduate education. Derek Lowe <a href="http://pipeline.corante.com/archives/2013/01/24/too_many_scientists_a_pyramid_scheme.php">notes the article and comments on the proposal to increase permanent lab staff</a> (i.e. how to fund it?).</li>
<li>Chemjobber has <a href="http://chemjobber.blogspot.com/2013/01/interesting-amusing-frustrating-quotes.html">some commentary and depressing statistics on the job market</a> and unemployment rate for chemists (spoiler: it's worse than the average rate for bachelor's degree holders).</li>
<li>Don't miss See Arr Oh and Chemjobber's <a href="http://chemjobber.blogspot.com/2013/01/podcast-see-arr-oh-and-chemjobber-on.html">podcast on amusing interview stories</a>.</li>
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<h3>
Other</h3>
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<li>This is a must-watch: several grad students from UC Berkeley do <a href="http://www.youtube.com/watch?feature=player_embedded&v=odxvp-3nSw4">a eukaryotic microbe-based parody of Gotye's "Somebody I Used to Know."</a> Be prepared to be singing it to yourself for a while.</li>
<li>A lot of people have been writing about malodorous affairs this week. First, Derek Lowe <a href="http://pipeline.corante.com/archives/2013/01/22/pick_your_stench.php">compares and contrasts a massive mercaptan spill and a large-scale goat cheese fire</a>. The Chemistry World Blog <a href="http://prospect.rsc.org/blogs/cw/2013/01/23/thiols-mercaptans-and-the-stench-from-the-french/">covers the matter</a> as well. Then, Sarah Everts at C&EN's Newscripts explores <a href="http://pipeline.corante.com/archives/2013/01/22/pick_your_stench.php">the history of deodorants and the biochemical basis for their need</a>. Finally, at The Curious Wavefunction, Ashutosh Jogalekar describes <a href="http://blogs.scientificamerican.com/the-curious-wavefunction/2013/01/25/chemists-and-bad-smells-and-sulfur-a-productive-pairing/">the chemistry of smell and some fascinating anecdotes</a>--read it! This post by Breanna Draxler at Discover talks about <a href="http://blogs.discovermagazine.com/80beats/?p=42521">the biochemistry of odor recognition</a>.</li>
<li>Check out these <a href="http://blogs.scientificamerican.com/artful-amoeba/2013/01/25/the-startling-mechanical-beauty-of-a-rotifer-in-motion/">videos of rotifers</a> and other microorganisms. Really cool stuff! </li>
<li>Breanna Draxler writes about a paper published recently in Science in which <a href="http://blogs.discovermagazine.com/80beats/">researchers stored a little under a megabyte of hard drive data in DNA and retrieved it with perfect fidelity</a>. It's been talked about for a while, and this instance happens to be faster and more accurate than previous attempts. It's a very, very cool thing---DNA is about as compact as you can get for reliable data storage! One might speculate, then, on the potential evolution of the first music-pirating bacteria.</li>
<li>Keith Kloor has an<a href="http://blogs.discovermagazine.com/collideascape/2013/01/24/why-science-fails-to-persuade/"> important post</a> commenting on <a href="http://www.sciencebasedmedicine.org/index.php/the-role-of-anecdotes-in-science-based-medicine/">another important post</a> (Steven Novella). Both discuss why science is not persuasive; though data and statistics are logically compelling, <a href="http://blogs.discovermagazine.com/collideascape/2013/01/24/why-science-fails-to-persuade/">we are fighting a reliance on heuristics and anecdotal evidence</a> that is likely ingrained due to evolutionary advantage.</li>
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