About this Author
Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases.
To contact Derek email him directly: derekb.lowe@gmail.com
Twitter: Dereklowe
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June 10, 2009
Posted by Derek
I had some requests to answer my own "Random Questions" from the other day, so here goes:
1. Does it bother you, or by contrast make you a bit proud, when you tell someone that you're a chemist and (as happens in about seven out of ten cases) they say "Oh, that was my hardest/least favorite/most boring subject when I was in school"?
Well, whether it bothers me or not, this happens all the time. Like pretty much every chemist in the world, I get to hear all about how people couldn't stand my subject in school. I take the point that mathematicians have it even worse, but it's not like we miss many of them with chemistry, either.
When people ask me what I do, I tell them "drug discovery", and I mention the diseases that I'm working on. That never fails to get some interest, and only then I spring on my listener the (often unexpected) info that this involves chemistry. Coming at it from that angle almost always leads to a good conversation, while coming at it from the "I'm a chemist" angle often leads to "Hey, look at the time!" effects. It's worth doing it in the right order, though - I like the effect when of showing that this boring/hard/useless subject actually leads to what most people find is a really interesting job.
2. How many thousands (10s, 100s of thousands) of dollars of unused equipment is sitting in dusty, unused storerooms at your company, because someone ordered it years ago and either (1) never got it to work, (2) was the only person ever to get it to work, or (3) found that it worked, but what it did wasn't worth doing that way?
Disused equipment? What is this disused equipment you speak of? Never have I seen such a thing. Why, those elaborate combichem machines in the sub-basement, they're just down there because they're so valuable. That rotating split-and-mix thingamabob and the multichannel parallel doohickey, we guard those closely.
Hah! Actually, I remember a couple of labs where this stuff wasn't in the basement at all. No, it was out there in the hoods, taking up space and slowly gathering dust, a standing reproach to everyone who walked past it. It would have been better off out of sight, but no one quite had the heart. And besides, it would sometimes get turned on for visiting groups - there was that.
3. Have you ever set up a reaction and thought "Boy, I sure hope that this doesn't work"?
I suppose that this is somewhat shameful, but yes, I have set up reactions hoping that they would fail. Usually it's been when I've had to use a particularly distasteful reagent (sodium ethanethiolate, for example), and I don't want to end up using it on a larger scale. I remember a fellow grad student presenting his work while we were trying to get our PhDs, and he detailed a deoxygenation step which only worked when his intermediate was made using a hefty excess of thiophosgene. "As fate would have it", said his long-suffering labmate from the back of the room.
And I've had less honorable instances, dating back to grad school or early in my industry career, when I was more or less forced to run a reaction a particular way even though I felt there was no chance for it to work. So yeah, in those cases I did look forward to saying "Yes, I tried your idea. And no, it didn't work any better than mine."
4. For the drug discovery people out there, what per cent of compounds you've made over the years would you guess dissolve in plain water to any real extent? Is that figure going up, or down?
The figure is hard to estimate, but it sure isn't high. Things that dissolve in straight water are hard to work with, y'know - they tend not to extract so well into ethyl acetate or dichloromethane, and they don't run so great on silica when you try to clean them up. That's worth another blog post in itself - the way that our standard chemistry techniques tend to push us away from a lot of polar molecules that might be just what we need for med-chem.
5. What, off the top of your head, would you say in retrospect is the most time-wasting chemistry you've ever ended up doing?
Tough competition. I'm tempted to say vacuum pyrolysis of corn starch to make levoglucosan, but I needed that for my dissertation, so it can't be called useless.
The real winner, in retrospect, has to be a series of reactions I did in my first couple of months in my grad school group, when I was still taking classes and working in the lab part time. I was presented with a route to a tetrahydropyran compound that we needed, a four-or-five stepper that involved an aluminum alkyne opening an epoxide, a Lindlar hydrogenation, a ring closure. . .I can still draw the damn thing on the board, now that I think about it, and it's been twenty-five years ago this spring. Being a first-year grad student, I hopped to it - and hopped right into the mud, since the route bogged down (and how) at the ring closure stage). I kept at it for a while, and then one evening I decided to look up my target compound in Chemical Abstracts.
That wasn't so easy in those stone ax and bearskin days - command-line access to CAS via a rockin' 1200 baud modem and a terminal was still a few months away. I paged through the five-year indices, and found. . .my compound. In a Tetrahedron paper. Two steps, from stuff you could buy from Aldrich, and you form the ring in the first step through a Prins reaction. I was shocked. Surely this couldn't be a known compound. Surely someone must have looked the structure up before coming up with that route I'd been given.
Surely not. And thus did my lab education begin. So you know, when I think about it, even though those first couple of months were a waste of chemicals and effort, perhaps they weren't as much a waste of time as I thought. . .
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January 23, 2009
Posted by Derek
A run of bad accident news today, and all of the same kind. The Chemistry Blog has the story of a fatality in the labs at UCLA. The short and painful details are: inexperienced student, t-butyllithium, flammable clothing, and panic (as in not running toward the safety shower).
This is very sad to hear about, and as with so many lab accidents, one of the saddest parts is how easily it could have been prevented. t-BuLi is, of course, a well-known fire starter, and the student did know about that problem. But one of the keys to working with dangerous substances is to think through what you’ll do if something goes wrong. For a pyrophoric compound, that means knowing where the nearest fire extinguisher and safety shower are. It’s very easy to panic when something goes wrong, but if you’ve rehearsed what to do beforehand, you have a much better chance of doing the right thing in tough circumstances.
I pass this along to the students who read this site, and I’m sure the other experienced lab workers here will agree: always think “OK, what’s the worst thing that can go wrong with this reaction?”, and think about what you’ll do if that happens. Fire? Explosion? Sudden leak of nasty toxic stuff? Think it over. Anyone working in a laboratory should always know where the nearest fire extinguisher is. That is, the nearest appropriate one – if you’ve got a separate Class D model for metal fires, or even just a sand bucket, then when you need it you’re really going to need it. And everyone should know where the nearest safety shower is, because no one ever just sort of needs to use one of those. I’ve had to run and pull one once in my career, and let me tell you, it was a damned good thing that I knew where to go when the chips were down.
The other news I have was communicated to me privately, so I won’t go into details other than to say that it appears to be another fatality, this time involving inhalation exposure to trimethylsilyl diazomethane. The problem with these sorts of reagents is that you might think that they’d cause breathing trouble immediately, but you’d be wrong. Diazomethane, phosgene, methyl bromide and others can actually take hours to kill a person, and for a good part of that time, the only symptoms might be a slight cough. But serious lung damage can be coming on slowly during that period, and by the time it’s clear that there’s a problem it’s usually too late to do very much about it. Unfortunately, in some cases, it’s too late right from the start, but that takes quite a bit of exposure, and indicates a serious mistake somewhere along the line.
Anyone who works with such volatile and damaging reagents needs to be completely aware of what they’re doing, and to only handle them under good ventilation. I’ve used such things many, many times in my career, without incident, and so have most working organic chemists. But we should never lose respect for what we’re holding in our hands.
I’m not trying to scare beginning chemists out of doing lab work. It has it hazards, but so does driving to work in the morning or cutting up food for dinner. (When I was in graduate school, my mother once expressed her worries about my lab work, but I told her that the most dangerous thing I did was to drive 650 miles back home on holidays). But every well-appointed chemistry lab is full of death in screw-capped bottles, and that bears thinking about. Random, unforeseeable accidents are, fortunately, very rare. But that means that the others didn’t have to happen, and that’s painful to contemplate.
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October 28, 2008
Posted by Derek
I’ve noticed over the years that my patience in seminars and talks has been eroding. This started in graduate school – I certainly sat through my share of lousy talks back then, but I was starting to skip out on the occasional one, after a certain level of grimness was reached.
For example, I remember walking down the hall with a new post-doc, when the building’s speakers came to life. “May I have your attention, please. . . “ We stopped to listen. “There will be a seminar in the main auditorium in ten minutes, entitled “Raman Spectroscopy of Synthetic Asphalt Roofing Materials” (I swear that this is a real title, or something very close; it was appalling). The new guy asked, in a slightly worried tone “Do you guys in the group usually go to these things?”
And at that point, one of my fellow group members came lurching out into the hallway, pantomiming elaborate choking gestures as he pointed desperately at the speaker up on the wall, slumping against the wall as the horror of the seminar’s title overcame him completely. We watched him slide to the floor, still gesturing at the intercom, and I said calmly: “No, we skip a few of them now and then”.
Well, over the years I’ve continued to skip a few of them now and then, and my threshold has been steadily creeping up. I realize that many of the topics that keep me glued to my seat are, by any objective standard, rather dry. Give a detailed talk about enantioselective hydrogenation, the thermodynamics of multivalent binding, or even the latest thinking about the patent office’s requirements for obviousness rejections, and I’ll be right there, practically munching popcorn. To me, those things are interesting. But plenty of things aren’t.
It’s to the point now where there are single phrases that give me that “late for the door” feeling. After that hits, it’s a major effort for me to stay in my seat. So, speakers, if you see me out in the audience and think that the ambience would be improved without me, it isn’t hard. Just spend a few minutes going on about “cross-functional goal setting” or the wonders of ISO nine-thousand-whatever. I’ll spray gravel on my way out. One day I’ll probably end up dangling from a bunch of knotted tablecloths, having rappelled down the side of my building from an upper-floor conference room. “Vision statement”, I’ll gasp to the passers-by as I drop to the sidewalk in relief. “They invited me to work on a new vision statement. . .”
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September 22, 2008
Posted by Derek
Science is taking a look at the 1991 members of Yale’s Molecular Biology and Biophysics PhD program. The ostensible focus of the article is to see what the effect of flat federal research funding has been on young potential faculty members, but there’s a lot more to pick up on than that.
The first thing to note is that out of 26 PhDs from that year’s class, only one of them currently has a tenured position in academia. Five others are doing science in some sort of academic setting, but only one of those is tenure-track. And you can tell that for at least a few observers, the response to those numbers is “What went wrong?”
Well, nothing did. As it turned out, the students didn’t necessarily come out of the program on a mission to go out and get tenure. But there was no particular way to blame the research funding environment for the numbers, because almost no one that Science interviewed mentioned that as a factor at all. Instead, many of them decided that there might be something more (or at least something else) to life than going from being a grad student and post-doc directly to. . .supervising more grad students and post-docs:
For some MB&Bers, academia was never really an option. "Even as an undergraduate in college, I never bought into the concept of being a professor," says Deborah Kinch, associate director for regulatory affairs at Biogen Idec in Cambridge. "Being a grad student is the last bastion of indentured servitude, and being a faculty member is pretty much the same thing, at least until you get tenure. Earning the same low salary and fighting for every grant--that was the last thing I wanted to do. . .
. . . Midway through their graduate training, a few MB&Bers hatched the idea of a seminar series to hear from former graduates working outside the academic fold. (Athena) Nagi said the group wrestled with the definition of an alternative career and decided that the answer was, in essence, "anything that didn't involve teaching at a major research university”. . .what (Tammy) Spain remembers most were their reasons for branching out. "They all said they didn't want to go into academia. None of them said, 'I failed.' None had even tried to find an academic job. It was the first time I got the sense that there was no shame in not going into academia."
That heightened sense of empowerment reinforced what some class members were already feeling. "At first, you think that academia makes sense," says Nagi. "But by your 3rd or 4th year, you start to get the lay of the land and look at the options. You realize that a postdoc isn't just for 1 year and that there are multiple postdocs."
I particularly like the way that a third-year graduate student had never realized until then that there was no shame in not going into academia. This is a major problem in academic science – the amount of this attitude varies from department to department, but there’s always some of it floating around. It’s no wonder that some of these people were baffled by the prospect of what they were going to do with their lives, because a large, important range of choices was being minimized or ignored.
But I have no room to talk – by that point in my graduate career, I wasn’t clear about what I was going to do, either. I was getting pretty sure, though, that going off and fighting for tenure at a major university was not in the running. I’d seen what the younger faculty put up with in my department, and it didn’t look much better than the life I was leading as a grad student. In many ways, actually, it was worse. Why would I want to do that?
As it turns out, a good number of the 1991 Yale people ended up at various small biotech companies. Some of them have made a success of it, and naturally enough, some of them are out of science altogether. But the rarest, least likely thing for them to do was to get tenure – or even to try. When I think back on the folks I went to grad school with in the mid-1980s, the picture is very similar. You just wish that there were a way to make this sorting-out process less painful. . .
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August 25, 2008
Posted by Derek
You need access to vacuum if you’re going to work at the bench in chemistry. In fact, you need more than one kind. Reasonably hard vacuum (well, by our standards, which is laughable by the standards of the physicists) is down in the single Torr or below – that is, less than about 1% of normal air pressure. We use that for pulling out residues of water or organic solvents from our compounds. You can’t usually see it happening from the solid ones, but the syrupy liquids will foam up or blow a long series of thick bubbles when the vacuum is applied. The foam can be an irritating problem at times; some things will fill your flask with sticky bubbles and go right on up into the vacuum line if you’re not watching them.
The lesser vacuum lines are used for bulk evaporation of solvent (on your rotavap) and for filtering things off. We do an awful lot of both of those, too, and a full vacuum-pump pull is too vigorous for them in most cases. Evaporating down reactions is a constant task in an organic chemistry lab; I’d rather not think about how much of it I’ve done over the years. As for filtration, there are many cases where a solid product can be filtered out of the bulk liquid (which is good) or where some undesired solid by-product has to be filtered out before you can go on (not as good).
The low-tech way to get the sort of pull-it-though vacuum you need for these things is a water aspirator. You don’t see these as much any more, and you don’t see them at all in industry, since they necessarily pull solvent vapors into the water stream. But they work. An aspirator is basically a narrowing tube that hooks up to a hard-spraying water tap and has a sidearm fitting. The accelerating blast of water pulls the air in the tube along with it as it goes, creating a useful vacuum. If you wanted to make one rather more environmentally friendly, you’d keep a well-stocked dry ice condenser in line with it to trap out the solvent vapors before they go down the drain (which is what your rota-vap should have on it, anyway), but even with that, you’re always going to be turning the water flow into a waste stream. As I say, you don’t see them as much these days.
But we used them back when I was in grad school, that’s for sure, mostly for the rotavaps. If you wanted to keep things from splashing around back in your hood, you attached some rubber tubing to the other end of the thing and ran it further down the drain a bit.
Well, one day, one of the guys in the lab next door to me was shocked to see water blasting around in his hood. It was a real fountain, just geysering out full blast from what must have been a cracked water line or something in the back. He ran over and immediately shut off every tap – but to no avail. Roaring, showering water everywhere. Getting a look at the source, he realized, to his consternation, that the water was coming up out of the drain in the back of his hood. I remember standing there with him, staring at this in disbelief. It looked like a special effect. How on earth could you get water blasting up out of a drain pipe?
Suddenly it hit me. I ran around to the other side of the lab, where a new Japanese post-doc had taken up residence. “Masa”, I asked him, “Did you just put that rota-vap in your hood today?” “Yes, yes, just started it today”. There was a water aspirator flooshing away back in the back of his hood. “Did you put some rubber tubing on that thing?” “Tubing? Oh, yes” “How much?!” “Whoaaa. . .” He spread his arms to indicate the mighty extent of the rubber tubing he’d added.
Mighty, indeed. He’d run the stuff down his drain, through a horizontal pipe and right through a T joint, and back up out of the drain of the other guy’s hood, which backed on to his. So when he turned his water on full throttle, he immediately started irrigating his labmate’s space. We finally go thing turned off, and trimmed back the rubber tubing to a more reasonable length (like, not seven feet), and order was restored. For a while.
Note: if you want to see How Not To Do It to a really expensive vacuum rig, try here.
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December 19, 2007
Posted by Derek
There is a pecking order in chemistry. That’s because there’s one everywhere. If it’s a human endeavor, staffed by humans, you’re going to have hierarchies, real and perceived - who you did a post-doc with, what huge company you're a big wheel in. But that doesn’t mean that we have to bow down to them, and it doesn’t excuse this sort of thing, from The Chem Blog:
” Waaaaaayyy back at the ACS in San Fran at the poster session, we were walking around and introduced ourselves to this guy standing in front of his poster. Now… old boy (a graduate student) engaged us in some dialog about his poster and we were getting along famously, my friend asking most of the intelligent questions (I was still recovering from giving blood a few hours before and drinking multiple beers immediately after.) As conversations normally flow, he asked us where we were from. I told him my fine institution and my buddy told him his. I assume he wasn’t put off my by school, but the look on his face when my buddy told him where he was from was at first a “are you serious” chuckle, which melted into one of those “do they have a department” and finally to a resound(ing), “I’m done with you.”
I stood there and watched it the whole time. So, my buddy being naive to the ways of the world, kept asking questions but the answers weren’t forthcoming any more. In fact, in the midst of a question my buddy was asking, the guy actually walked away from his poster and started talking to his friends. . .”
Read the rest of the post for the rest of the story, which goes off in a different (and still interesting) direction. But as for this behavior, there’s just no call for it. As far as I’m concerned, if a person is asking intelligent questions, they’ve already provided all the credentials they need to show. Likewise, I reserve the right to discriminate against time-wasting bozos (just as I reserve the right to define that class, although I’ll bet that most of my picks would easily pass a show of hands). But if you’re presenting a poster, you have, whether you realize it or not, entered into an agreement to take on the broad unwashed masses.
Tactfully dealing with the clueless is a learned skill, but no such skill seems to have been called on here. This is tactfully dealing with the intelligent and informed, and if you can’t do that, you have some serious problems. It takes an awful lot of red-hot results to make up for a really obnoxious attitude, and a degree from Big Name U is only partially going to offset one as thick as this. Now, it's true that there are certainly some pretty abrasive folks from BNU, but the ones with the proven big-time track records can at least get away with it. Too many other morons take the shortcut, deciding that the nasty attitude is some sort of essential first step – in some cases, deciding that it and the Big Name is all they need.
Out here in the real world, where Poster Boy has yet to tread, it becomes clear that the wonderfulness of a marquee school background eventually goes stale. There are places in the drug industry where working for particular academic bosses will give you a leg up – for a while. It’s a real advantage to be able to get in the door that way, no doubt, but once you’re through the door you generally have to produce something. (And it’s good to keep in mind that even these advantages don’t necessarily last forever. A rollicking management purge can destabilize an old-boy network very quickly).
No, doing lots of work and doing it really well is a better long-term strategy. (Another part of that strategy is to make sure that people know who’s doing it, but that's a topic for another day). And having a personality that makes people grit their teeth and wait for you to leave is not such a good long-term plan. I wish Poster Boy well, but I hope that he has a lot to talk about. This isn't one of those businesses where you can get by on looks.
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November 20, 2007
Posted by Derek
I had a hard drive failure the other day, which naturally got me to thinking about backing up data, and about the times I’ve been more paranoid about it. I wrote my PhD dissertation back in those far-off days (1988) when you could put Mac versions of Word and Chem-Draw on one 3.5-inch disk (yes, that was possible, and I still have the disk to prove it). But I went to the disk-swapping trouble of putting my dissertation-in-progress on a separate floppy.
So there I was, with a couple of week’s worth of dissertation draft on my floppy disk, when one fine day I insert the thing into the slot, and. . .it can’t be read. Hrm. I try other machines. I try them all. None of them can read the disk, under any conditions. It slowly dawns on me that my two weeks of work have evaporated, and a little later it dawns on me that things could have been much, much worse. I converted to the Backup Religion.
Grad students writing up tend to get a bit paranoid under the best conditions. Once I made my backup copy, I realized that I might run into a problem with the floppy drive – what if it subtly ruined my disk? Then one floppy would apparently be bad, so I’d feed the next one in, and the evil drive would chew that one up too. Hmm – better have three copies. I decided to keep one in my lab dsek, one at home, and one in my car. But then I started thinking of the unlikely – but still possible! – combinations of drive failures, fires, accidents, etc. that could still wipe me out. In the end, I had, I think, five separate copies of the dissertation in progress: one back at my apartment, one in the car, one in the lab desk, one back in a drawer by my hood, and one in my coat. I never needed any of the backups at all.
But it was a comfort to know that they were there, and mentally I needed all the backup capacity I could get in those days. Late one night I was awakened by a host of fire trucks roaring down the street. I lived only a quarter-mile from the chemistry building, and I found myself wondering, there at three in the morning, if that’s where they were headed. Ah, but I had my latest dissertation disks. But. . .I also had all the hard copies of my NMRs there in my lab. Aargh. (I should note that digital backups of NMR data were quite rare back in that era, at least in much of academia). What if the building caught on fire?
Worse, what if I’d been the cause? Had I really turned off that heating mantle when I left at midnight? Or did I just think that I had? Wasn’t there a bottle of hexane in my hood? (I did mention that this was three in the morning, right? Why the brain gets into these loops at that hour is a mystery, because that kind of thinking is normally alien to me, as my wife, to whom it’s second nature, will tell you). So I sat there, wondering if my lab and my data were at that moment going up in flames, until I finally rolled out of bed and called the lab. Ring. Ring. Ring. “Hello?” I recognized the voice – it was Randy, down the hall – but I suddenly realized that I didn’t know what to say to him. “So the lab’s not on fire?” didn’t seem like a good conversation starter, so I just hung up, and went back to sleep.
The next day I made my late-morning entrance into the lab, and ran into Randy. “How late were you here last night?” I asked him. “Oh, really late”, he said, and looked at me. “How did you know?”, he asked, and I looked embarrassed. “Hold it,” he said, “that was you, wasn’t it? You must have heard all those fire trucks going past! Thought the lab was on fire, didn’t you?” All I could do was turn red, because he had me.
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October 25, 2007
Posted by Derek
A colleague reminded me the other day of a project that he and I had worked on back at the Wonder Drug Factory seven years ago. "Seven years ago", I thought. . .I was the project leader on that one, trying to keep things alive as weird toxicology kept torpedoing everything. In the end, we held it together long enough to get four compounds into two-week tox testing, whereupon every one of them wiped out for yet another set of ugly reasons. Ah, yes. No one's going to have to work on that stuff again, that's for sure.
Hmm, I thought. What was I doing seven years before that? Well, I was back at my first drug industry job in New Jersey. The company had just moved into a new building the year before, and the old site was on its way to becoming a Home Depot. I was spending my days cranking out molecules hand over fist. Boy, did I run a lot of reductive aminations. It's safe to say that during those years I ran the majority of all the reductive aminations that I'll ever run in my life, unless something rather unforeseen crops up. We made thousands of compounds on that project, and I remember pointing out in a talk that nobody makes that many compounds if they really understand what they're doing. This was not a popular line of reasoning, but it's hard to refute, unless saying how much you don't like something counts as a refutation.
And seven years before that? Still in the lab. I was midway through grad school, wrestling with the middle of what turned into twenty-seven linear steps by the time I pulled the plug. (At this point, I began to reflect that I've been doing chemistry for quite some time now). In 1986 I didn't know that I wasn't going to end up finishing the molecule, and I was still hauling buckets of intermediates up the mountainside, only to find them alwyas mysteriously lighter and smaller by the time I got to the top. My response, naturally enough, was to start with larger buckets - what else was there to do?
And seven years before that? That finally takes me over the chemistry horizon, back to my senior year of high school in Arkansas, and to what might as well be a different planet entirely. Although I was interested in chemistry - as I was in most all the sciences, something I've never lost - I'd never heard of a Grignard reagent, and I didn't know what a nucleophile was. Counting up, I see that some time next year will mark the point at which I will have spent a slim majority of my lifetime doing organic chemistry, which is an odd thought. And it makes me wonder what I'll be up to seven years from now. . .
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October 18, 2007
Posted by Derek
My graduate school lab, like most of them, had an assortment of people from different countries. That kept things at all sorts of hours, since we’d get the occasional Japanese post-doc who never really seemed to get off JST and worked the zombie schedule. It also made for some adventures in communication. English was the lingua franca of the lab, naturally, but there were a lot of varieties spoken (and attempted).
And although it’s risky to generalize, I think that the ones with the biggest language gap were the aforementioned Japanese. Friends of mine from the country have blamed the problem on the traditional state of English teaching there, and the way that too many students are taught the language as if its phonics really did conform to what’s available in Katakana.
That’s the writing system used in Japan to render words phonetically. Reading fancy Japanese (Kanji) takes some real practice, but any hack (like me) can plow through Katakana with a chart and a little practice. I’ve been asked many times, in wondering tones, if I read Japanese after I pulled out a useful reagent name from a Japanese patent, but I wasn’t reading Japanese – I was reading English. Sort of.
Sounding out the words makes you sound like the most unfortunate expatriate Japanese post-doc you’ve ever heard. “Cyclohexyl”, for example, comes out as “Sa-ki-ru-he-ki-sa-ru”, and “chloro” is “ko-ru-ru”. I’d probably sound even worse than that if I had to speak Japanese, but it does give you some insight as to where the stronger features of the accent come from.
One way or another, we all did communicate in the end. I remember talking with one of our post-docs, trying to learn some Japanese profanity (a well-known gateway into a foreign language, of course). But I couldn’t get the concept across. “Bad word?” he asked, puzzled. “Curse word?”
An idea hit me. “OK”, I said, pointing at his rota-vap where a 1 mL flask was spinning. “How long did it take you to make that stuff?” That stuff, he informed me, was step 17 of his synthesis, and had taken weeks and weeks of work. “Fine,” I said, “what happens if it falls into the water bath?” “Ah! Terrible!” he said, looking fearful at the very thought. “Right”, I told him: “If that happens, what do you say?”
Enlightenment! “Oh! Yes! Those words! Bad word, yes, now I understand!” A great moment in international understanding. We went on to explore the sorts of phrases that are absolutely guaranteed to come in handy in any research lab, no matter where.
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August 26, 2007
Posted by Derek
This is the first post from the new Blogging Room of Stately Lowe Manor here in Massachusetts. The internet is hooked up, the lights are on, and I'm surrounded by boxes no matter where I turn.
I had a few requests to do more posts on graduate school and what goes on there. Problem is, it's becoming an increasingly distant event for me (which in most other ways is not much of a problem at all!) There's one immediate thing I can think of to say to people who are still in the middle of it, though: Don't worry. You're not going to be stuck like this forever.
I'm thinking of what a generally foul mood I was in throughout my PhD work, compared to my overall sunnier disposition since. I didn't like having to work on the exact same molecule for years, and I didn't like having to do it days, nights, weekends, and holidays. I especially didn't like that little voice in the back of my head that took up residence there, telling me - every moment that I wasn't in front of my fume hood - that I should stop goofing off and get back to work.
And I wondered if the experience had permanently damaged me. I really worried about that. When you're younger, these thoughts occur to you if you've got any introspective tendencies at all, and my working hours gave me plenty of time for thinking about such things. Was I ever going to wake up and feel enthusiastic about going to work in the lab? If not - and there seemed a real chance that the answer was, in fact, "Never again" - how was I going to make any sort of worthwhile life for myself? After all, here I was committing a good slice of my 20s to getting an advanced degree in a field whose same advanced degree might be ruining my chances of ever using it.
No wonder I was surly. I wasn't sure I was doing the right thing, and I wasn't sure what shape I'd be in if I stopped or if I kept going. Admittedly, I never seriously considered the first option. The going didn't get really rough until I was in far enough that the shortest way out was at the other end. I knew that I could hang in long enough to get the degree; what I didn't know was what kind of shape I'd be in after I got it.
Well, as it turned out, I was fine. My worries, though real, were overblown. It took a while on my post-doc in Germany, but my brain proved to be more resilient than I'd feared, and it soon bent back to its usual shape. I stopped feeling as if the dogs were chasing me when I wasn't in the lab on, say, Sunday nights or the day after Christmas. And I started enjoying the times that I did go in. Not being up to my elbows in lab work all the time made it fun when I did it out of choice. No permanent damage seemed to have occurred.
Actually, I came out of the experience stronger than when I went in, for having gone through it without breaking. So, if you're trying to finish up your last year or two of a degree, and you feel as if it's never going to end, take it from me: it does. And if you think that you can't stand the time remaining, prepare to surprise yourself, because odds are very good that you can. And no, you won't always feel like you do on your worst days in your grad school lab. That's not the real world; it's just pretending to be.
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August 23, 2007
Posted by Derek
The FASEB folks have collected a large amount of data on training and employment in the life sciences (start here), and see the discussions over here at the AAAS).
Many of the conclusions are not going to surprise people, but it's good to have some data to back up everyone's impressions. I can sum the whole presentation up in a sentence: academic life science is a hard place to make a living, and getting harder every year. For example, the average age of first-time R01 grantees has been going up for the past thirty-seven years. And over the past twenty years, the number of doctorates awarded has roughly doubled, while the number of people employed in tenured (or tenure-track) positions has stayed exactly the same.
So where is everyone going? Well, down the hall from me - industry is where the job growth is. I know that my pharma/biotech readers might be startled by that statement, but compared to academia, we're a boom town. (I mean, look at it, no head count increase since 1987?) The problem is, as far as I can see, many PhD candidates and post-docs have been trained in environments where an tenure-track academic position is seen as the natural and desirable goal, and industry is just the fallback for the also-rans. If this ever was congruent with reality, it isn't now. As a commentary in the latest Nature put it:
More effort is needed to ensure that recruitment interviews include realistic assessments of prospective students' expectations and potential in the academic workplace. And training should address broader career options from day one rather than focusing unrealistically on jobs that don't exist.
Chemistry doesn't have this mindset problem to the same extent. There do seem to be some research groups who don't so much look down on industry as over-exalt academia, but there are plenty of strong people from the top-ranking groups all over the pharma landscape. But the hiring problems, well, I'm sure those track pretty close to the FASEB story.
And that gets us back to the ever-popular topics of medicinal chemistry employment, outsourcing, restructuring, and so on. For now, I'll reiterate my strongest opinion on these subjects, which is that this is not a good time to be an ordinary medicinal chemist in the US. You need skills, you need to keep them sharp, and you need to be ready and able to move into new research areas as they get interesting. It's not easy. But at least it's easier than trying to make it as a professor. . .
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August 13, 2007
Posted by Derek
One of the comments to my brief post earlier today brought back some memories. Back in graduate school, we were a comparatively well-off group. That is, we graduate students lived off grant money after our first year - no more teaching assistant duties. Compared to some of the other professors, whose students were TAing in their fourth years and beyond, this was luxury.
But luxury went only so far. We still had to watch our expenditures in the lab, and ordering of reagents and supplies was kept under tight control. We didn't go as far as recycling our wash acetone (well, most of us didn't - see here for what happened to the fellow who did), but If you wanted a fresh bottle of something, you had to justify it: what's wrong with the one we've got, heh?
I was pushing a big pile of material through the early stages of a long synthesis, so I (and the people like me) needed larger amounts of things. I remember getting in a fresh 800 mL bottle of borane/THF, of which I was going to use about 700 mL in one big ol' hydroboration reaction. Ready to go! Got my starting material on the pump, got my freshly distilled solvent, got my untouched bottle of. . .wait a minute. That's not on the shelf where I left it. And it's. . .it's. . .
What it was, was about half empty. Yes, one day in the lab was all it took for my pristine stockpile of borane to be raided. To add that extra emotional touch, when I unscrewed the cap and looked at the seal, the person who'd pirated the stuff had apparently used something the size of a knitting needle to remove it. The "Sure-Seal" was surely hollowed out, to the point that I could see the borane solution sloshing down there in the distance.
I didn't take it well - it was grad school, so I didn't anything too well. I went stomping through the labs, beard bristling out, hands making involuntary strangling motions in the air, asking who, just who, had helped themselves to half a liter of borane/THF in the last day? Eh? Well, as you'd guess, no one had. Nope, nobody at all had used that there borane, no-sir-ree, didn't even know it was there. Some of my colleagues assured me that they'd never used borane in their lives, and a couple of them seemed surprised to find that there was a chemical with such an odd and catchy name. What you say, boh-rain?
I never did find the culprit. Most of the time, you never do. I gritted my teeth, used some more foul language, ordered another bottle of reagent - and used it right out of the box this time, trailing little flecks of vermiculite packing material behind me.
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April 17, 2007
Posted by Derek
The doctorate-or-not discussion is roaring along in the comments to the last post, and they're well worth reading. I have a few more thoughts on the subject myself, but I'm going to turn off comments to this post and ask people to continue to add to the previous ones.
One thing that seems clear to a lot of people is that too many chemists get PhD degrees. I'm not talking about the effect of this on the job market (more on that in a bit) so much as its effect on what a PhD is supposed to represent. So, here's my take on what a PhD scientist is supposed to be, and what it actually is in the real world. I'm going to be speaking from an industrial perspective here, rather than an academic one, although many of the points are the same.
Ideally, someone with a doctorate in chemistry is supposed to be able to do competent independent research, with enough discipline, motivation, and creativity to see such projects through. In an industrial applied-research setting, a PhD may initiate fewer projects strictly from their own ideas, but they should (1) always be on the lookout for the chance to do so, (2) be willing and able to when the opportunity arises, and (3) add substantial value even to those projects that they themselves didn't start.
That value is both creative and managerial - they're supposed to provide ideas and insights, and they're supposed to be able to use and build on those of others. They should be able to converse productively with their colleagues from other disciplines, which means both understanding what they're talking about and being able to communicate their own issues to them. Many of these qualities are shared with higher-performing associate researchers, who will typically have a more limited scope of action but can (and should) be creative in their own areas. Every research program is full of problems, and every scientist involved should take on the ones appropriate to their abilities.
So much for the ideal. In reality, many PhD degrees are (as a comment to the previous post said) a reward for perseverence. If you hang around most chemistry departments long enough as a graduate student, you will eventually be given a PhD and moved out the door. I've seen this happen in front of my eyes, and I've seen (and worked with) some of the end results of the system. The quality of the people that emerge is highly variable, consistent with the variation in the quality of the departments and the professors. Unfortunately, it's also consistent with the quality of the students. But it shouldn't be. The range of that variable shouldn't be as wide as it is.
There are huge numbers of chemistry PhDs who really don't meet the qualifications of the degree. Everyone with any experience in the field knows this, from personal observation. You will, I think, find proportionally more of these people coming out of the lower-quality departments, but a degree from a big-name one is still far from a guarantee. The lesser PhD candidates should have been encouraged to go forth and get a Master's, or simply to go forth and do something else with their lives. They aren't, though. They're turned loose on the job market, where many of them gradually and painfully find that they've been swindled.
Over time, the lowest end of the PhD cohort tends to wash out of the field entirely. There are, to be sure, many holders of doctoral degrees in chemistry who go into other areas because of their own interests and abilities. But there are also many jobs that make an outside observer wonder why someone with a PhD is doing them, and that's where many people end up who shouldn't have a doctorate in the first place. Others, somewhat more competent, hold on to positions because they're able to do enough to survive in them, if no more. While there are plenty of bad or irrelevent reasons for people not to be promoted over the years, some cases aren't so hard to figure out.
Those, then, are my thoughts on the doctoral degree. What can be done about this situation, if anything, will be the subject of a future post. I have another set of opinions on the Master's degree and its holders, which I'll unburden myself of a bit later on. Comments, as mentioned, should go into the discussion here.
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April 15, 2007
Posted by Derek
There's been a lively discussion in the comments thread to this post about the differences between hiring PhD and associate-level chemists. Anyone who's interested in the topic should have a look, because there are a number of issues in play: chemical knowledge, ability to manage direct reports, adaptability, and more.
There's little doubt that non-Phds have an easier time getting hired. There's almost always a ceiling over their heads, rarely one as transparent as glass, but finding a place under it isn't as hard as finding one off to its side. One question that's come up is whether chemists with doctorates could (or should) apply for associate-level positions.
This has been done - but it usually involves deception. If you have a PhD on your CV, most places just aren't going to consider you for an associate job - thinking (probably correctly) that you're going to be more trouble than you're worth. The feeling is also, even in down job markets, that you're selling yourself short by going for these jobs, and that there must be some good reason why you're doing so. . .
I have personally seen a case that bears on this. Karl (as I'll call him) was a pretty good associate. Not (I'd say) the absolute best we had at the time, but definitely above average. A vacancy appeared in the PhD ranks in the group, and Karl stunned the group leader involved by marching in to his office and revealing that he actually had his doctorate, and that he was interested in applying for the position.
What happened to him? Well, he was fired. He was fired reluctantly, and people in the organization found him a position with a small company in the area, but he was fired. He'd lied on his job application materials, and the company's legal department had only to hear that before they ruled that there was no other choice. How could we deal with people who lied about other things on their applications if we kept him on?
The problem was that as things stood, Karl would have moved from being one of the best associates to being one of the lesser PhDs. His strengths and weaknesses at the time fit better for an associate position than as a lab head. And that brings up another question from the comment thread: are too many people going on to get doctorates? I have no idea myself, but I have to say, it's not an unreasonable thought. . .
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March 7, 2007
Posted by Derek
The grad-school advice topic from the other day got me to thinking about another issue in that line. Everyone knows about how hot all the mixed chemistry-biology stuff is (and has been). Chemical biology, biological chemistry - call it what you like, a lot of people are doing it (and a lot of people are getting funded for it).
That's fine with me. I find a lot of the work very interesting (though not invariably), and some of it looks like it could lead to useful and important things. My worry, though, is: what happens to the grad students who do this stuff? They run the risk of spending too much time on biology to be completely competent chemists, and vice versa. Instead of being seen as well-rounded modern scientists, ready to take on the blurred boundaries of the new research, they might end up unacceptable to their potential colleagues in any given discipline.
I'm sure these fears have come up every time a new field of research opens up. ("Organometallics, you say? So, are you an organic chemist or an inorganic one, hey?") They've taken care of themselves in the past, and they probably will this time, too - eventually. But I'd have to think that there's going to be a lag time, which we're surely still in, during which the people who've done hybrid projects are going to have a hard time proving themselves in the traditional categories.
I should qualify that to the traditional industrial categories. Academia, following the hot topics and following the grant money, is surely more more hospitable to the new breed. But many of the tools of chemical biology are still a bit blue-sky for use in the drug industry (or are seen to be), and even the ones that are already in use tend to be used by people who are more easily classified. Probably the smaller companies are out in front on this, having less invested in the standard organizational charts and often being closer to the academic worldview anyway. Thoughts?
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March 6, 2007
Posted by Derek
I've had an e-mail from someone going off to grad school in chemistry. He wants to eventually do drug discovery work, and is wondering which way to go:
I have it narrowed down to two departments. One is a large, well funded and well respected university with a specific research advisor that is actively recruiting me for his lab. He is a leader in his field and my place in the lab would be in the capacity of synthetic chemist (making various inhibitors). Although his lab is in the chemistry dept it is more on the bio-organic side. My other choice is a smaller less well respected school with fewer resources (lots of TAing) but I could do total synthesis. I would like to join the first group but obviously I want to be able to get a job. If I joined the first group, would I be unemployable in pharma? With a post doc heavy in synthesis would I be able to get a job?
My answer to him was that I'd go with the first lab. A larger school with a more well-known advisor is worth more than the chance to do total synthesis for a PhD - and just as he mentioned, he can do a synthesis-heavy postdoc if need be. Connections mean a lot - ask someone who's job hunting! - and a PhD advisor is generally the first major source of them at the start of a career. The work described is definitely not so far afield that it's going to mess up later job-hunting.
I told him, though, to be sure to get a varied chemistry background in whichever group he joins. You don't want to get too specialized - for future med-chem employment, that can be a killer. A seminar full of same reaction (or class of reactions) over and over isn't going to impress anyone later on - you need to show that you can pick up new chemistry and get it to work, and that you've had to deal with the things that didn't.
One of the reasons that we like total synthesis people is because they've had a wide range of experience, as well as practice with overcoming difficulties. Total synthesis is probably the most efficient way of getting a wide background in synthetic problem-solving in the shortest amount of time. Admittedly, it doesn't always seem like the shortest amount of time while you're doing it, but you can't have everything.
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February 8, 2007
Posted by Derek
Here's another one of those topics that is a bigger concern in academic labs than in industrial ones: stealing supplies from each other. The difference is easy to understand, and can be summed up (as a terrifying number of things can) by the word "money". Industrial labs generally are the Land of Research Plenty, so people don't spend much time looting and pillaging.
But boy, do they have to unlearn those habits. Most academic labs run on tight budgets, so valuable reagents and pieces of equipment get hoarded. People would practically steal things out of my lab coat pockets. I remember going on vacation in graduate school and leaving notes in the drawers in my lab: "Please don't take this. It's the only one I have" or "Go steal one of these from So-and-So. He has more of them than I do". When I came back, people told me how much they liked the notes.
Deprivation leads people to all sorts of money-saving (but time-wasting) attempts to economize. I mentioned a disastrous attempt to recycle lumpy, brown waste acetone here, and there are more stories like that to be found whenever chemists gather. Graduate student time is the one cheap commodity in academia, so you see people redistilling used solvents or washing and re-using silica gel, both of which are (to me) roughly the same as trying to dry out uneaten pasta so it can be boiled again later.
A group down the hall from me in those days used all sorts of exotic mixtures, and whoever made up decent quantities of them was sure to see pilferage. A friend of mine got tired of making things for his colleagues to steal, so he started labeling his bottles with the names of freshwater fish. A midnight raid on his cabinet would present the would-be shortcutter with a row of jugs labeled "Rainbow Trout" and "1:1 Catfish / Smallmouth Bass". That slowed things down for a while, anyway.
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October 19, 2006
Posted by Derek
Three days before: go to the local supermarket and ask to buy a case of corn starch. Ignore the puzzled looks, which come your way since you don't look like you own a Chinese restaurant. Pay for the stuff out of your own pocket (this is grad school, y'know) and head back to the lab. Ignore the puzzled looks of colleagues who haven't seen you walking around with boxes of corn starch before.
Two days before: mix up a kilo or two of the starch with some dilute acetic acid into a weirdly dilatant fluid. Hold on to the memory of it, unknowingly, for fifteen years or so until you have kids of nursery school age. In the meantime, pour the stuff into a cheap baking pan and put it into a drying oven that no one, since you started in on it, will use for anything else.
One day before: take the baking pan out of the oven, wheezing into the waiting faceful of acetic acid fumes if you try to rush the process. Break the cracked, slightly shrunken white cake into chunks small enough to be loaded into your apparatus. Wonder to yourself if this is how other famous scientists started during their doctoral work, and if it is, how come you never read about it.
Day of prep: load up the reactor, a metal box with a glass tube and ball joint poking out of it, with the chunklets of corn starch. Hook up to a connecting adaptor, with a vacuum take-off on it, which you're going to need, big-time, and a large round-bottom flask at the bottom, ditto. Pour plenty of liquid nitrogen into the dual traps on the vacuum pump, regretting the day that you ever told your summer undergrad, who isn't around, of the potential dangers of LN2 traps, because now he won't get near one.
Hook up the vacuum line and pump down the system, and break out a Fisher burner, without realizing (naturally enough) that you won't use one again for at least twenty years. (Not using corn starch as a starting synthetic reagent for at least twenty years, on the other hand, is something you actively yearn for). Take a deep breath and begin flaming the bottom of the metal box with the burner, making sure to get the whole surface and not to linger too long on any one spot. Moderation, moderation in all things.
Note the wisps of vapor flashing through the glass part of the apparatus, accompanied by a throatier note from the vacuum pump. As the heating continues, look for the appearance of an ever-darker flow of thick heterogeneous syrup. This sticky ooze with black flecks in it is your desired product, damn it all. Continue heating until the lava flow dwindles and its color becomes darker than you think you can ever lighten.
Cool down the apparatus, bleed in some air, pull the vacuum line and kill the pump - in that order, unless you really want to suck oil back into the traps, and you really don't. Now would be a good time to lift those traps out of their liquid nitrogen Dewars, to guard against just that oxygen-condensing explosion risk you foolishly warned your undergraduate student about. Make sure that the pump system is open, though, and that the hose is draped into a fume hood, because some of that odd stuff that's condensed in there is probably carbon monoxide and it will be evaporating shortly.
Turn your attention to your product, which has now cooled into a tarry reddish-brown glass. Dissolve it in water and transfer it to the three-foot-tall liquid-liquid extractor, which you will eventually describe to people who will look at you as if you are describing how you used to hunt mammoths. Start heating up a three-liter pot of ethyl acetate, make sure that all the hose fittings to the water condensor are tight (about three times should be enough to relieve your paranoia), and go to what passes, for now, for home. Your product will be ready for the next phase of its purification, which involves the irreversible blackening of a thick column of ion-exchange resin, in just under a week.
After that and all the rest of it (the evaporation, the decolorizing charcoal, the methanol, the crystallization), take a small sample of your product and put it in a glass vial, hanging a paper label around its neck. Pack it and take it with you on your every move over the next twenty years so that you have it, with its now-yellowed label with the faded ink structure on it, as you sit down at your computer.
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October 15, 2006
Posted by Derek
Back when I was a first-year graduate student, I had to do something that I'm not sure that folks today have to worry about: pass a German test. Mind you, it wasn't much of a test - you got a passage from a journal article, and could use a dictionary, and you had a couple of hours. Fast page-flipping would get you through it, which is basically how I did it, since I'd only had one semester of the language as an undergrad (and not much of it took). Little did I know that I'd have a year coming up when I'd have to speak the language in order to eat.
You couldn't substitute another language, either, because German is a uniquely important one in chemistry. A lot of the older physical and inorganic (and a huge amount of the early organic) work was done in Germany, which also produced huge reference works like Beilstein, Gmelin, and Houben-Weyl. But perhaps all the verbs in those sentences should be in the past tense, because both of those references are now appearing in English.
Beilstein switched over with the 5th printed supplement, which appeared only after massive delays which led many scientific libraries to give up on their subscriptions. At one point, the print edition was a good thirty years out of date. Organic grad students had regarded Beilstein with awe back in the 1950s and before, but by the 1980s many of them had never used it. The switch to electronic database searching, which was done in English right from the start, brought them back to relevence. Now libraries are having to remind people that the computer-based service used to be part of a printed handbook.
Houben-Weyl, for its part, switched to English in 1990 or so, but that doesn't seem to have raised its profile in the non-German-speaking world. I recall a Dylan Stiles post where he didn't seem to have heard of the work, for example. The publishers finally caught on to the fact that printed reference works are in trouble, and have moved into the electronic age.
So, here's a question for the grad-student readers: does anyone have to take a German exam any more? The importance of the language in chemistry has been in steady decline for decades, and (if anything) accelerated decline for the last fifteen years. And if you do have to take a test, does anyone at your department still know why?
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September 18, 2006
Posted by Derek
So I see that Dylan Stiles is going to close down his blog next month. I'll miss it, but I can't say that I'm completely surprised by his decision. He's in the home stretch of his PhD work in a demanding group, and there will doubless be some stretches in the next few months where he'll be lucky to have time to go to the john, much less update a blog. I wish him luck, and hope that his eventual transition to Dr. Stiles is as quick and painless as possible.
And yes, that's my theory as to why he's calling a halt. I'm sure that questions of future employment and so on have crossed his mind, but his kind of site definitely won't hurt his prospects, should he decide to go into industry. Dylan obviously knows his synthetic chemistry, enjoys doing it, and can pick up new material quickly - those are some of the key things that you look for when you're hiring. I second the suggestion made by one of the commenters on his site that anyone who's offended by the blog is someone you wouldn't want to work for, anyway.
When I first linked to him, I wrote that it was a good thing that the internet didn't exist when I was a grad student. I meant that two ways - first off, I'd have wasted huge amounts of time rooting around on the web, naturally, not that I didn't make do with what was at hand. But the second problem would have been that I would have probably been tempted to start a blog myself, which would have taken up even more time that I couldn't have afforded. As I've written here before, the purpose of graduate school is to prove that you can get out of graduate school. After allowing for a certain amount of down time needed to maintain your sanity, things that distract you from that main purpose are not your friends.
If I'd had a blog, I'd have spent a good amount of time venting. That surely would have gotten me in trouble sooner or later, given the amount of steam that I had available. I'm pretty sure that I wouldn't have wanted future employers reading what I had to say after I messed up some reaction at 3 AM, what I wanted to do to my summer undergrad student after he blew us all up, or after one of my ever-helpful labmates had stolen a lab jack out from under a distillation of mine while it was still going. No one knowingly hires someone who sounds like a cranky, hyperverbal maniac, which is what I sounded like much of the time back then. (My current co-workers who read this site can, I hope, restrain themselves from further comment).
As for my situation now, well, I blog mostly at night, and I post from home. That's because "night" and "home" are real times and real places now, as opposed to graduate school, when they were crammed over into that little area on the left-hand side of the dial marked "Not in the lab, for some reason". Life's extras fit into place better after you've had the time to get a life to fit them into.
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September 13, 2006
Posted by Derek
Talking about my old optical spectroscopy class brought a couple of other things to mind. One of them is that I have never used a good solid 95% of the material I learned there, ever again. Not even once. I worked on a big ol' honking normal coordinate analysis for a class project during that time, and looking back at it, I'm shocked to see the stuff in my handwriting. I supposed there must have been some benefit to learning all of this material, but it is a benefit that time has managed to obscure.
The main thing I took out of the class was the incident I spoke of earlier in the week - hitting the wall of what I had already learned or could pick up on the fly. I'd been warned for years, while growing up, that I was going to have to buckle down and study someday, which news I absorbed in an abstract sort of way. I thought that the prediction had come true in college, but in those courses I could still show up unprepared and understand what was going on. This spectroscopy class was a different order of experience, and a useful one. Fortunately, I left academia before running into the experience of a subject that not only could not be understood in real time, but couldn't be understood after long and careful thought, either. I am reliably informed that they're out there.
The other result of the class was the following work of art, which I composed one day in lieu of doing the assignment. I posted some of this a few years ago, but many readers will not have seen it. It is, of course, a parody of Lewis Carroll's White Knight's song from Through the Looking Glass, which is in turn a parody of Wordsworth, who seems to have tuned up many parodists to concert pitch.
He waved his hands and asked me why
Some peak would polarize
But I was thinking of my lunch
And looked up in surprise.
He then showed me a diagram
And I found to my shame
I didn't know what good it was,
And couldn't say its name.
And if now I chance to put
My tongue in super-glue
Or madly cram my chiral foot
In its enantiomeric shoe,
I weep, for it reminds me so
Of that old class I used to know,
Of ligand fields and planar nodes
And symmetries of normal modes.
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September 10, 2006
Posted by Derek
OK, the votes in the comments to the Explain This! post came out with NMR/MRI as the clear winner, with a strong plurality wanting to make sure that Fourier transforms are part of the explanation. So that's what I'll take on, but it's not going to appear this week. I'm going to try to pitch the explanation to an intelligent lay reader who doesn't have any particular physics, chemistry, or math skills. I'm out of my mind.
In second place were various suggestions about X-ray crystallography, and perhaps that'll be topic number two. Chirality would be tied with that, except there were actually more votes against it than for it, with people finding it not all that hard to explain. (They've clearly never tried to explain to someone whose specialty is running a Morris water maze assay why all the compounds flipped from R to S just because a group changed out on the far end of the molecule). Other multiple-vote getters were Woodward-Hoffman/FMO, structure determination in general, and antibiotic resistance.
Many of the single-vote topics would be good as well, and some of them would be quite tricky. The person who suggested point group symmetry, though, brought back some memories. I'd never covered anything in that area as an undergraduate, for one reason or another. So there I am in my first year, taking an optical spectroscopy class, and on about the second day the professor launches into a discussion of symmetry operations and their relevance to infrared absorption bands (which is considerable).
And this was the first lecture I had ever heard where I understood nothing but the common verbs and the minor parts of speech. I listened to the whole thing with mounting alarm. It had taken me all the way to graduate school to come definitively to the limits of my knowledge, but the pavement ran out right there. I was so stunned I couldn't even take notes - I'd never tried to take notes on something that I wasn't comprehending at all, so I didn't know how.
That evening, I stalked over to the chemistry library and checked out, among other things, Harry Gray's book on group theory, renowned as the first one on the subject "that you could read in bed without a pencil in your hand". And I didn't go to bed myself until I understood just what I'd been listening to that morning, because I didn't enjoy the experience one bit, and wanted to make sure that it never happened again.
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July 31, 2006
Posted by Derek
One of the things I've noticed over the years is that I rarely stay on a project long enough to have the kind of familiarity with the molecules that I had with the ones I worked with in graduate school. I'm not complaining. I knew my PhD project molecules like an infantryman knows the hundred-pound pack on his back - that is, much more than I ever wanted to or believed possible. I knew tiny details in their NMR spectra, things like long-range coupling constants and NOE enhancements, and the moment something changed I would point like a hunting dog.
But now, my lab stays on a project for a few months, maybe a year at the outside. And during that time, we'll work on several varied groups of molecules - usually with the same core, but with all sorts of things coming off of it. We get a working knowledge of them, but we're always being surprised by little details that would have been second nature after a good solid three years of the same series. Of course, after that good solid three years we'd all be good and solidly sick of the chemistry, too, but that's the price tag.
I used to tell people in grad school, while I hauled yet another load of synthetic intermediates up the mountainside, that the grunt work left me a choice of two moods: bored, or angry. If everything was working just the way it always had, I was bored. And if a reaction decided to unexpectedly fail, then. . .not much of an emotional range, is it? No, I'll take what I have now, where boredom doesn't have as much of a shot at me, and I don't have the chance to stay angry about any one thing for long. Variety, the spice of chemistry. (One of my "Laws of the Lab" covers this topic - I'll get to that later in the week).
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June 27, 2006
Posted by Derek
When I was in graduate school, I had a law student as a neighbor for a while. We were both pretty quiet, and got along fine in our respective dinky efficiency apartments, but we couldn't help but notice some differences between our studies. The biggest one became clear around this time of the year: he left, and I stayed. I still remember the look of surprise on his face when I told him that we didn't have any time off.
Well, I know that law students don't generally go off and laze around on the ol' hammock during the summer, but they at least get to go somewhere else for a while. But grad students just keep banging away, and if they're in the sciences, they're up there nights, weekends, and holidays.
Ah, those holidays. I still have in my files a memo from my old chemistry department, reminding everyone that the university (undergraduate) vacation schedule most definitely did not apply to us. Do not attempt to take these holidays was the very pointed message, because we will notice if you do. I sure didn't. I did take off some time at Thanksgiving and Christmas, and I didn't work every single July 4th, but otherwise it was a rare, rare day when I wasn't in the lab.
I've written before about my physical surroundings during that time, but things like this memo didn't add to the festive atmosphere very much, either. On the university level, it became clear pretty quickly that we weren't students, and we weren't staff - well, not all the time, anyway. We were whichever caused the least expense and inconvenience to the school at the time you asked the question.
But the biggest factor was the work. It was a strain. I like variety up here in my head, and this was the first time I'd ever had to do the same thing, think about the same thing, day after day (and night after night). It brought on, eventually, the mental equivalent of a leg cramp - I know for sure that I was in a much crabbier mood during my grad school years than I was afterwards, and I'm sure that it was largely because I was venting off some of the pressure. My project had the usual twists and turns, which during one point just about had me tearing my hair in frustration, but the real problem was that there was no escape from it.
Every hour I spend doing something else, besides necessities like eating and laundry, I found myself thinking about how I'd just added another hour to my graduate studies. When I could have, you know, been back in the lab trying to find a way out of the place. That is to say, doing something useful with my time. In the end, anything that didn't directly involve getting out was classified as a luxury, and I tried to ration such things. I remember going past a TV set at one point that had a golf tournament on, and I found myself amazed at these people - not the golfers, the spectators, these people who felt free enough to just wander off and spend the whole day in a sunny park watching a sporting event, without having to worry the whole time about what it was taking them away from.
All of which is why I reiterate my advice to my grad-school readers, who may be watching the summer weather out the windows of their labs (if they have windows, that is): get out. As far as it's compatible with taking a reasonably honorable and complete degree and not leaving any bad blood behind you, get out. The whole point of graduate school is proving that you can make it out of there.
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March 20, 2006
Posted by Derek
I spent the day giving the Wonder Drug Company good value for their money - cranking out a load of intermediate for other folks on the project and getting analytical data on some other samples. And talking about that sort of thing reminds me to link to a chemistry blog that I wasn't aware of until recently: a grad student named Dylan Stiles, who's working for Barry Trost out at Stanford.
Stiles is running just the kind of blog that I would have if. . .well, if the Web had existed back in 1985 when I was a grad student. Actually, it was probably a good thing for my graduate career that it didn't, come to think of it. That's the era of the "old timey" NMR machine in this post of his, which makes me wish I could find a photo of what we considered an old-timey machine. Ah, here we go: scroll down to the middle of the page, to the picture under "1976-1977". I used one of those things, and no, you didn't have to load coal in the back of it and wait for the boiler to fire up. It just looks that way.
At any rate, Stiles talks about the reactions he's running, with drawings and schemes, and takes photos of the crystals he gets and other oddities around the lab. I really wish I could do something similar once in a while. I obviously can't talk much, though, about (for example) the heterocycle I finished up today, except to note that the reaction used an unseemly amount of straight hydrazine, like nearly half a liter, and I was very glad to see the back of it. And I'd like to show some photos, too, but the Wonder Drug Factory has a "no camera" policy, and I can see why, what with chemical structures drawn all over the place.
But there would be some things to show off: I dropped a big stirbar right through the side of a one-liter pear-shaped flask the other day, for example, producing a perfect Pyrex analog of a gourd birdhouse. All I need to do is flame-polish the hole and find a way to stick a stopper permanently into the ground glass joint, which is a task that I've always seemed to be pretty skilled at, and I'm in business. See what you're missing?
Anyway, give Stiles a look if you're a hard-core organic chemistry geek like me, and if anyone knows of some other chemistry grad student or post-doc blogs, please send them along. I need to differentiate my blogroll a bit more, and that would be a fine category to have.
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+ TrackBacks (0) | Category: Graduate School | Life in the Drug Labs
November 13, 2005
Posted by Derek
I haven't worked in a US academic chemistry lab since 1988, so you'll have to take that into account as you read today's post. But I don't think that things have changed enough to invalidate this observation: many grad-school science labs are so depressing as to defy belief. This isn't universal, but I've seen enough examples to convince me. The atmosphere doesn't correlate well with the amount of money around, either, because I've seen some lower-level departments that weren't so bad, and a couple of Ivy League lab corridors that would pull the serotonin right out of your brain just to walk down them.
Many of the students and post-docs working at these places don't realize this, though, which is surely to their benefit. It's only after you've gone out into the Real World for a while and come back for a visit that it hits you. That's certainly how it dawned on me. I believe it says over there to the left that I went to Duke: maybe someone there could tell me if that second-floor "graduate student lounge" in the chemistry building is still there? I sure hope not.
This was one of the most cheerless rooms I've ever seen; it made laundromats seem warm and inviting. There was no ceiling as such, just the fluorescent lights hanging down from the industrial clutter above. Some scuffed paneling on the walls surrounded an assortment of worn, stained, mismatched thrift-store furniture. A small damaged table in the middle of a couple of sprung couches held an assortment of torn, dogeared cycling magazines, some of which had been there when I arrived and were still sitting there when I defended my PhD. A scarred counter held a 1970s-vintage microwave, which might as well have had "X-1 Prototype" stenciled on it. A bike frame without wheels, furry with dust, was chained to a rack in one corner. That was still there when I left, too.
You feel bad enough at 3 AM on a Sunday morning up in the lab, running a reaction for the twenty-third time. Taking a break by wandering down to a dingy room full of junk is not the recommended antidote. Why more people didn't just decide to end it all after a session in there is a real mystery.
Update: Reader LNT, in the comments to this post, passes on this news:
"I graduated from Duke in 2001 and the graduate student lounge hadn't changed from what you described. I don't know why university chemistry departments can't budget a couple thousand bucks a year to keep a decent communal area for their slave labor pool..."
Oh, dear.
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August 2, 2005
Posted by Derek
I was trying to think back to the least useful chemistry I ever learned in undergraduate and graduate school, and let me tell you, it's a tough league to play in.
I know, I know, many of you are thinking "Yeah, I hated quantum mechanics, too", but that's not what I'm talking about. Quantum stuff is actually interesting to me, although I am glad to not be obligated to finish any paragraph that begins with "Consider the Hamiltonian. . ." No, I'm thinking of things that were presented as techniques that I'd be using and had better understand and commit to memory.
How about. . .electron spin resonance? ESR was sold to us as a parallel world to NMR, full of its own utility, well worth getting to know. Sheep dip. ESR is interesting and useful to that subset of people who deal with reasonably stable free radicals, but to very few others indeed. I take that point that it's a fine technique for those people, but I'd like to point out that my chances of becoming one of them were never very high. The time and effort I put into learning it could have been spent much more profitably.
"But hold it," says my memory. "You didn't spend any time getting to learn ESR spectroscopy. You read the newspaper during the lectures. You didn't buy the textbook. You only exerted yourself during the hours leading up to the exams, and sometimes not even then. It's no wonder you don't know squat about it."
Er, well, I suppose there's something to that. I recall that the class was divided up into groups of three or four, and assigned regular problem sets to work out and hand in. My group of three became increasingly demotivated as things went on, and by the time of the last problem set, we spent our time complaining about how much we couldn't stand the stuff any more and never got around to solving any of the problems.
Come that Monday morning, I realized that I hadn't put anything together for us to hand in. So I just dug around and found a sheet or two where we'd taken a listless stab at working a problem. That seemed a bit lacking in heft, so I bulked it out with a random handful of paper from a disused notebook, put our names on it, stapled the pile up, and turned it in. There were blank sheets of paper in there; there was a paper towel. The sheets with writing on them often weren't even from the course in question, and many of them were upside down, anyway. What the hey.
Looking back, it's hard to believe I actually did that. My problem set partners found it a bit difficult, too, even at the time: "You did what?" I awaited our grade with interest. A few days later, the professor stopped me on my way out of the class and asked "Do I have your group's problem set?" "Sort of," I responded. "Oh, yes!" came his answer, "that was a messy one, wasn't it?"
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August 29, 2004
Posted by Derek
When I think back on all the things I learned in grad school. . .well, let's say that not all of it has come in handy. Chemistry, like all the other sciences, long ago split into all kinds of sub-specialties, so it's no wonder that I haven't had to worry much about Tanabe-Sugano diagrams (to pick a representative example from inorganic chemistry.) Nor has normal coordinate analysis featured much in my work of the past twenty years, since I'm not some sort of theoretical spectroscopist. And, thank God, I haven't had to sit down and do any quantum mechanics since the day of my final exam in that well-known rite-of-passage course.
But I haven't had to use things that are nominally in my area of expertise, either. Electron spin resonance, for example - that's something that free radical chemists care about, but I did a whole post-doctoral year doing free radical chemistry, and never did the subject come up. Makes me glad that I didn't spend any more time learning it.
How about chiral aldol chemistry? That's close to home. It's organic synthesis, my very own subfield, and it was the subject of the first question I was asked during my PhD orals. Have I ever done a chiral aldol reaction? Not a one, and I don't have any plans to. Was my time well spent learning all the various theories about how they work? Doubts have crept in.
Moving even closer to how I earn my living, how about all those med-chem graphs and equations they try to teach you? My first year in the business, they sent me (and a number of other folks) off to a well-known summer short course in medicinal chemistry, to teach us the ropes. Now, I can't pretend that I didn't learn anything useful there, although it was all material that I was going to learn anyway. But those equations, those fine equations for pharmacokinetic behavior, for clearance and absorption and distribution. . .I haven't had call for one of them since.
I mean, I think about those phenomena all the time, but not in mathematical terms. The real systems are just too messy for that, and most of the time we don't understand what's going on, anyway. I can just see myself back in that classroom, copying these things down. Did I have the suspicion right there that I'd never write them down again, or did that take a little while longer?
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June 2, 2004
Posted by Derek
It's been a while since I returned to this topic. Many differences remain for me to talk about, but I though that it was time to address the biggest one, which is psychological. Some of you probably thought that the biggest difference was money. Can't ignore that one - it probably contributes to some of the effects I'll be talking about. But there's a separate mental component to graduate school that never really recurs, which should be good news to my readers who are working on their degrees.
Some of this is due to age, naturally enough. The research cohort out in industry ranges from fresh-out-of-school to greybeards in their fifties and sixties. (I can say that, since I'm in my early forties, the color changes in my own short beard notwithstanding.) Everyone in graduate school is a transient of one sort of another, usually someone whose life is still just getting going. But in the workplace, most people are more settled in their lives and careers. There are still some unsettling waves that move through industry, mergers and layoffs and reorganizations. But people respond to them differently than they would in their 20s - often better, sometimes worse, but differently.
And not all your co-workers in grad school are actually stable individuals, either. Some of these people wash out of the field for very good reasons, and you don't see as many of the outer fringes later on in your career. It's not that we don't have some odd people in the industrial labs, believe me. But the variance isn't as high as it is in school. Some of those folks are off by so many standard deviations that they fall right off the edge of the table.
Another factor is something I've already spoken about, the way that most graduate careers come down to one make-or-break research project. The only industrial equivalents are in the most grad-school atmospheric edge of the field, small startup companies that have one shot to make it with an important project. But in most companies, no matter how big a project gets, there's always another one coming along. Clinical candidate went down in flames? Terrible news, but you're working on another one by then. There's a flow to the research environment that gives things more stability.
The finish-the-project-or-die environment of graduate study leads to the well-known working hours in many departments. Those will derange you after a while: days, nights, weekends, holidays, Saturday nights and Sunday mornings. I worked 'em all myself when I was trying to finish my PhD, but I don't now. If a project is very interesting or important, I'll stay late, or once in a while work during a weekend. But otherwise, I arrange my work so that I go home at night. For one thing, I have a wife and two small children who'd much rather have me there, but even when I was single I found many more things to do than work grad-school hours. It took me some months after defending my dissertation before I could decompress, but I did. Having a life outside the lab is valuable, but it's a net that graduate students often have to work without.
But beyond all these, there's one great big reason for why grad school feels so strange in retrospect, and I've saved it for last: your research advisor. There's no other time when you're so dependent on one person's opinion of your work. (At least, there had better not be!) If your advisor is competent and even-tempered, your graduate studies are going to be a lot smoother. If you pick one who turns out to have some psychological sinkholes, though, then you're in for a rough ride and there's not much that can be done about it. Everyone has a fund of horror stories and cautionary tales, and there's a reason for that: there are too damn many of these people around.
Naturally, there are bad bosses in the industrial world. But, for the most part, they don't get quite as crazy as the academic ones can (there's that variance at work again). And they generally aren't the only thing running (or ruining) your life, either. There's the much-maligned HR department, which can in fact help bail you out if things get really bad. Moving from group to group is a lot easier at most companies than it can ever be in graduate school, and it's not like you lose time off the big ticking clock when you do it.
I can see in retrospect that I was a lot harder to get along with when I was in grad school. I responded to the pressure by getting more ornery, and I think that many other personalities deformed similarly. When I've met up with my fellow grad students in the years since, we seem to be different people, and with good reason. It isn't just the years.
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March 18, 2004
Posted by Derek
A reader's e-mail got me thinking about this topic. It's worth a number of posts, as you'd guess, since there are many substantial differences. Some are merely of degree (funding!), while others are of kind.
But the funding makes for larger changes than you'd think, so I'll get that one out of the way first. When I was in graduate school, my advisor's research group was actually pretty well-heeled. We had substantial grant money, and none of us had to be teaching assistants past our first year. But even so, we had to watch the expenditures. For example, we didn't order dry solvents, in their individual syringable bottles, from the chemical companies because those were too expensive. Instead, we had our solvent stills, which (to be fair) produced extremely good quality reagents at the price of the occasional fire.
Grad student labor is so cheap it's nearly free, so making expensive reagents was more cost-effective than buying them. (At least, it was if you weren't the person making them.) I had a starting material that's produced from pyrolysis of corn starch (levoglucosan, it's called, and I'd be happy to hear from anyone who's worked with the stuff.) At the time, it sold for $27 per 100 milligrams, and since I used it in fifty-gram batches, that was out of our price range for sure.
So I pyrolyzed away, producing tarry sludge that had to be laboriously cleaned up over about a week to give something that would crystallize. (I saved the first small batch that did that for me back in the summer of 1984, and it's sitting in the same vial right next to me as I write. The label looks rather distressingly yellowed around the edges, I have to say.) A kilo of corn starch would net you about fifty grams of starting material, if everything worked perfectly. And if it didn't, well, I just started burning up another batch, because it's not like I had anything to do that Sunday night, anyway.
When I got my first industrial job, it took me a while to get all this out of my system. I needed an expensive iron complex at one point, about six months into my work, and sat down to order the things I needed to make it. My boss came by and asked what I was up to, and when I told him, asked me how much the reagent itself would cost. "About 900 dollars", I told him, whereupon he told me to forget it and just order the darn stuff. He pointed out that the company would spend a good part of that price just on my salary in the time it would take me to make it, and he was right, even at 1989 rates.
So we throw the money around, by most academic standards. But there can be too much of a good thing. There's a famous research institute in Europe, which I'm not quite going to name, that was famously well-funded for many years. They had a very large, very steady stream of income, and it bought the finest facilities anyone could want. Year after year, only the best. And what was discovered there, in the palatial labs? Well, now and then something would emerge. But nothing particularly startling, frankly - and from some of the labs, nothing much at all. You'd have to have a generous and forgiving spirit to think that the results justified the expenditure. There are other examples, over which for now I will draw the veil of discretion.
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| Category: Academia (vs. Industry) | Graduate School
December 9, 2002
Posted by Derek
As I mentioned in that last post, I did carbohydrate-based chemistry back in grad school. (I still break out the sugars once in a while, but there aren't as many opportunities in medicinal chemistry.) Back then, I was on a project that was using them as starting materials to try to synthesize a large antibiotic molecule from scratch. The idea's fairly sound - the antibiotic has a lot of chiral carbons in it, and sugars are a rich source of strings of chiral carbons.
But there were complications. There's no carbohydrate with just the sort of backbone you'd need (if there had been, the synthesis would have been pretty trivial.) So the project involved taking some of the available ones and tweaking them around - remove a hydroxy group here, flip one over down there, change this to a branching carbon over around this way. The synthetic steps really start to add up after a while, I can testify. A lot of the difficulties came from starting out with such highly functionalized molecules. You had to first protect all those hydroxy groups, and do it in such a way that you could take each protecting group off at just the time you needed it. Pretty soon, you run out of possible protecting groups!
I pulled the plug on the whole thing at about 27 linear steps, and it wasn't finished then. It really seemed to me that we had reached the point of diminishing returns, which opinion of mine time has completely confirmed. It would have taken me another year, at the rate things were going, and that would have been a really bad trade. Even as it was, I was spending most of my time making starting material (as my readers in the organic synthesis field can readily imagine.) And no matter how large a flask (flask? how large a bucket) I started the chemistry off in, I always seemed to get to the frontier of the synthesis with about 20 milligrams. I felt like the guys painting the bridge - as soon as I finished, it was time to start again.
Some time I'll tell the story about what my PhD advisor did when I shared the news with him that I wasn't going to finish the molecule. He wasn't taken with the idea.
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February 18, 2002
Posted by Derek
I won't be posting for another day or two; I'm taking tomorrow off from the Wonder Drug Factory and heading out with the family. My chemistry can get along without me just fine, and the people that report to me will most likely be even more productive without me around.
Leaving the lab for a few days was much harder back in graduate school, of course. The main reason was psychological. It took at least six months after I got my PhD for that voice in the back of my head to stop telling me to get back in lab, that I was wasting time. Every hour that I wasn't trying to finish my project was an extra hour that I was going to spend in grad school. This mental nudging didn't just occur when it should have. No, I felt this way when I was doing frivolous stuff like buying food, or putting gas in the car.
The second problem with leaving the lab was that I had a lot of chemistry going on simultaneously. I persisted in thinking that I'd remember every tiny detail when I got back. So I'd return and find a bunch of flasks, helpfully labeled with things like "large batch," "other fraction," or "N." My first day back in the lab always involved a lot of staring up at the ceiling, trying to remember what the heck I was doing.
Of course, many of my days in the lab involved some staring up at the ceiling. The difference was, on those occasions, my lips were moving.
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