Tuesday, August 31, 2010

PIs, students, and academic misconduct

With the Marc Hauser misconduct situation making waves all over the blogosphere, and even at the NYT, academic fraud has been on my mind. Yesterday, DM reminded us about the collateral damage academic misconduct leaves in its wake, namely the careers of the blameless trainees. In a Science update on the 2006 case of Elizabeth Goodwin, who was a biologist at the University of Wisconsin (UW), Madison when she falsified data and was turned in by her students. Goodwin's punishment, in which she

...has agreed not to participate in federally funded research for 3 years and will pay $50,000 to the Department of Health and Human Services, according to the Justice Department press release.
Seems minor compared to what happened to her students. In doing the right and proper thing and blowing the whistle on their cheating and lying PI, the six students lost pretty much everything:
But the outcome for several students, who were told they had to essentially start over, was unenviable. One, Chantal Ly, had gone through 7 years of graduate school and was told that much of her work was not useable and that she had to start a new project for her Ph.D. (The reason wasn't necessarily because of falsified data but rather, Ly and the others thought, because Goodwin stuck by results that were questionable.) Along with two of the others, she quit graduate school. Allen moved to a school in Colorado. Just two students chose to stay at UW.
Ethics aside (where it seems obvious that turning in a cheater is the right thing to do), whistleblowing is really important in that it ends the cheating behavior ASAP, and stops the literature from being polluted with additional incorrect and falsified results. As noted in this 2006 article in Science, even retracted papers endure and pick up citations. I've noticed in my class last year that students will summarize and cite retracted papers in their coursework, unaware that the information contained is incorrect. From the outcomes in the Goodwin case, it seems that scientists expect trainees who become aware of misconduct to take one for the team, and give up their careers in favor of the benefit to science as a whole. This sucks. How can giving up on your desired career compare to 3 years of giving up Federal support and a $50k fine?

Whistleblowing is immensely risky as a student--there is such an imbalance of power, that the tendency is to assume sour grapes on the part of the student and not that the "proven" PI is cheating (maybe because outright fraud is so rare?). The case much be really, really strong for students to go forward. The easiest (and most self-serving) outcome is to switch groups as soon as possible for the student, before any taint or investigation occurs. Goodwin's students were really brave and really strong to go ahead and turn her in.

On the other hand, maintaining the meaning and value of a PhD degree is important as well. Clearly Goodwin's students can't just get degrees for time served, given that their mentor screwed them over and prevented them from actually doing scholarship. That said, the six students had enough scientific training to notice the inconsistencies and collect enough data to prove a case to the point that Goodwin did not contest the charges. That should count for something, right?

Marc Hauser was also turned in by trainees. He gets a year off from Harvard, and they get?

Friday, August 27, 2010

Paper managing software

Endnote has pissed me off for the last time (I hope)! Now that I have a really large library, it is difficult to find things in it. I sometimes have formatting issues, and it can be annoying to add something to the library. Basically, the software is layer on layer of new stuff on old, and it is just not working for me anymore. Now that I am finishing up an old collaboration (where we used to send each other drafts with Endnote libraries), I am taking this chance to try something else.

Lots of people recommended Papers to me (since I have an old Mac in my office), but I find I am using the Mac less and less (since my lab instrumentation is all Windows based, and I like to look at the raw data occasionally). It looks like I will probably start hooking my PC subnotebook up to my big monitor. So I want at least a cross-platform solution.

I decided to try out Mendeley, and I like it so far. I let it grab my paper data out of the pdf files, which took a little while. Once set up, I found that while most of the details it grabbed were correct, I do need to look at entries before using them. Rather than wasting time fixing stuff, I am fixing entries as I use them. There is a tool to look papers up by title in Google Scholar if the data grabbed from the pdf is incorrect, and that is pretty handy.

I am not used to using anything but Adobe to read pdfs, but the ability to add notes to my papers (and highlight text) seems like it could be pretty handy. It is also possible to share annotated papers, which I may eventually do with my group. I signed up for the Web account, but I don't know if I will use it. For now, I just want something that can insert references properly into my manuscripts (I am not a LaTeX person) and search through my library of pdfs.

I'll post a more extensive review after I use Mendeley for the manuscript I started yesterday. Anyone else have paper/reference management software suggestions?

Wednesday, August 25, 2010

Impressions and realities on the job

Inspired by posts by Dr. Isis, Gerty-Z, and Prof-like Substance, plus my own panic here in year 2 at Prodigal U, I've been thinking about training and preparation along my career track.

When I was an undergrad, I did research. I worked in a lab for 1.5 years (full time over the summer), participated in group meetings, did my share of lab maintenance, and worked with grad students. I thought I knew what grad school would be like. I was completely wrong--grad school threw me for a total loop. I felt lost (there was no clear path to get to my degree). I had all this time, but yet no time at all. Progress was really, really slow, and I was so clueless. I had no idea how to manage my time effectively without classes and deadlines to help me. I didn't know how to properly test things or document them, so I had to repeat a whole series of experiments. I didn't know about all the time TAing takes, all the different pressures on students to study and finish experiments and do this side project quickly and train this new student and help this undergrad in lab while still making progress on my own stuff.

When I was a grad student, I worked with postdocs. I thought I knew what being a postdoc would be like. I was wrong. As a postdoc, I was now THE expert on my technique. My National Lab colleagues were relying on me, ME! to tell them if certain experiments were possible, if certain data was reasonable, if certain timelines were realistic. I had no backup. There was no one else on the project who knew my technique (which is what I was brought in for), but I knew nothing of the system I was studying (which is what I went to learn). I panicked quite a bit when I realized that, then knuckled down and did it. Being a postdoc (at least in my case) was a lot more responsibility and a lot more independence than being a student. It took a lot of getting used to be considered an expert after all those years as a student.

When I was a student, we used to sit in the lab and wonder what our advisor did all day. We would laugh about it actually. Now, I am drowning in it.

Monday, August 23, 2010

What is a degree worth?

There were a lot of interesting points in the comments of my last post from Dr. G, Hope, and GMP about the value of a PhD, and of higher education in general. I agree with the sentiments expressed by all three that in an ideal world, all PhD candidates would be trained to be scholars to the same standards, regardless of where they started from or plan to end up.

But reality is a lot messier than that. There are many pressures that support the admission of "unqualified" students to grad school, including state funding per student, the need for warm bodies as TAs or RAs, or the desire to grow a program. There are more spots (at least in my STEM field) than truly qualified applicants. Students with good recommendations, great grades, and research experience are admitted immediately, often without the whole admissions committee seeing the file. This doesn't fill up our whole program.

There are two kinds of "unqualified" that we will consider admitting--students with mediocre to poor grades, but great research experiences/recommendations and students with mediocre grades from well regarded programs (students with mediocre grades from unknown programs are just not admitted). The first group are often students who had to work a lot in school, students with learning issues (like diagnosed or undiagnosed dyslexia), or students who had to learn English while undergrads in an English language program.

The second group is full of students who got into a good undergrad program and then coasted and directionless students. Some of these students will be late bloomers, and be wonderful grad students--that is the case for one of my collaborators. In this case, the student had pretty poor grades from a pretty good undergrad program (which was used as an excuse for admission). The poor grades were clearly due to lack of effort, since this student discovered true passion for the field in their senior year as an undergrad, and excelled in research as a grad student. Alas, this is generally the exception and not the rule. The result is a department full of mediocre, poorly motivated, and difficult students with a few gems that are heavily sought after.

A huge additional problem for faculty members is the quality of the BS degree (which is no fault of the students, to be sure). As GMP said,

Another issue is the complete devaluation of the BS degree. It's become almost what a high-school degree used to be 30 years ago. Now you can't do almost anything without a BS; also, in order for everyone to get a BS, it has become watered down, with emphasis on breadth rather than depth, so basically all in depth technical training is now deferred to grad school.

When I was a grad student, I and my fellow US-educated students noticed how far ahead technically the European and Asian students were than we were. We had all received good grades, and did well in our programs, but the emphasis on liberal arts meant there was a lot less time for core instruction in the details of our field. This is a mixed blessing--several of my European colleagues are jealous that they never got to take classes in history, literature, or art (which I thoroughly enjoyed myself). On the other hand, I lacked a lot of depth in my field. This causes a few problems down the line. First, incoming students must be treated as if they have limited technical knowledge and skills at best, which means lots of training for people running labs. Second, lots of people don't really know/understand what the field is really like, which leads to a relatively high attrition rate of people abandoning their programs after a year or two.

This devaluation of the BS degree means that the MS and PhD have followed suit. Since the BS students are coming in with less knowledge, more of the PhD has to be spent on bringing them up to speed and less on more advanced training. We also don't want PhD training to last more than 5 years or so. Given that a fair fraction of the admitted students are less qualified, and that we want to maintain the value of degrees in our department, we end up tailoring expectations and experiences of the PhD to the students' end goals. Otherwise, too many would not make it through.

Personally, I will not grant a PhD to anyone not capable of doing PhD-level technical work, but I can already see that some of my students will be better than others at things like writing (papers and proposals), idea generation, working independently and other scientific skills. The department has a line in the sand to get a degree, but in practice, this is worked out by the PhD committee. What are the requirements of a PhD scientist? How can we make uniform standards for people with uneven skills? As a committee member, it is really, really hard to see someone working hard who will not make it. Sometimes, it isn't apparent until the student has been around for a while. I am a replacement committee member for someone on the bubble (who had been in our program for 3-4 years), and it is really difficult.

And what about my standards? Should I not allow a brilliant researcher who writes poorly in English to graduate? What about someone who is wonderful at scholarship in general, but is weak at generating new research ideas? These people would be valuable assets in the right position, but will never be successful faculty members because they are good scientists, but not necessarily good scholars. They have PhD level training and PhD level skills in some aspects of science. Do we restrict PhDs only to people who are capable of TT-like positions? I don't think there is an easy answer.

Friday, August 20, 2010

Overproduction of PhDs?

I saw this interesting post and follow-up comments at Inside Higher Ed by Monica Harris, a professor of Psychology. In her post, Prof. Harris discusses the poor academic job market in psychology and how she tried to warn potential students about it. In the end, she says:

After a few years of watching the academic job market collapse into a seeming death spiral, I also started to wonder whether my "full disclosure" strategy of trying to scare off prospective graduate students was adequate. I started to entertain the possibility that if the problem was too many qualified applicants for too few jobs, then perhaps the responsible – even ethical – course of action would be for me to stop contributing to the oversupply of applicants.

So, a few weeks ago I revised my departmental web page to include the following statement: "Notice to prospective graduate students: I will not be accepting new students in my lab for the indefinite future."

This seems like a total overreaction to me. Now, I am in a STEM field, so even though the academic job market is poor, there is still pretty good demand for Masters and PhD holders in my field outside of academia, especially in non-research positions. According to the scientific societies that track such things, unemployment is low among PhD-holders, and in general remains much lower than the general unemployment rate even in times of recession.

Furthermore, what percentage of grad students go in wanting to become academics? In my field, it is pretty low--maybe 30%? None of my current students (or in fact any of the many students I have interviewed for my group) have said they want to be professors, which is similar to what GMP has experienced in her field. Maybe this is not the case for the social sciences and humanities. Even so, I find it hard to believe that the skills of a PhD in anything (statistics, research skills, writing, analysis) are not transferrable to other job areas.

In my own experience, I have a friend who went to a top-10 University, published in Science, and uses his PhD to teach high school (which was his plan all along--he just loved his field, and wanted to spend a little time delving into it before starting his career). Another former classmate is now an ordained clergy person, after getting a PhD in our field (also for the love of it). This on top of all the PhD holders I know in law, business, non-research science, and other occupations by choice, not as a last resort. Given the HUGE variety of motivations for getting a PhD, it seems kind of patronizing to say "I am going to save you from yourself, kid." Especially in fields where the main cost is opportunity cost, and grad stipends are livable.

I can understand the feeling that there are too many PhDs, but I think that is because there are more people in general, and more of those people than ever before have opportunities that used to be reserved exclusively for rich, white, Christian, heterosexual men. I do not believe that academia is a pyramid scheme, any more than I believe admissions to prestigious Universities are a pyramid scheme. My fear is that if we restrict admissions to PhD programs, we will go backwards on the progress we have made towards diversity. Tightening admissions requirements would screw over the disadvantaged in our society. I would much, much rather allow people to make their own choices and roll the dice on a TT job if they so desire.

Wednesday, August 18, 2010

Tenure (on a personal level)

FSP and GMP both discussed tenure, why it is important, and why it is unlikely to go away any time soon. On a more personal note, I am contemplating when I should go up myself. Since I am not a brand new scientist, when I started at Prodigal U, I negotiated the right to go up for tenure any time after my 3rd year (though I can wait the normal 6 if I want to). If I am denied early, I can go up again at the normal time (in theory with no penalty).

I was talking in the hall a few days ago to 2 of my colleagues, one tenured and one not about the issue of going up early. My tenured colleague asked "why would you want to?". My untenured colleague said "I totally would if I could."

On a personal level, I would like to have the certainty of tenure. We moved to Prodigal City, which is far from National Lab City, because I am pretty sure I will get tenure here. I have no desire to uproot my family again after 6 years, especially since the Prodigal kids will be in school by then. Going up early means fewer years of tentative roots just in case. Professionally, I'd get a 5-6% raise (which is nice, but not really a motivator). When recruiting, I'd be able to tell students I have tenure (which can be a big deal to some students).

So what are the costs to early tenure? It is true that in my department assistant professors are somewhat protected from onerous service obligations, so I'd be giving that up. I would be giving up eligibility for "young investigator" and "new investgator" awards, but I am already not eligible for any of the shiny Federal young investigator awards anyway, since I am too far out from earning my PhD (which is totally fair, since I have a lot more experience than a new grad). If I am denied early, that could put a black mark on me for future rounds.

In the short term, going up after 3 or 4 years won't really change what I am doing. I feel like I had a great first year, and would like to capitalize on that momentum. If I can get some more funding next year, maybe it becomes worth it to push for tenure after 3 years in case I have a dry spell later. So, what would you do?

Friday, August 13, 2010

Using startup money

I am through my first year and also mostly through my startup money. I have a little "nest egg" of about $20k that I plan to nurse along for emergencies/a little boost sometime in the future. I've been told that the accountants at Prodigal U start to get antsy about unspent startup after 4-5 years, so I have a few years to worry about it.

When I started my position, I saw lots of advice about balance, teaching, recruiting, setting up, etc, but not much about how to best use startup funds. Startup funds are magic money--not tied to any particular project or any particular budget, they can be spent on anything. This type of money is so amazingly rare in academia that I am unlikely to ever have significant amounts of it again. Watching funds disappear from the account can be painful, since they are in effect irreplaceable.

When I started at Prodigal U, all I had was my startup money to buy equipment and supplies, to pay salaries, to travel, and to cover user fees for instrument access. The temptation (at least for a cheapskate like me) is to horde it--what if nothing else comes in? My new chair and my PhD advsior both told me that it is more common for new profs to cheap out on buying stuff than to burn the startup too quickly, and that you can always ask the department to help you pay for students, but you can never get wasted research time back, so I decided to spend. I took a "burn the ships" approach to my startup. I would turbocharge my first year by spending on anything that would get me going faster and worry about the funding situation later.

This was a deeply considered decision. To be at the cutting edge in my research area requires some very expensive equipment. I decided to buy most of what I will need rather than depend on instrument access in other labs. I was thinking 1) I have priority usage, so we can work 24 hours a day if necessary, 2) we can modify the equipment as needed and make permanent installations of commonly used setups, and 3) equipment money is hard to get and user fees can really add up. That said, burning through my startup like this means I cannot hire a postdoc or technician until I get some decently funded proposals.

So far, it has been a good decision. My equipment is humming along and producing nice data. I had 3 proposals funded this year (1 new investigator, 1 solo small grant, and one as co-PI with 2 other profs). None are huge money, but I can probably support 4 grad students with what I have in hand. I have 2 grad students plus myself as personnel (augmented by 3 summer students), and I will probably take 2 more grad students if I can find the right ones. And then I need to find more money.

The postdoc thing weighs on my mind a bit--would I be going faster if I had one? In my field, postdocs last 1-3 years, so it just didn't seem worth it to me to invest so much time into someone so temporary in the very beginning. Mine is a student-heavy strategy that is only possible because my first 2 students are doing amazingly well in terms of research productivity. Sometimes I wish I had hired a postdoc right away, especially when things are not going well in the lab and there is troubleshooting to be done. But then I see some colleagues waiting around for instrument time while we are using our own, and I am happy again.

Tuesday, August 10, 2010

Looking back at grad school

Inspired by Ambivalent Academic, as a submission for Samia's zomg grad skool carnival!!!1, and in honor of the 10th anniversary of my PhD defense (yikes, has it been that long!), a look at the things I took too long to learn in grad school (or things I should have learned in grad school, but learned later):

1. Ask questions. In high school, classwork came really, really easy to me (you can hate me now). In college, I quickly learned things would be different, but I also had this notion I should keep my ignorance to myself. This notion followed me into grad school and is dumb, dumb, dumb!

Your professors want you to come to office hours to discuss the course material (assuming you are doing all the work and keeping up in class). They especially want you to dig deeper into the material and have fun with it, and then come ask questions about your digging. Going to seminars with fancy, famous speakers is great, but only if you get something out of it! If you are confused, ask. I guarantee you are not the only one. I was one of those people who was always afraid to look stupid, and I missed out on my opportunity to ask the experts questions about their science. Now I have to learn that stuff myself, without the benefit of an expert.

2. Attend seminars (and pay attention). You never know what you will end up doing. It is really important to keep up in areas other than your research sub-field. I was so sick of my project after my PhD that I completely changed sub-fields for my postdoc. I was able to pick something else I was excited by from the great seminars I saw as a student, which narrowed down my interests to a manageable degree.

3. Push to attend meetings. In my PhD program, students could attend one meeting on the department. This was not advertised, and my PhD advisor only really encouraged his Golden Boy (tm) to attend meetings with him. Well, fuck him--I want to go too! I asked around a little, and lo and behold there was a fund to help students with tightfisted advisors travel.

When I found out about this money (it is a dollar amount per student), I was pretty annoyed, but I also wanted to get the most out of it, since advisor wasn't going to give me anything else. By proper budgeting, I used my money to attend 1) local society meeting, 2) International technique meeting which happened to be in my city (I volunteered to help out to defray costs), 3) national society meeting in a far away city (also did some volunteer work there), and 4) local society meeting in a nearby city. If there truly is no travel money in your department, apply for grad travel awards.

Meetings are super important for networking, job hunting, inspiration and feedback. You need to go if you want to stay in science!

4. Decide what you want to do with your degree. I was one of those idealistic idiots who just wanted to get paid to do research without any real plan for what happens next other than "industrial research, I think." This post show what a huge role dumb luck played in my career. This is not a good idea. You should think about what you want to do next so you can tailor your PhD to get the experience you need to actually reach that goal. Do you want to teach? You might want to do some more advanced TAing. Do you want to work in industry? You should meet with all the speakers from industry and try to work on an industrial collaboration if possible. Work at a government lab? You need to work on getting contacts. Whatever your goal is, there are things you can do to help yourself.

5. Let your advisor help you. It is what they are there for, and not just in the lab. You need to communicate when you are having problems. Your PI isn't a mind-reader. An example--I was assigned to TA a very time consuming class that I hated TAing. I was assigned it 3 semesters in a row. The 4th semester, they assigned it to me again (over my objections). I complained to my PI and he said "I didn't know you hated it so much! You should have said something earlier." He got on the phone. An hour later, I had a much better TA assignment, and I never was assigned my hated class again (yes, I TAed a lot--see point 6).

6. Be aware of your PIs career trajectory. My PI was winding down. He took a lot of students in a short period, but soon after stopped taking new ones. And he stopped writing new proposals too. So this meant we were cash strapped. If I looked carefully, I would have seen that he was getting towards the end of his active research career, but I fell in love with my project and didn't care. Projects come and go, but your funding comes from your PI. If they stop writing, you start TAing (in departments where that is possible).

7. You are at a major University--take advantage! Even though you are in grad school, you can probably see great theater, attend wonderful music performances and enjoy great art. Take advantage of the other things found at PhD U. You definitely have time to do stuff outside the lab, so go for it. Your PhD is a marathon, not a race. You don't want to burn out early. I actually took an intro class in another department for fun my second to last year, though this option is not available everywhere. I definitely started paying more attention to the art museum after 3 years at PhD U. Why did it take me so long?

8. Pick your advisor, not a project. See #6. I don't regret my choice, but I also followed an a-typical career path for a TT prof. Your labmates are also crucial, so make sure you meet your potential group before you join.

9. At most Universities, you can find someone to deliver pizza to any building at any time. And nothing tastes better at 2 am than hot, fresh pizza with your labmates!

10. Have fun! I really enjoyed my first 4 years of grad school. I loved learning, I loved my project, I had hobbies, I had a life. I could even save some money (I bought a few shares of Apple stock at its historic low. If I had more money to burn then, I would be rich now!) The hours could be grueling, but I was also working almost completely independently and following my interests. My labmates were smart and fun. If it is all painful, you should quit. Life is too short to suffer for some letters after your name. If you hate everything about grad school, you should reconsider a career in science.

Monday, August 9, 2010

Feeling refreshed!

For the first time in a long time, I am feeling relaxed (or at least I was, before I went in to Prodigal U today). Limiting Internet access to 1 hour a day greatly enhanced my vacation. I could handle important work mails (and not abandon my students), but blow off unimportant stuff. I didn't feel cut off, but I didn't feel too connected to work. And the weather in our vacation spot was great all week!

In my absence, I see the science blogging arena has blown up. I'll have to get around to fixing my blogroll sometime this week.

Tuesday, August 3, 2010


I am away this week and trying to limit my Internet access. Thus far, I've only been online once a day for about an hour. I am going to call that a success, since I am pretty aware of my Internet addiction. Have a nice week!