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phd / graduate student stuff

give the academic gift that keeps on giving

I hope everyone has been enjoying the holidays!

Yes, it’s the season of giving and what better way to show you care than to give authorship on one of your papers.  This can be a very touchy subject sometimes and I’ve heard of some pretty crazy and ridiculous situations where people have been included as authors on papers (some even including extortion and blackmail).  But, what I’m talking about here is including people in your research–getting people involved in the process.

One concern I’ve heard is that having a lot of authors on a manuscript dilutes the authors’ acknowledgement, which really is not true.  To this day, I still only pay attention to the first and last authors (sometimes second-to-last author as well)–I find this to be true of almost all of my friends and colleagues.

So why should you actively try to involve others at an authorship level?  Well, another brain thinking about your project certainly can’t hurt.  That’s a given, but maybe you don’t think it’s necessary plus there are people who would think about your project without having to be an author.  From a practical standpoint, when you include someone with the understanding that he/she will be an author, you can demand a lot more–time, resources, thought, etc.–from that individual:  What do you mean you can’t?  You’re going to be an author right?  Do it!

More importantly–and I think this is more important for some of us junior academics–including someone else in your research at an authorship level shows your appreciation for that individual’s thoughts/abilities and contributions with the most valuable currency in academia and ultimately helps to build new professional friendships as well as solidify already established professional friendships.  Some of my closest friends (professional and now even personal) are people who I’ve met through research collaborations and they remain as people who I know I can rely on for help when I need it.  And in the often cut-throat world of academics, it is awesome to have such friends.  So as you are working on your research, keep this in mind and use it to your advantage to make important professional connections and friendships…

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graduate programs in translational research gaining in popularity

The draw of translational research and the desire of many graduate students to gain some clinical exposure and to have opportunities to do research with tangible clinical impact has caused academic institutions around the country to address these objectives by designing graduate programs with a focus on translational research.  I’ve known a number of people who have gone through these programs and all have been very satisfied with their training.  The primary differences between these programs and more specific, traditional Ph.D. graduate training programs (e.g. “the graduate program in biochemistry”) are the faculty comprising available mentors as well as program-specific course requirements and offerings.  Whereas in more traditional graduate programs there are more opportunities to research the biological sciences at a more basic level (e.g. studying the structure and function of a specialized protein), translational research-focused graduate programs tend to include faculty members whose work has greater immediate clinical impact (e.g. studying biomarkers or pharmacology).  Moreover, course offerings through translational research-focused graduate programs have specific focus on exposing students to clinical problems and disease processes, for example through pathophysiology, pathology and pharmacology courses.  Even more unique are some courses offered by a few programs that give graduate students the opportunity to go out into the wards and see patients firsthand.  I personally think that the clinical exposure in these programs should really be extended to all graduate programs in the biological sciences.  Maybe it’s my own personal bias, but I think all research in the biological sciences, whether in the short term or long term, should offer some benefit to patient care.  And at the very least, I think clinical exposure for graduate students (or anyone) just offers more motivation and inspiration for doing research.

Anyway, for those who are interested in translational research, these programs go far in fostering that interest through many opportunities that don’t otherwise exist in full at the more traditional graduate training programs in the biological sciences.  For some personal stories of people who have gone through these programs and a list of translational research-focused graduate programs across the country, check out this article on Science online.

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finding an endpoint for your phd - part 2

So you have decided–mind and body–that it is time to finish your PhD but you have to get your advisor onboard.  What to do?  Before I go on, I make the disclaimer that I am not giving out advice on how to trick or bamboozle your advisor into handing a PhD over before you actually deserve it.  First of all, if you haven’t done enough work to have earned a PhD, it will be painfully obvious to both you and your advisor.  And in the off chance you manage to slip one by your advisor, it’ll never fly with your thesis committee–so don’t even try it because it’ll make you look really bad.

With the disclaimer out of the way now, I will say that it is a fact that your advisor will never come up to you and say, “You know, I think it’s time for you to graduate.”  It’ll never happen so the responsibility is left to you to approach your advisor when it is the time, which naturally works out against you because you will think long and hard before getting into that discussion.  In some cases, the thesis committee meetings are helpful because a committee member may throw the idea out there.  However, this isn’t always effective because after the thesis committee meeting ends, it will be back to just you and your advisor, which means that it will be up to you to follow up on the “graduation” discussions.

So it’s always great if you have a “reason” to bring up graduation.  For example, family/spousal reasons/circumstance or funding reasons.  In my case, I had a number of first author publications with some more on the horizon and it was generally accepted by all that I was done except the conversation had never come up, when I received an email from the registrar’s office telling me that either I had to register for clinical rotations or put off going back to the wards for another year.  That was a perfect opportunity for me.

Next, how do you make the approach?  I lucked out in that I had a very shrewd friend who went through this process many years ago.  He said, that the key to this conversation–and again all founded on the assumption that you have, in fact, done enough work to graduate–is to not give any opportunity for your advisor to say no.  The key is that no one likes to start a conflict.  Which is why when you present the idea of graduating, you do it more as a statement than a question.  Resist the urge to ask “what do you think?”  I know you respect your advisor–so do I–and it is natural to ask your advisor’s opinion but asking “what do you think” could be the kiss of death.  If your advisor says, “Well, I think you need another year” or “I’m not really sure about that right now”, then what are you going to do?  Disagree?  Of course not because no one likes to start a conflict.  On the flip side, if you present a compelling case for why you should graduate, then your advisor will be unlikely to disagree.  Why?  You know it by now… 

But how do you make a compelling case for graduating.  This consists of two parts, (1) what you already done and (2) what you will do.  You need to very clearly state what is the body of work you have already finished and contributed to your field.  This should be easy.  The second part requires some planning on your part.  You need to outline what you have left to do in order to wrap up open projects/experiments and show that it is feasible to do so (in addition to some other little things…like your dissertation) within your time frame.  The plan is critical to how this plays out because it shows that you are serious and committed to finishing (i.e. you have actually thought out the logistics).  Having a really good plan also lends a sense of inevitability–like the wheels have already started rolling–to the whole discussion.

Finally, how do you deliver the first strike?  Two choices: face to face or email (the coward’s way out).  After much discussion with many comrades, I think email is actually the best way to drop this bomb because you can take your time to write a very well thought out and eloquent statement in contrast to a face to face meeting where the uncomfortable nature of the conversation could have serious impact on your eloquence or even ability to get everything out.  An email with a request to have a sit down and then it’s all you after that. 

So I take this opportunity to again reiterate that all of the above should be considered only in the situation where you have actually done enough to have earned a PhD–actually, probably more like more than enough work so it is obvious to all parties that you have done enough for a PhD.  Insisting that you have done enough for PhD (remember–you are becoming a “doctor”) when you in fact have not will only make you look like a complete slacker with no understanding or appreciation for what the PhD is all about.

Anyway, I hope this two-part post, based on my experiences and others I have known, has been a little helpful to you all in figuring out how to wrap things up at the end of your PhD.  It is a tricky time and so much of it rides on uncomfortable situations that most graduate students are not used to.  Relax, think it through, and go to it with a rock-solid plan.

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finding an endpoint for your phd - part 1

Finding an endpoint for your PhD (agreed upon between you and your advisor), is one of the last major hurdles to overcome before finishing your PhD.  This two-part blog entry is inspired by a recent comment that was left on this blog, which got me thinking about my own experience with this:

Speaking of anything related to leaving the lab can be a touchy subject, so how do you go about it?  First of all, every project (and by extension, body of work) should in theory be started with an endpoint in mind (but the subject of goal-oriented projects vs. fishing expeditions deserves to be dealt with in a separate post).  But of course, endpoints may change as the research progresses and more possibilities are either uncovered or eliminated.  That’s just part of the game and also what makes it so difficult to set an endpoint.

But as time goes, you may find diminishing returns (i.e. training and research) from your time in the lab and then, all of a sudden, determining an endpoint becomes a more tangible inevitibility.  Two major considerations need to be made: (1) how to wrap up the research and (2) how to get your PI on board.   Let’s talk about how to wrap up the research.  Even a month before the decision was made to wrap up my PhD, I still had about a million experiments that I could do and three or four more papers that I could potentially write.  I think the thing you need to remember when weighing the pros and cons of finishing your Phd is that the grad school experience is filled with millions of possible experiments that can be done, each the foundation of Nature paper, but how many of them actually pan out?  In my experience, the answer was none.  In your experience, perhaps 1, perhaps 2–which are still long odds.  Is the risk of spending another year for few returns worth the chance for hit it big on those long odds?  Of course, your risk depends on the work up to that point.  But I don’t know how objective, as graduate students, we can be in determining how realistic it is that the next set of experiments will land the coveted Nature paper.  Sadly, sometimes I don’t think that even one’s advisor is capable of providing that objective view (another reason not to put off your thesis committee meeting)–actually from mine and other peoples experience, this might actually be most of the time. 

I ended up publishing a few papers from my PhD research.  But, the ultimately published work for my last, big paper–my flagship paper–in its final form was actually finished over a year before I even started writing up the paper.  The problem: I had a some really exciting and possibly high impact findings that could have comprised a solid paper as-is, which I decided nonetheless to buildup with some follow up experiments.  The bigger problem (which you may or may not have): it was obvious to me there was no real logistical support for the project.  And yet I pressed on because of the potential impact that of those last few experiments.  Well, a year later, the experiments hadn’t worked and the ever looming specter of getting scooped (on what I did have) continued to grow, which ultimately convinced me to write up and submit what I had finished before I continued with the follow-up experiments.

From my own experience and talking to a number of graduate students who have gone through, I think you just know when it is time to wrap things up.  There are always more experiments to be done, so the first step to finding that endpoint is to commit to finishing up the PhD.    Assuming that you have had the realization that it’s time to wrap things up, committing to it will drive you to define what exactly needs to get done and then a plan for how to do it–which is the next step. 

So you’ve come to the realization that it’s time to finish your PhD, you’ve committed yourself to finishing the PhD and have developed a plan.  You are good to go.  Wait a minute…  Oh yes, one last, small detail–your advisor has to agree.

How to get your advisor onboard in Part 2.

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little magnetic beads saved my phd

One mainstay method for cell sorting is with flow cytometry. However, this can be a time intensive procedure and depends on the availability of a flow cytometer with sorting capability and someone who can run the machine. And while most major universities have flow cytometry cores with dedicated technicians, who often know waaaayyy too much about flow cytometry, you will have to schedule an appointment along with everyone else in the university who needs cell sorting.  At the institution where I did my PhD research, there were several sorting facilities but only one of them could handle my samples and the technician who ran that facility worked from 10am to 3:30pm (what is this, a bank?!?!?) performing only two sorting runs per day.  And with the number of people who wanted to use that sorting facility, I was left having to schedule my cell sorting 1 month ahead of time. The problem I ran into was that most of my experiments were dependent on getting purified cell populations from blood samples and when I could get blood samples was quite unpredictable. Plus on top of that, the sorting tech wouldn’t let me schedule more than 2 sorting runs at a time. At the rate I was going, I would be able to do maybe 1 experiment per month and my PhD would take on the order 10 years to finish. Painful. Just painful.

brilliant!

brilliant!


But then one of the older mudphudders to whom I was venting turned me onto cell sorting using magnetic beads and it saved my thesis project. Magnetic beads, attached to antibodies specific for a particular cell surface marker are used to label all cells with that marker and a magnet is then used to pull those cells out of an otherwise heterogeneous population of cells. Brilliant! All of a sudden, my cell sorting needs were no longer dependent on the availability of anyone but myself and I could do my sorting whenever I needed to—day or night. I will point out for anyone interested that sorting with magnetic beads: (1) is probably best characterized for isolation of specific cell populations from blood samples although can be used well with cell suspensions isolated from a tissues; (2) may be toxic to cells, depending on the cell type and the company you buy your beads from (beads from different companies–e.g. Miltenyi or Dynal–are made of different components); (3) will stay on the cell’s surface a lot longer than antibodies used for flow cytometry and may block any receptor/ligand interactions involving the cell surface protein in future experiments with those cells; and (4) usually does not allow sorting for the presence of more than one cell surface marker (i.e. you can only isolate cells that are positive for marker X *and/or* marker Y not cells positive for marker X *and* marker Y), unlike flow cytometric cell sorting—there are exceptions to this, in particular any bead that can be removed from the cells after sorting. Using this technology, I was able to get specific cell populations (sorting on 2 markers, actually) at purities and yields comparable to flow cytometric sorting (after some optimization of course).

When I was starting my PhD, cell sorting with magnetic beads wasn’t nearly as well known as it is today (…definitely aging myself…) so probably everyone reading this is already aware of that technology. but I wanted to mention this story because anytime you are dependent on a core facility for a necessary part of your research but are getting held up by logistics—odds are that there is technology out there that can let you get around it. I think the most frustrating thing is when you want to do work but can’t—and the worst is logistical problems, like when you are working 12 hours per day and you are dealing with a tech who works 5-6 hrs/day (in all fairness, I will say that the techs at another sorting facility that couldn’t handle my sorts were extremely helpful and really taught me everything I know about flow cytometry). You just gotta keep talking to people—graduate students, postdocs and PIs—and looking at product catalogues. If you are getting jammed up by logistics, odds are that many others have too and so some company has probably developed some solution that you need to find.

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choosing a research project

You are starting in a lab and deciding on a project to work on. If you will be in the lab for an extended period of time, say >1 year, or if you are a graduate student, sometimes there is a temptation to work on something really interesting related to the field in which the thesis advisor works in, without much consideration of the advisor’s most immediate interests. Even if your advisor tells you that it is okay and he/she is willing to devote time to learning about that particular topic, don’t do it. Do NOT fall into that trap. PIs are great when you are joining the lab, and they often have every intention of following through on the promise to learn about your interests. BUT, (surprise surprise) PIs are too busy with grants to keep the lab afloat and other already established projects in the lab to learn about some new topic in their field because of a new graduate student. Unless there is some obvious benefit for the PI—and I mean that there is some connection or natural progression from a previously established project in the lab which promises near certain success—do not get baited into starting a completely brand new project for which the PI has no expertise (even if it is within the PI’s field) or current interest.

Here is why: inevitably, the PI will no longer have the time or energy and in the worst case, money, to support you and your project. There will be a time when you will run into logistical problems outside of your control and the PI will just not have the time, energy or desire to help. There will be problems with the research–technical problems and directions in which to take your research–that the PI will not be able to help you with.

All of this is not to say there aren’t situations were it could be wise to start down a new avenue of research in your thesis lab.  One advantage is certainly that you wouldn’t be competing with anyone in the lab.  In general, choosing such a project is usually a high risk, high reward enterprise.  So, if you are one of the people who is successful, it will be worth it.  However, this is certainly not the most conservative approach and despite a potentially high impact paper, I don’t know if it’s worth risking your training (which is exactly what will happen if you are stuck in a project that your PI cannot/will not advise you on and there’s a reason why a graduate student is called “student” and not assistant professor). 

I’ve known a few talented graduate students who joined the labs of well-known PIs and then chose projects that were in the field of the PI but not within their PIs’ realm of expertise.  Every one of those students functionally ended up going through their PhDs without an advisor–only a funding source.  In the meanwhile, their labmates were in and out of the PIs’ office getting regular advice and mentoring.  Not a good situation. 

Therefore, I leave you with this message: if you are joining a lab to do research, work on something the PI is interested in.  Don’t say the Mudphudder didn’t warn you…

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graduate student mentorship

A meeting with one of my clinical mentors yesterday got me thinking about the importance of mentorship in general and, in particular, the importance of mentorship in medical school, which now has me thinking about good mentorship in graduate school.

Graduate school (PhD training) is unique amongst other doctoral training in that the mentor (thesis advisor) plays a central role in one’s training (at least theoretically… see one of my previous posts)–in fact, one’s training is from the mentor very much like a traditional apprenticeship.  So practically, what are we looking for in mentorship from a thesis advisor?  I think that a thesis advisor guides or teaches you:

  1. how to develop scientific problems
  2. how to think about and approach scientific problems
  3. how to solve scientific problems
  4. how to explain/write about your research for others in your field
  5. how to explain/write about your research for others not in your field
  6. some of the unpleasant aspects of academics and science (e.g. politics)
  7. how to circumvent or deal with some of the unpleasant aspects of academics and science (e.g. politics)
  8. things he/she wishes they knew when they were starting out

and finally, the thesis advisor is someone who will promote you and help you get to the next level (e.g. postdoc, faculty job or industry).  Disclaimer: of course, these functions of a devoted mentor in graduate school are predicated on the assumption of an equally devoted graduate student.  I do not believe that it is at all reasonable or fair to expect a thesis advisor to be devoted to a student who does not take his/her graduate studies seriously. 

Anyway, I will group these: #1-3 as how to do good science; #4 & 5 as how to develop good communication skills whether it is related to a paper, editorial or conference; #6-8 as dealing with B.S. in academia and the last point is just looking out and caring for your career.

On teaching you how to do good science:

I’ve never been a big fan of advisors who hold their student’s hand through a PhD.  In some respects, graduate school should be a trial by fire.  I think mistakes are some of the most valuable learning tools ever.  And when your career is riding on how you continue after mistakes, you’d better believe that you will take something–a learning point–away from every mistake.  But there is a fine line between letting a graduate student learn through self-directed learning and neglect.  I’ve seen advisors who “guide” their students with gentle nudges here and there when the student is veering off onto an ill-advised course.  In contrast, I’ve seen advisors who let their students flounder about for years on fishing expeditions that ultimately yield nothing.  I think the ideal is an advisor who let’s you do your thing for reasonable stretches of time (e.g. a month or longer) and then checks in on your progress, but is available in the meantime to talk if you need it.   What you absolutely do not want in graduate school is an advisor who welcomes you to the lab and then stops by to see you four years later to see what you have been up to.  I think that completely defeats the purpose of graduate school.  The reason I harp on this point is because to learn how to do good science, you can either re-invent the wheel and do it entirely on your own–hopefully it doesn’t take you too long–or you can pick up some of tips from your advisor, who is the pro.  It’s really about a solution to your scientific problem, but more so how the solution is arrived at that matters most.  I remember listening to my advisor at some lab meetings giving advice to people on how to progress with their projects and really thinking about how he would come up with his suggestions and the underlying objectives he was getting at.  He was almost always right, but I think his students got more out of the reasoning for his suggestions than the actual solutions to their problems.

On communicating your work to others:

Communicating one’s research to the world is extremely important.  Science is not done in a vacuum and we obviously seek answers to certain questions because someone cares about it.  Otherwise, one’s research would just be an exercise in mental masturbation.  On a more practical level, career promotion, recognition and funding all come through one’s ability to communicate one’s results and the importance of those results.  Writing a scientific manuscript is not an easy task, but gets easier and easier with experience.  However, organization, clarity of thought and expression as well as more subtle issues like citing the proper references and people are not easy skills to master in scientific writing.  A lot of these skills can come from the thesis advisor.  I have worked with scientists who fall into one of two categories: either they write the whole thing for you (sometimes with you sitting there in the room) or they will tear your manuscript up with “track changes” on in your Microsoft Word document file with suggestions like “more in-depth discussion here” or “good place to make this point” or “not necessary–take this sentence out”, etc.  I think I got very little out of my writing experiences where I sat in the room and watched a PI re-write a 25 page draft of my manuscript.  In contrast, after going over my manuscript for the 10th time (c’mon–give me a break already–it was my first one!), you’d better believe I had learned a set of skills that I wouldn’t forget for the next one.

Finally, how to communicate your work also depends on who the audience is.  Yes, yes, this is quite obvious, but actually, much harder than (at least I) expected.  After being in the lab for so long and so much, it is easy to forget that not everyone speaks with the same scientific jargon.  Moreover, there is clearly a spectrum of understanding from the lay-person all the way to the PI who works down the hall on thing else.  Learning how to clearly communicate your work and, again, it’s significance to all of these people is an important skill that comes from the opportunities the advisor gives and then offers guidance on. 

On dealing with the negative aspects of academia:

Academia is a rude-awakening for many graduate students. I think many people go into graduate school to do work with the potential of making novel findings of significance and perhaps making impact on the lives of others. It is an admirable goal, which by its virtue also brings to mind a collegial and ethical atmosphere, conducive for collaboration towards a greater good: everyone working together to better mankind. And then, you get to graduate school and need someone to do a small task—but critical to your work—which will take about 10 minutes of their time. Sure that person will do it, but not unless you promise to list them as an author on your paper—and all subsequent papers that arise from your use of that information. For 10 minutes of work?!? Does this person know that I and the other authors have put in about 2 years of work? Does this person even care? If someone has you in a tight spot, they will likely squeeze you for 100X more than what you are asking for. Then you request information from a publically funded open-access database, but the caretakers of the database (who are specifically paid to do this) will put you through the ringer with paper work then have you wait about 9 months for a 5 minute database search, unless you repeatedly tell them how great they are and then list them as an author on your paper for doing their job. Again, are you serious? Serious as a heart attack.

Yes we are all working together for a common good but the means towards that end are sometimes questionable, and sometimes plain and simply unethical. Academia is filled with egos and people who are (like you and me) struggling to make it. This is an absolutely inescapable fact, which happens at every institution. These conditions necessitate frequent stroking of egos, to a sometimes disgusting extent, and then getting taken advantage of when you are most vulnerable—and this is the best case scenario. And as a graduate student, you are the most vulnerable. I found these aspects of academia in graduate school really tough to swallow. Same is true for others I have talked to. The problem is that, as a graduate student (in truth at most levels of academia as well), you have no recourse. I stress this point because it is hard not to become cynical and disillusioned—and over time, to become the same as those people. This is where an advisor’s guidance can be really helpful. For one, a graduate student’s adjustment to these aspects of academia can be greatly facilitated by an advisor, who can help you to navigate these somewhat touchy areas, and when necessary, take over for you. Moreover, these aspects of academia exist—it is a fact—so why not learn about and hear about them? I’ve found over the years that the more I learn about all of the ethically “questionable” problems that others have had to deal with, the better that I am prepared for these problems when I encounter them. And certainly, I believe that a mentor has an important role in giving their graduate students straight-up, honest advise this aspect of academia.

On promoting your career:

I wrote about this with regard to medical student mentorship a couple of days, and it is really no different in graduate school. At such an early stage of training, one needs as many opportunities to flourish as possible. This comes through opportunities to participate in different projects at authorship level, within the lab and through external collaborations as well. Presentations are another great way that advisors promote graduate student development. There are some labs where the advisor, when invited to give a talk, will ask a student in the lab working on that subject to give the talk instead. These are really golden opportunities that show your academic community of peers and colleagues that your advisor thinks highly enough of you to send you in his/her place. I have known a few graduate students with such advisors, and they are all the better off for it—before finishing their PhDs, they already have established name recognition and respect in their fields. And clearly, there are other ways through which a thesis advisor can give a graduate student opportunities to shine but I will not dwell further on this topic. Finally, a graduate student needs an advisor who will write a stellar letter of recommendation, talk to colleagues and make calls when the time comes to find a post-doc, apply for faculty jobs or a job in industry. I think this is a fairly obvious point, but it should not be assumed that last two points are automatically obvious to all advisors.

Okay, before I continue, I will reiterate that what I described above are qualities to look for in devoted graduate school mentorship (i.e. a thesis advisor) with the assumption of an equally devoted graduate student. I would not join a lab expecting these kinds of mentorship qualities without putting in 110% effort. However, if one is giving 110%, the most one can do is try to find a situation in which that effort is maximally repaid in mentorship.

I hope that some of the points above will have been helpful in thinking about what is and isn’t important to you out of a thesis advisor.  The best resource for finding out how well a PI has provided mentorship in the past is obviously the PI’s graduate students.  As you look for labs, look at past and current graduate students. Look at their publication records on PubMed.  Ask the PI if and where these students did post-docs and where these past students ended up taking employment (e.g. academia–tenure track faculty posts–or industry, etc).  Read some of the lab’s past papers.  Ask past and current students how much the PI meets with them and provides guidance.  And see how easily past students have moved on to postdocs or jobs and how active the PI was in process.  These questions and others will hopefully help you find the PI most likely to give you everything you need out of graduate school.

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good mentorship is so key…

Just came back from an hour-long coffee break with one of my mentors in my medical field of choice, in which I am currently applying for residency positions.  When I think about the factors that lead me to head down the various paths that I have traveled, so much of it has been due to the mentorship that I received.  Good mentorship is so key!  Finding someone who has the right personality, attitude, and work habits to jibe with your own and at the same time is both sympathetic to your situation and generous with opportunities to get name out there. 

It’s weird but in hindsight, people just find each other.  I think the key is to just talk to as many people as you can and eventually you’ll bump into like-minded people.  I’ve been blessed (and I really mean blessed–academics can be so vicious sometimes) to have three faculty members (one of whom is at another university) who have all, in different ways, mentored me through graduate school and medical school–in research and on the wards.  It is interesting that all three are young, junior faculty members.  Perhaps that is as much a reflection of my own tendencies as it is of theirs. 

At this point in my career, I just want to produce as much meaningful research in my field as possible and to learn as much as possible.  So I guess it’s not too surprising that I met all three through various research projects–either approaching them or by being approached to collaborate on one project that has turned into multiple with each.  I think working with someone on a research project really tells you a lot about them: their personality type (easy going or uptight), their level of commitment to their work, their commitment to teaching (accessibility–can you go and knock on their door?  how long does it take for that person to return your emails?) as well as more personal qualities (goal-oriented, picky, lacksadaisical, punctual, detail-oriented, generous, open-minded, stubborn, etc).  Usually, by the end of one paper, you can tell if this is someone who you can work with/interact with in the long term and if this is someone who will guide you in your training. 

For people early in their careers (e.g. me), I think you gotta figure out how to get your name out there as much as possible through publications and national presentations in order to develop some name recognition in your field.  At the same time, I think this is the time where we need to figure out how to balance “life” (e.g. family life, “you”, etc) with work.  I think a good mentor can give you so much insight into how to do this or at least how to figure it out for yourself. 

Finally, a good mentor lifts you up and nurtures your career by giving you opportunities.  There are a lot of people out there who would love nothing more than for you to do work for them and then take all of the credit.  Believe me I know.  I’ve been there.  It’s pretty rotten when the choice is either to give you an opportunity or to just pass it up all together and the latter is chosen.  But, despite my bad experiences, I honestly believe there are people out there who are committed not only to their own careers, but also to mentoring others as well–who are committed to your success (isn’t that a crazy concept given what many of us have experienced?)–who see it as a part of the tradition of academia.  The people who I work with now are constantly giving me the chance to present at national conferences, are signing me up as an official reviewer at scientific journals and continue to involve me in collaborations.  And I really, really appreciate.   

My bad experiences have often at the time motivated me to go at it (i.e. academics) alone.  But, from what I’ve seen, that’s a path few make it through in academics.  I think you gotta keep trying, keep talking to different people, keep working with different people and when you find those few who are really committed to mentoring you, it really makes it all worth it. 

But that’s just my opinion…

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european academic career fair

If you are interested in pursuing training or a career in academic medicine in Europe, here is some information I recently received:

Are you interested in the European job market? Do you want to pursue a PhD, a post-doc, an academic or a professional career on the other side of the ocean? We invite you to join us at the 13th European Career Fair (ECF) in Cambridge, MA, the largest career fair of its kind.

Get started!
submit your resume today, by registering online for the ECF2009 at www.euro-career.com.
Deadline for resume submission has been extended to Wednesday, Dec 10th 2008. Resumes need to be prepared in PDF format.

The 13th European Career Fair in short

  • January 23, 2009 - Lunch meeting about Entrepreneurship in Europe. Afternoon panel discussion hosted by the European Commission and the MIT International Science and Technology Initiatives (MISTI).
  • January 24, 2009 - Career Fair Day with exhibits and presentations by employers from industry, academia and research.
  • January 25-26, 2009 - Interviews for selected candidates. Science careers panel discussion on careers in European industry. Information sessions about working in German and Dutch academia and industry.

Why should you attend?

  • Unlike many career fairs, ECF aims to represent the full breadth of the European job market. Whether you are looking for a job in industry or a non-profit sector, you will find something of you interested at ECF.
  • All areas of research and study are welcome! Recruiters are looking to fill vacancies at all levels. Graduate students, professional degrees and post-docs are especially encouraged to apply.
  • By submitting your resume before the deadline, employers can invite you for interviews prior to the fair. In addition, you can connect face to face with >140 employers from industry, academia and research on the fair day!

More information
For a list of employers that participated in previous European Career Fairs, or more detailed information go to the website:
http://www.euro-career.com

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unreasonable manuscript reviews getting you down?

It’s happened to me and it’s probably happened to you.  I was talking to a buddy of mine today who has been having a heck of a time with a manuscript review.  The unreasonable manuscript review.  Yes, it can be a very touchy subject and a bad review can cut you deep.  But have you ever had a reviewer who wants you to demonstrate some additional step that is waaaaaay beyond the quality scale of that journal–i.e. you’re thinking, if I could do that, I’d be submitting this article to Nature or Science rather than this journal?  Those kinds of reviews really get to me because there is really nothing you can.  I was discussing this with my buddy today, and he really has no options.  His manuscript has been in review for almost a year now and he can spend another 4 months working on satisfying this insatiable reviewer, but what will he have to show.  (1) If he can’t do it–experimental limitations make it unlikely that this is even doable–then has lost 4 months where the paper could be in review at another journal.  (2) if he does get it done and the paper gets accepted at this journal, he will have lost a Nature Medicine quality article to a second tier journal.

This happened to me on review for a manuscript to a journal one notch under Nature Medicine where if I could do what the reviewer demanded, I’d have won the Nobel prize.  But what to do?  You can’t tell a reviewer that their demand is too good for that journal.  I ultimately had to submit to another journal.  I’m afraid that my buddy will have to do similarly. 

I suspect that these types of reviews happen when competitors review the manuscript.  I don’t think the quality of articles in most journals is any secret so it is generally quite obvious when reviewers ask for ridiculous things.  Actually, I received some ridiculous reviews on another manuscript, which the editor luckily ignored and when the manuscript was published, the reviewers were revealed and it was indeed a competitor who was making the ridiculous reviews.  In my buddy’s case, he submitted to a specialty journal where the editor-in-chief is one of his competitors and left a specific note in his reviews stating that he needed to do X. 

If anyone has suggestions on how to reply to such types of reviews,  please let me know.

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grants, scholarships, fellowships

There are now over 100 grants, scholarships, fellowships for research (or just for you!) for medical students, graduate students, postdocs, residents, clinical fellows and investigators now on my funding opportunities page.  On the way to two hundred!

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choosing a research topic

So you’ve decided to do research and are wondering what to do it in. 

Two pointers that I picked up during graduate school are:

1) do research in something you are passionate about

and

2) do research in something that is important to the lay-person. 

Okay, so where do I get this from?  I ended up choosing my PhD topic because I found myself thinking about the topic at all hours of the day–watching T.V., at the gym, etc.  This served me extremely well.  When you are in a long-term research project, you are bound to hit bumps in the road.  And grad school can be one awfully bumpy ride.  People talk about the peaks and valleys but in four years I can count the number of peaks on one hand.  What kept me going through all of the valleys was my belief in the question I was trying to answer.  Finishing the PhD was secondary.  Sure you could power yourself through the hard times of research and the dark times of graduate school without necessarily having a great deal of passion for the research (e.g. some people choose a research lab only because of the PI).  And depending on what you get out of research, it may be worth it.  But I for one have seen too many good people leave/finish graduate school (or their research term) quite bitter and angry with the scientific process.  I didn’t understand why or how that could be until I went through it myself.  The one thing that kept me from heading down that dark path was the fact that I loved my project and believed in it (even though sometimes it felt like no one else did). 

Work on something that lay-people will understand and appreciate.  I don’t think this is critical like what I mentioned above (so don’t send me angry emails about it) and I offer this point more so as a consideration and a shout out to an old friend.  This point is important on two levels.  When I was a first year medical student, I hung out with a much older MD/PhD student in our program.  He was a really smart guy, quite talented and successful in the lab.  But, his research centered around how the two ends of a protein (no one had ever heard) interacted with each other.  He won many awards but lamented that he could not talk to his parents or even friends in different scientific fields about his work.  He once said that if you cannot tell your parents what you do in under 5 sentences, then that is a problem.  At the time I thought that this was not a valid argument–there are many important problems, which need to be solved that aren’t well known to most others.  But as I have thought about it over the last 6 years or so, I can see his point on some level.  For one, research funding in a lot of ways depends on getting lay-people (i.e. the taxpayers) to appreciate what you do.   On another level, perhaps it is a part of our natural tendency to work on translational research (i.e. research that clinical implications), which would, of course, have importance to the lay-person.  Now that I have written it down, I suspect that this may have been a big reason for my friend’s feelings.  As a physician, physician-scientist, or scientist with a desire to make a clinical impact, it is difficult to reconcile one’s career goals (helping patients) with research that has very little chance to make any clinical impact anytime soon–especially if no one even understands the work.   I don’t know.  I don’t think this is critical (so again, please don’t leave me angry emails/comments), but it is something to consider. 

 

gotta have the passion

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world aids day 2008

December 1 will be the 20th World AIDS Day.  Take some time to think about the fact that over 30 million people are infected with HIV worldwide–as well as the tragic extent of the AIDS epidemic in Sub-Saharan Africa, where 2/3rds of the world’s HIV+ population live and 2/3rds of AIDS-related deaths occur.

For more information and resources, check out:aids red ribbon world aids day

And for those interested, here are links to the first two articles published describing the clinical entity AIDS in the December 10, 1981 issue of the New England Journal of Medicine:

Neither article is available online at nejm.org, so refer to your local medical library but it’ll be well worth the effort.  These articles make for an amazing read and it can be quite eerie–putting yourself in the shoes of the authors who were writing these case reports and then thinking about the extent to which HIV has since spread.

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game on

Okay, funding opportunities are searchable now. 

It’s a work in progress!

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funding opportunities

Funding opportunities for medical students, graduate students, post-docs, residents, clinical fellows and investigators are now up and searchable.  I will be adding many more in the coming weeks–all with direct links to the actual grant applications and/or information urls.

Still working on making it more user friendly, but it is use-able for now.

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happy thanksgiving

To go to work or not to go to work?  That is the question.  The ultimate dilemma.  Of course, if you are in the medical field, there is no question–you’re either on or off.   But if you are in the lab, do you go in for that quick experiment before your thanksgiving day meal? 

I mean, it is a university holiday.  But as one world-reknowned faculty member at our institution told someone I know who tried to use that reasoning to put off an experiment: “they don’t lock the doors.”  They don’t lock the doors indeed. 

Happy thanksgiving to everyone!

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had a thesis committee meeting recently?

Yes, thesis committee meetings can be such a hassle. Depending on when your last meeting was (if ever), you may have to go over months or years worth of data, positive and negative results (bringing back all of those bad memories)–and then assimilate it all into a presentation. Sadly, you have to come to terms with the fact that, yes, in fact the last 12 months of your life can be compressed into a 1-2 hour presentation. At the same time, you may have to confront the fact that despite the hard work, not much has been accomplished. (If you have accomplished a lot–kudos to you!). There is often a tendency amongst graduate students to avoid the thesis committee meeting until there are some really good results, or if there are good results, wait until the hot streak is over–or in most case, wait until the graduate program mandates a committee meeting. I’ve been through it and every other graduate student I know has gone through it. And almost unanimously, in hindsight we wish we had done it differently.

There really is never a good time to have a thesis committee meeting. I bring this up because I was talking to a buddy of mine who is in year 5 of graduate school and has had only one thesis committee meeting. (Actually, this describes more than one of my buddies).  In hindsight, the thesis committee can be a valuble resource. Sitting down and gathering all of your thoughts, writing a summary of the work, or putting a Powerpoint presentation together can often times be a much needed break that allows an objective look at one’s work.  At the same time, if you are headed in the wrong direction (especially if your gut tells you so), the committee may be able to help you get back on track.

Now in my buddy’s case, his project was never well defined and when he had his first thesis committee meeting at the start of his tenure in his lab, it was okay because he had just started. Three years later, his project has remained largely undefined.  He has done a lot of work–most of it though very undirected with no particular purpose.  And, he has received little to no guidance.  He is in a large lab where it is easy to get lost and left behind, and this exactly what has happened to him.  In a situation like this, a thesis committee meeting–even with no result–will provide the sometimes necessary confrontation, i.e. the thesis committee saying “what the heck are you doing?”, that will get the attention of both the student and advisor to rectify the situation.

I am happy to report that my buddy now has some direction through the intervention of another graduate student who has been collaborating with him on a new project. I really hope it works out. He’s got a pretty strong thesis committee so I suspect he will get some good feedback in the next few months when he finally gets them together.

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where to buy sodium borate electrophoresis buffer

There was some interest in the sodium borate buffer DNA electrophoresis so I thought that I would look around for companies that sell the stuff.  I actually had a hard time finding anyone who sells sodium borate electrophoresis buffer (e.g. couldn’t find it in Invitrogen, Biorad, etc.), but the company Labsupplymall does sell a 20X stock of sodium borate buffer for nucleic acid electrophoresis–in case you don’t feel like making it yourself…

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sodium borate nucleic acid electrophoresis buffer

Sodium Borate Electrophoresis Buffer (SBE buffer) is an excellent alternative to traditional TBE (TRIS borate-EDTA) and TAE (TRIS acetate-EDTA) electrophoresis buffers. SBE buffer allows for higher voltage runs, extremely rapid running times, and high-resolution band separation.

Brody and Kern described sodium borate buffer for nucleic acid electrophoresis several years ago (Sodium boric acid: a Tris-free, cooler conductive medium for DNA electrophoresis, Biotechniques 36, 214-216, Feb, 2004).

FYI - sodium borate buffers for gel electrophoresis are compatible with gel purification and most other applications.

You can buy pre-made sodium borate stock solutions or you can make it yourself. There is a recipe for 20X stock in the Brody and Kern article or here is one I found online:

for Borate Buffer: pH 7.4-9.2
Borax (sodium tetraborate) 0.2M = 76.2 gm/L
Na2B407*120H20 (MW = 381.37)
Boric acid 0.2M = 12.37 gm/L
H3BO3 (MW = 61.83)
Add boric acid to borax solution until desired pH is reached. Dilute to desired molarity with ddH20

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gordon research conferences

Every year there are many “Gordon Research Conferences,” each on different topics related to the biological and physical sciences.  These conferences are generally limited to small numbers of attendees that includes graduate students, post-docs, and faculty members who are some of the world’s leaders in those fields.

If you can find a Gordon Conference on a topic you are interested in or working on, you should definitely check it out.  Everyone I know who has gone to a Gordon Conference has come back raving about it.  One of my regrets from graduate school is not having gone to one of these conferences.  If you go to the website, you can see for what topics there will be conferences this year and hopefully see the schedule of speakers as well. 

From their website www.grc.org

“The Gordon Research Conferences [(GRC)] provide an international forum for the presentation and discussion of frontier research in the biological, chemical, and physical sciences, and their related technologies…

For over 75 years, GRC’s high-quality, cost-effective meetings have been recognized as the world’s premier scientific conferences, where leading investigators from around the globe discuss their latest work and future challenges in a uniquely informal, interactive format. Apply to a Gordon Research Conference now and see why attendees consistently rate them ‘the best conference I’ve attended this year’…

GRC is committed to bringing young scientists together to discuss their current research and build informal networks with their peers that may lead to a lifetime of collaboration and scientific achievement.”

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career resources for PhDs

The situation for scientists is becoming constantly more tenuous with increasingly more competition at all levels: in graduate school, as a post-doc and on the job. 

Advice on everything from succeeding in graduate school, as a post-doc, writing cover letters, getting and exceling at a job in academia as well as industry is offered at: http://www.phds.org/career-resources.  While this website is targeted primarily to those in the physical sciences and mathematics, the career resources section contains general advice that is useful to those in the biological sciences as well.

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predicting microRNA binding sites

Are you interested in or researching microRNA regulation of gene expression?  MicroInspector (written by Vesselin Baev and Ventsislav Rusinov at the University of Plovdiv in Bulgaria) is a web-based program that predicts the existence of microRNA binding sites in a given sequence (you can enter the actual sequence or GENBANK accession number) for many different organisms (including humans, nematodes–e.g. C. elegans, arthropods–e.g. drosophila, plant species–e.g. arabidopsis, and viruses–e.g. EBV).  Here is the link: http://mirna.imbb.forth.gr/microinspector/

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funding opportunities for medical and graduate students: grants, research, and fellowships

I have updated the funding opportunities page with a new and easy to read/search format that includes grants, funded research opportunities and fellowships.

Keep checking because I will be adding a ton of new content to the funding opportunities page in the next few weeks!

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asking P.I. taboo questions when choosing a lab

So I made a post last night about previous graduate students’ records being a factor to consider when choosing a lab for your PhD research / graduate school.  A similar argument can be made for medical students who will be taking a year or two off to do research.  Anyway, in choosing a lab there are many factors that are important to you, to me and to every graduate student, which may be taboo to talk about (e.g. publications and how long it takes to finish).  Certainly you should feel comfortable to talk to other graduate students about it, but is it okay to ask the P.I. about such things?  I would argue yes.  In fact, I did when looking for a lab to do my PhD in. 

First of all, everyone (and I mean everyone) knows how important it is get publications and to finish in a timely manner.  Moreover, each of those taboo topics is also something that everyone cares about.  Therefore, that you are asking these questions of the P.I. reflects the fact that you have thoroughly thought about the process of graduate school and also demonstrates that you care enough about your career to ask.  At the same time, when you ask, make sure to express your understanding that e.g. graduating in 4 years or having a ton of publications is not the most important thing in the world–but that you are just curious of how previous students did.  Implicitly, these questions also gauge the mentoring ability of the P.I.  In other words, if it takes most students 10 years to finish their PhD with 1 paper, you gotta wonder about the quality of mentorship as well as the P.I.’s drive to publish. 

The time to ask these types of questions is before you join the lab.  So at the end of each lab rotation or as you are going through your decision making process, sit down with each P.I. and ask these questions. 

Other good questions to ask of the P.I. before joining the lab are about: funding (grants and if they will be running out soon–you can half jokingly express interest in whether your salary is secure), and whether the PI plans on leaving the institution anytime soon (or is looking for a job elsewhere).  P.I.s that leave can destroy a graduate student’s training.  I’ve seen too many of my buddies have to start over after 2 years in a different lab or move to another lab where they are treated as second-class citizens or otherwise have to move across the country to be with their advisor. 

If you think of other topics that are important to you, ask about those too.  As long as you maintain a respectful attitude and express an understanding that these things are not necessarily the most important factors that go into choosing a lab, you should be alright.

Finally, there will be some who give you flack for asking these tough questions no matter how you phrase them.  I won’t lie to you–it may happen.  BUT–anyone who thinks publications, timely graduation, funding and/or assurance that he/she will stick around are not important issues, then that person either 1) doesn’t know what they are talking about, 2) is completely naive or 3) has a bad track record and is trying to minimize the significance of that.  In any case, it’s not a good sign. 

Remember you are talking about your career and where you will be working everyday for the next several years–it really behooves you to ask the tough questions.  You are interviewing them as much as they are interviewing you.

Good luck!

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precedent of graduate student success in choosing a PhD advisor

If you are a graduate student in the process of finding a thesis advisor, one factor that you should consider is how well previous graduate students have done.  Some objective measures to look at are:

1) How many publications did each graduate student finishing in the last 5 years have?

2) Does the lab produce high quality or high impact articles?  And if so, are graduate students the first authors or is it mostly post-docs?

3) How many years did graduate students finishing over the last 5 years take to complete the PhD?

You may find that some graduate students in the lab get tons of publications and others get none.  If this is the case, consider probing a little deeper to find out why.  Even if it as simple as a matter of some students just not working hard, then you should also wonder why that is the case.

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traveling for interviews?

I’m traveling a lot these days for residency interviews and it is expensive.  I do a lot of my traveling by amtrak to avoid the hassles at the airport and I found this website for amtrak promotion codes to use when booking amtrak tickets online or by phone:

http://www.promotioncode.org/Amtrak

It looks like the main site, http://www.promotioncode.org/, has promotion codes for other travel and almost anything else you can think of too. 

If you are interviewing too, good luck, have fun and safe travels!

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networking and schmoozing in the world of academics

I was talking to a buddy of mine who is interviewing at various universities for a faculty job right now and he mentioned to me that some of his interviewers remembered him from his residency interviews. This reminded us of an important point–

Good grades and professional accomplishments will get you only so far. The highest levels of academia are largely ruled by politics and social interactions. It’s a fact, so get used to it.

This makes some sense because at the level of post-doctoral/clinical fellows and above, most everyone is quite talented. What sets certain people apart (in terms of getting promotions or the jobs they want), is their knack of knowing the right people or schmoozing on the fly. Keep this important aspect of academics in mind from an early stage (e.g. graduate student or medical student) and practice meeting people of all levels at conferences and national meetings (this is probably the best reason I know of to go to a conference)–or even at your own institution. Meet and talk to as many different people as you can. I stress practicing as a student because no one expects much out of a student so there is no pressure on you. And, if you make a particularly good impression, you will be even more likely to be remembered.

The more comfortable you get at initiating and maintaining professional/scientific/medical conversations, the easier it will be when you are interviewing to move up the academic ladder–both in the interview process and in having interviewers who either have previously met you or have heard of you.

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graduate student / post-doctoral fellow labor unions

I read a very interesting article (click here to go to the article) in today’s issue of Science magazine that highlights the changing nature of research training and mentorship in academia producing a place for academic unions.

Here is an excerpt from Taken for Granted: Joe the Plumber and the Postdocs by Beryl Lieff Benderly:

“Supervisors have largely abandoned any pretence of promising a career, except to the handful of star students usually designated early by mega-prestigious awards and publications…

In the old days, professors considered finding jobs for their students a moral responsibility… the system also encouraged professors to recruit only the number of grad students they could reasonably expect to place in suitable posts… There grew up within the funding research system what Michael Teitelbaum of the Alfred P. Sloan Foundation calls “perverse” incentives that instead encourage principal investigators (PIs) to take on as many grad students and postdocs as they possibly can… they came to view students not as future guild members but rather mostly as cheap labor useful for doing the work needed to get and keep grants. Instead of the old contract between master and apprentice, graduate training these days… ‘resembles a pyramid scheme.’  But most professors no longer worry because they know that the majority of those aspirants will never become competitors. Professors’ own reputations among their peers now depend much less on the fate of their students and trainees than on their ability to win grants… That leaves grad students and postdocs not as promising aspirants to a prestigious trade but rather as employees of large organizations, namely, the research universities that pay their wages out of PI grants. As such, these young scientists are exactly the sort of worker for whom the… industrial union… was devised, [which] serves the interests of workers drawing their pay from a given large company or organization.”

keywords: graduate students, post-docs, training, mentoring, unions

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P.I. recognition in choosing an institution or lab for graduate school (or post-doctoral) research

One of my mentors once advised me that the number one predictor of becoming a Nobel prize winner is working in the lab of a nobel prize winner.  That the number one predictor of being elected to the National Academy of Sciences (NAS) is working in the lab of an NAS member.  I don’t know if this is actually true (or if anyone has even studied this)–but it makes sense.  When choosing a lab for your PhD or other graduate work (or even post-doctoral research), many many many factors should be considered.  But this may be one consideration to keep in mind. 

If you are in the process of looking for a graduate school or a post-doctoral position, I wouldn’t limit your institution search by the presence of Nobel prize winners, but consider investigating prevalence of National Academy of Sciences members at the institutions you are considering:

http://www.nasonline.org/site/Dir?sid=1011&view=basic&pg=srch

Also consider looking at prevalence of investigators at the various institutions you are looking at who are members of the Howard Hughes Medical Institute (http://www.hhmi.org/) (a prestigious group of recognized biomedical investigators consisting of some of the most talented scientists in the country):

http://www.hhmi.org/cgi-bin/scientist_search/search.pl?kw=&it=INVESTIGATOR&x=48&y=12

That said, (I repeat) many factors go into choosing a lab or institution for graduate or post-doctoral research.  And I might add, so many other factors besides the quality of science go into election to these groups, that there are many incredibly talented investigators who are not in the NAS or HHMI but also consistently produce cutting edge, high-impact and important research.  I offer this information as just another factor to look into.

keywords: research, advisor, graduate student, post-doc, HHMI, Howard Hughes Medical Institute, National Academy of Sciences

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genechip / microarray experiments - spending on analysis

Don’t scrimp on the analysis of your genechip / microarray experimental results!

Genechip / microarray experiments are now very important and useful tools in biomedical research.  Genechips, while decreasing in price as cheaper technology is developed, are still expensive.  And in a lot of cases, many samples (i.e. microarrays) must be run to have the statistical power to tease out the differences between experimental groups–in particular when you are dealing with human tissue and biological noise is a significant factor to be dealt with.  I know many labs that have spent anywhere from $30,000 to almost $100,000 on running the microarrays–getting only the raw data in return for that sum of money. 

However, I also know many who then turn around and try to save money by being cheap on the analysis of that raw data.  This is so wrong, in particular if you plan on publishing your microarray data rather than just using it as a screening tool to chase targets.  For publishing microarray data, the analysis is what makes or breaks your experiment, since the raw data is uninterpretable.  You can save some money by using the most basic tools that are available to find some genes that are differentially expressed, but you will get what you pay for.  You’ve already spent so much money on the genechips, go on and spend on the analysis too.  Regardless of how complicated and sophisticated an analysis you do, it is highly unlikely that you will spend anywhere near what you spent on your genechips (either through buying analysis software, access to databases for your analysis or hiring trained statisticians to show you the cutting edge methods for microarray analysis and then doing the analysis for you if choose not to do the statistical programming yourself).  And at the same time, the more sophisticated your analysis (which will hopefully yield more biological insight), the more impact that your final article will have.  Microarray papers continue to be published at all levels–from the big 3 of biological research (ie. the journals Nature, Science and Cell) to the most obscure journals you’ve never heard of.  If you don’t believe me that your analysis makes your paper, then look up microarray papers in Nature, Science and Cell and compare them to microarrays in any journal you’ve never heard of. 

Yes, yes, I know, money is a real factor for many labs.  Avoid the problem of money by discussing with your P.I. or advisor the importance of the analysis before you begin your microarray experiment and plan ahead so you balance the number of genechips you use in order to maximize the analysis you can perform after.

Bottomline: don’t scrimp on your microarray analysis!  It will hurt you much more than the cost will hurt.

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