Wednesday, April 30, 2014

Post #5 Learn the Rules - My PhD Process: How I Survived a PhD in the Biological Sciences and Succeeded Afterward

Post #5 in this series is all about learning the rules. Some of these rules are written down, some are not. Some of these rules are obvious, some are not. Some of these rules make sense, some do not. Therefore, I would like to talk about a lot of these rules and I would suggest that if people read this post and have their own experiences to share, use the comments section below.
These aren't in any specific order because it depends on your personal situation.

Vacations, Holidays, Weekend - In a "normal" job it is understood that for the most part, baring emergency, these should be days off where you are not working. In graduate school, I have found that isn't true. There is a wide amount of variation but personally, during my PhD, vacations, holidays, and weekends were work days. What was really great, is when we did take a vacation day, we had to explain why we were taking it, and were judged on how we used it. I had to sit down with the dean of the graduate school because I took a Friday off to go watch North Dakota State University's (NDSU) March Madness debut. To them, that wasn't an adequate use of vacation time. I was still in my first year. I didn't realize this interaction should have been a big clue as to the behavior and culture of the school and department.

During my third and fourth years of my PhD, I worked between 300-330 days per year. If you just subtract holidays and vacation days from a normal year, you are already down to 340 days. If you work all holidays and don't take any vacation days, but just take weekends off you are down to 261 days. I hated it. But if you want to make it worse, add to the fact that my advisor and the chair of the department still didn't think it was enough. This is crazy. Those are extreme hours and working that much is stupid.

You are going to want to determine what the rules are for vacations, holidays, and weekends before you join a department or lab. Graduate school is going to be hard, you are going to have to work a lot. No question. However, there are advisors out there that are reasonable and won't work you to death, or won't be passive aggressive when you do want to take a vacation. Many times what will be written down, isn't what the department believes. We were told that we got 10 vacation days per year and holidays off. In reality, any day we took off was a strike against us.

Free Time - Free time or down time in the lab is inevitable. Even if you are doing multiple experiments, there will always be incubation times or centrifuge times or time points, etc. What you do with that intermission time is up to you right? Possibly, but you may have a advisor that has a lot of input on what you should be doing. I would call them micromanagers and terrible, but that might be what you have to deal with. Intermission time is important, there is a lot of research that shows that letting your brain reset is helpful throughout the day. There are also other useful things that can be done such as read manuscripts, studying, actual human interaction (as if that exists anymore in academic labs), or just stopping, looking out the window, and thinking about experiments or ideas.

If you have questions, use the comments section below!

Computers and Social Media - Most graduate students will have either a program or personal computer for use. Ideally, keep it personal. I hate having to have institutional software and spyware installed on my computer. So since I have a computer in the lab what can I use it for, only work? This is a pretty big question and everyone deals with it differently. I know there are many offices that block certain sites (especially social media). I know a lot of places that frown on usage of social media at work. Personally, I can see both sides. On one hand, you don't want people falling down the YouTube rabbit hole, or pinning things on Pinterest for hours on end. On the other hand, what did people do before they had social media? They played cards, they literally talked around the water cooler, they brought photographs from their vacation into work, the read the local newspaper, etc. Nothing has really changed except platforms and attitudes.

Reading Papers in the Lab - This is a no brainer right? I mean if you have a little downtime between experiments and want to read papers then by all means go ahead. Wrong! (Okay well probably not wrong, I just like mimicking this old Saturday Night Live sketch) Most labs are not going to have a problem with this. I only include it because at RFUMS the chair of my department (and therefore my advisor) didn't like us reading papers in the lab, because it wasn't lab work. Reading was homework, lab time was for experiments. You've been warned. There is a lot of crazy out there.

Work Day - This is another good example of the wide range of variation allowable by certain advisors. I have heard that a mythical land exists where some advisors let their students come in and work on their own time. If there are experiments to do, they do them. If there is a long incubation or writing to be done, they don't have to do it in the lab. Personally, I have never experienced these things. I was given a few weeks out of the lab to write my dissertation, but by that point in time my advisor was actively trying to stop paying me, (which was against the bylaws in the graduate school handbook that stated students would get paid for one month following their dissertation defense because there are always edits, and things that need to be cleaned up in the lab, etc.) so it was obvious he just wanted me gone (and I wasn't arguing). Personally, paper writing was done in the lab, experimental design was done in the lab, everything had to be done in the lab. Honestly, I think this is a pretty stupid approach. Yes, some people have control issues and if they aren't in the lab, they aren't getting work done. Don't hire those people. However, if you have made it to graduate school, chances are you are going to be fairly self-motivated and driven. You also should be allowed to work creatively (which is an idea that currently, in academic science, seems to be dying a slow death). Smart people should be allowed a decent amount of freedom to be creative, work in a way that is productive for them, and not be figuratively held to a lab bench all day, regardless of the time it takes, or the task they are preforming.

Please share your own experiences using the comments section below!

Publications - There are a couple things to be aware of when it comes to publication expectations, but the first thing I want to cover is "how many?". For most PhD programs, there is going to be some lower limit. For me it was two first-author publications. For others I know it was one, some it was three. There are some instances I have heard of where people graduate and get a PhD without any first-author publications. This is not a good situation. You aren't going very far without at least something that says you were productive. There isn't much to discuss here because it is a fairly straight forward question. But you need to be aware of not only departmental expectations, but individual mentor expectations as well.  

Grant applications - Similar to publications the more of these opportunities you have, the better. Even if you aren't planning on staying in academia, the ability to understand, write, and construct grants is a valuable skill to have on the CV. Getting one is just a bonus.

Teaching and Other Extracurricular Activities - Is teaching required, or mentoring medical students or summer undergraduates in the lab? What about serving on committees or running for student government offices, being active in a graduate school association etc.? Personally, I think a lot of these things are good and important. Now, if you don't want to teach, you shouldn't have to. However if you do want to teach, you should be allowed to (as long as you are in good standing). In my personal experience, this is a very inflammatory subject. The department that I was in highly frowned upon any extracurricular activity. I was tapped to be President of the student council (not just graduate students, but all students, including the medical school) but by that time I knew enough to at least ask my advisor if it was okay (I didn't know enough to already know the answer) and obviously he said it wouldn't be worth my time (in hindsight he was wrong). Later, I was tapped to help start up the INfluence Student Potential and Increase Representation in Education (INSPIRE) organization. By that point in time I had lost all respect for the decisions of my advisor and knew that he wasn't making decisions that even remotely considered my best interests, so I got involved and it has been a success that I am very proud of. If you don't want to get involved in extracurricular activities, that is fine, just make sure that you aren't required to. The same goes for if you do want to participate, make sure that your advisor is accommodating to your decisions.
Plans Postgrad - For decades, there was a somewhat hushed cold war between scientists. Academia vs. Industry. If you stayed in academia, you were noble, pristine, honorable. If you went to industry, you were a sellout, no longer in it for the betterment of human society. And if you went into teaching, non-profit work, writing, etc. you had to turn in your scientist badge. You were kicked out of the club, basically not even worth being considered. I have three comments on this.
  1. It was all lies.
  2. It is so stupid that it has hindered the entire infrastructure of biomedical science in this country and around the world
  3. There are people out there that still think this way. If you find one, hit them with a stick.
Most of the advisors I have dealt with have been completely clueless about opportunities outside of academia. Most of them don't even have ties to industry. This is a huge problem. One of my most recent posts on the excellent manuscript published in PNAS Rescuing US Biomedical Research From its Systemic Flaws discusses broadening the career paths for young scientists. I think this is absolutely necessary and I highly recommend that even if you are planning on going into academia, you find an advisor who can help you with multiple different career paths.

Personal Items - Would you want to eat lunch with your advisor every day for the entirety of your PhD? Maybe...but, I doubt it. Now imagine that it is required that the whole lab eats lunch together...every day. There are some labs that are like this. There are also some that function more as a family than a work environment. This can be a very positive thing or it can be an extremely negative thing. It might sound attractive to have that level of closeness to your fellow graduate students and lab mates. But, what happens if you don't particularly like them, or your mentor is a walking inferiority complex? Personal items like lunch, family events, after-work functions, etc. are all handled separately by each lab. Birthdays and holidays are another good example. Is there a celebration, are there gifts involved? Depending on your thoughts on these items, it can get somewhat uncomfortable if the lab or your advisor is totally different.

Graduation Requirements - These are straightforward and should be in a contract, or handbook that was given to you when you started graduate school. However, graduate advisors and faculty will try to add things, change things, make you do extra, etc. If you feel like what they are doing is helpful or beneficial by all means, do it. If you feel like what they are trying to do is harmful, or not in your best interest go back to the guidelines and make sure they are aware that what they are doing is wrong. The guidelines and contract are there to protect you. Make sure you know the rules and make sure they aren't changed on you at any point in time.

There are a handful of other random thoughts I didn't have much input on, but wanted to include.
  • Maternity or Paternity leave
  • Funerals
  • Other leave of absence (illness)
  • What journals (high profile vs. open source)
  • Marriage
  • Dual-Degree (MD/PhD, PhD/JD, PhD/MPH, PhD/MBA) opportunities

And honestly even with all of these points above to consider, faculty advisors rarely even know what they want. They are fickle, they are stressed, and a lot of times they will take it out on you by changing their mind constantly.
I encourage everyone to use the comments section below! 

  • Lance D. Presser has a PhD in microbiology and immunology and is a public health laboratorian.
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
  • Follow Lance @ldpsci

Friday, April 25, 2014

Hepatitis C and Heroin on the Rise in Minnesota (and most of the U.S.)

Health officials in Minnesota are seeing an increase of people being diagnosed with hepatitis C virus (HCV), and suspect that it is related to the rising rate of heroin use. HCV is known to be transmitted via blood, and injection-drug use is known to spread HCV.
HCV Plush from Giant Microbes
32 Minnesotans were diagnosed with HCV in 2012, but the actual number of people infected is certainly higher. Many people do not develop symptoms immediately, and in some cases infections can smolder for years.

In May 2013, the Minnesota Health Department estimated 39,000 people were living with HCV statewide.

Needle exchange programs are one way to combat the spread of blood-borne pathogens like Human Immunodeficiency Virus (HIV), or Hepatitis B and C viruses. Needle exchanges have been successfully used in other countries, however in the United States they often come under scrutiny due to misunderstanding and stigma.

I found a list of five needle exchanges in the state of Minnesota. That doesn't seem like enough.

The heroin problem in the Minneapolis-St. Paul metro area has been worsening. 54 people died of heroin overdose in 2013 in Hennepin county, the deadliest year on record.

I encourage everyone to use the comments section below! 

  • Lance D. Presser has a PhD in microbiology and immunology and is a public health laboratorian.
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
  • Follow Lance @ldpsci

Wednesday, April 23, 2014

Meta-Research Innovation Center at Stanford

Stanford just announced a new center, named the Meta-Research Innovation Center at Stanford (METRICS). The press release says that it will focus on ways to transform research practices to improve the reproducibility, efficiency, and quality of scientific investigations.

I absolutely applaud this venture by Stanford and one of my personal science idols John Ioannidis, MD, DSc who I recently wrote about here.

As biomedical research presses on both in difficult and amazing times, the need for reproducibility, efficiency, and quality will be key in keeping the system productive. I am excited to see what this center and Dr. Ioannidis can achieve.

I encourage everyone to use the comments section below!

  • Lance D. Presser has a PhD in microbiology and immunology and is a public health laboratorian.
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
  • Follow Lance @ldpsci

Tuesday, April 22, 2014

Tuberculosis at the Zoo

Happy 52nd birthday to Packy, the oldest Asian elephant in North America. The celebration was held at the Oregon Zoo on 14 Apr 2014. The 40 lb cake that Packy enjoyed was made with whole wheat, fruits, vegetables, and about four pounds of butter.
Packy the elephant on his first birthday at the Oregon Zoo on April 14, 1963. Photo by Christina Christensen, courtesy of the Oregon Zoo
More importantly, for our purposes, it was announced by the zoo that Packy is currently battling latent tuberculosis (TB), which was discovered in July 2013.

Packy, and one of his sons, Rama, were diagnosed with tuberculosis in 2013. Rama responded well to the treatment, however Packy has struggled with the treatment. Similar to humans, the effects of the TB drugs vary from patient to patient, and Packy seems to be more sensitive to the cocktail.

The Oregon Zoo tests its elephants for TB yearly. Rama was diagnosed in May of 2013 at the age of 30. The illness was announced promptly by the zoo and employees working closely with Rama took precautions and isolated the elephant.

If you have questions, use the comments section below!

The treatment for TB in elephants lasts more than a year. The quantity of drugs required is massive, considering the size and weight of the animals. The same drugs are used for both humans and elephants. Neither Packy or Rama has any signs of illness, what the zoo is trying to control is the asymptomatic shedding of the Mycobacterium tuberculosis bacteria.

January of 2013 some zoo employees were reported as having tested positive for TB and undergoing treatment.

Previously, in 2009 the Centers for Disease Control (CDC) reported on a similar scenario that occurred among humans working as employees of an elephant refuge in Tennessee.

Tuberculosis is a common zoonotic disease. Elephants and elephant handlers, bovine TB in humans, etc. The treatment for TB in elephants is through oral medication for at least a year, and it costs between 5,000 and 50,000 USD.

Keep Packy in mind. Hope the treatment takes!

I encourage everyone to use the comments section below! 

  • Lance D. Presser has a PhD in microbiology and immunology and is a public health laboratorian.
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
  • Follow Lance @ldpsci

Sunday, April 20, 2014


Recently, I was involved as a mentor with the Milwaukee School of Engineering (MSOE) Center of Biomolecular Modeling (CBM) Students Modeling A Research Topic (SMART) teams. Holy acronyms!

2013-2014 SMART Team Shirt
I wanted to take a short moment and not just brag about how amazing the experience was, but also to give credit to everyone involved, for making it so.

I have been involved in a handful of high-school related science programs (LeadAmerica, INSPIRE) as well as a big brother for Big Brothers Big Sisters, and coaching football and baseball. The SMART teams were the most well-run, organized, productive group I have experienced.

Great year everyone! Thanks for the shirt!

I encourage everyone to use the comments section below! 

  • Lance D. Presser has a PhD in microbiology and immunology and is a public health laboratorian.
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
  • Follow Lance @ldpsci
  • Science Macrocosm Forum

Thursday, April 17, 2014

Review of John P.A. Ioannidis - "Why Most Published Research Findings Are False"

One of the most interesting essays I have read, John P.A. Ioannidis' "Why Most Published Research Findings Are False" discusses the increasing concern that most current published research findings are false.

This essay, published in 2005 didn't have an effect on me at the time (I was just starting my MS degree at Pitt's GSPH). But once I found it during my PhD, it really resonated with me.

I was having problems in the lab with RT-qPCR and western blots, etc. and how to interpret results. One of the main issues was my advisor was so certain that his hypothesis from his grant was correct, he would often pre-write the manuscript. If my results didn't match his hypothesis, then clearly I was doing something technically incorrect. Since I was doing something technically incorrect, his answer was repetition. Over and over until the results matched his hypothesis.

When you run a RT-qPCR and it "fails" the first three times (or twenty), but succeeds the 4th, and you only use the data from the 4th, I think that those are disingenuous results, and I argue that they aren't valid.

Likewise when you run a western blot or other qualitative experiment, (IFA, IHC, etc.) if you have to run the experiment 10 times, and only see your desired results once or twice, just how valid is that experiment?

These were issues that I struggled with (and I assume many others do as well) so when I read Dr. Ioannidis' essay, I felt slightly validated in my opinion.

If you have questions, use the comments section below! 

I want to discuss a few things about this essay. First, the summary:

"There is increasing concern that most current published research findings are false. The probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of true to no relationships among the relationships probed in each scientific field. In this framework, a research finding is less likely to be true when the studies conducted in a field are smaller, when effect sizes are smaller, when there is a greater number and lesser preselection of tested relationships, where there is greater flexibility in designs, definitions, outcomes, and analytic modes, when there is greater financial and other interest and prejudice, and when more teams are involved in a scientific field in chase of statistical significance. Simulations show that for most study designs and settings, it is more likely for a research claim to be false than true. Moreover, for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias."

Several methodologists have pointed out that the high rate of nonreplication (lack of confirmation) of research discoveries is a consequence of the convenient, yet ill-founded strategy of claiming conclusive research findings solely on the basis of a single study assessed by formal statistical significance, typically for a p-value less than 0.05. Research is not most appropriately represented and summarized by p-values, but, unfortunately, there is a widespread notion that medical research articles should be interpreted based only on p-values.

  1. The smaller the studies conducted in a scientific field, the less likely the research findings are to be true. I agree!
  2. The smaller the effect sizes in a scientific field, the less likely the research findings are to be true. I agree!
  3. The greater the number and the lesser the selection of tested relationships in a scientific field, the less likely the research findings are to be true. I agree!
  4. The greater the flexibility in designs, definitions, outcomes, and analytic modes in a scientific field, the less likely the research findings are to be true. Eh, this one I could go either way on.
  5. The greater the financial and other interests and prejudices in a scientific field, the less likely the research findings are to be true. I agree! However, if there are false results, there is a better than normal chance that another scientist overturns them.
  6. The hotter a scientific field (with more scientific teams involved), the less likely the research findings are to be true. I disagree. I think this is the pinnacle of science. More teams working on the same findings. The author does call this a paradoxical corollary, but I don't know if I buy it. The more people validating research the better.
The author does have some suggestions about how to improve the situation.
  1. Better powered evidence, e.g. large studies or low-bias meta-analysis
  2. Diminishing bias through enhanced research standards and curtailing of prejudices
  3. Instead of chasing statistical significance, we should improve our understanding of the range of R-values, the pre-study odds
I would highly recommend anyone involved in research to read the paper itself. It is fairly accessible, but a working knowledge of statistics is helpful.
I encourage everyone to use the comments section below! 

  • Lance D. Presser has a PhD in microbiology and immunology and is a public health laboratorian.
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
  • Follow Lance @ldpsci

Wednesday, April 16, 2014

Rescuing US Biomedical Research From its Systemic Flaws

For roughly four years now I have been on the "biomedical research needs reform bandwagon" tossing around heretical ideas like; there isn't enough funding to sustain the number of PhD and postdocs, alternative "non-traditional" career training, downfalls of hypercompetitiveness, etc.

If you have questions, use the comments section below!

When Rosalind Franklin University of Medicine and Science (RFUMS) School of Graduate and Postdoctoral Studies (SGPS) started putting together its strategic plan (and didn't think it was prudent to involve any students or postdocs) I took it upon myself to get involved and get on that committee. There was plenty of resistance, but I firmly believe items #5-8 wouldn't exist if I wasn't involved.

I am thankful that the number of faculty, and well-know researchers that are getting involved is growing. This week a manuscript was published in PNAS that everyone involved in the "Graduate School Industrial Complex" needs to read.

The abstract reads; "The long-held but erroneous assumption of never-ending rapid growth in biomedical science has created an unsustainable hypercompetitive system that is discouraging even the most outstanding prospective students from entering our profession - and making it difficult for seasoned investigators to produce their best work. This is a recipe for long-term decline, and the problems cannot be solved with simplistic approaches. Instead, it is time to confront the dangers at hand and rethink some fundamental features of the US biomedical research ecosystem."

And the first paragraph of the Conclusion and Future Plans section; "The US research community cannot continue to ignore the warning signs of a system under great stress and at risk for incipient decline. We believe that the American public will continue its strong support for biomedical research and that larger budgets are possible, defensible, and desirable. However, because of structural flaws in the system, such increases can only partially ameliorate a worsening problem."

Here's hoping for reform in the next decade

I encourage everyone to use the comments section below! 
  • Lance D. Presser has a PhD in microbiology and immunology and is a public health laboratorian.
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
  • Follow Lance @ldpsci

Tuesday, April 15, 2014

Post #4 Know your Advisor and Department Chair - My PhD Process: How I Survived a PhD in the Biological Sciences and Succeeded Afterward

Post #4 is all about getting to know your professor and department chair. Most everything I have seen in the "self-help" graduate school category is about getting to know your mentor/advisor.

A few examples:

Rackham Graduate School - University of Michigan
Graduate School - University of Washington
Science Magazine and another

This is a very important topic. No question, your advisor is going to own your career (and most of your life) for 4+ years, and will definitely have an influence afterward. What gets forgotten though, is the effect of the department chair.

Let's talk about the advisor position first.

When starting at a graduate school, it has become common to have a set amount of time (for PhDs usually your first year) to rotate in a number of labs in order to get a feel for how you work, get to know professors, and eventually pick your dissertation lab. At Pittsburgh, for the M.S. program, I was allowed to rotate with two faculty members. At Rosalind Franklin University of Medicine and Science (RFUMS), for the Ph.D. program, I was allowed to rotate with three faculty members (and in some cases they made allowances to rotate with four).

These rotations are crucial. Depending on the size of your department, and how many faculty are available to chose from, you should already have narrowed down your list, even before you arrived. When I arrived at RFUMS, I had two faculty in mind, a Kaposi's Sarcoma-Associated Herpesvirus (KSHV) researcher, and a hepatitis C virus (HCV) researcher. When I arrived I became interested in two other researchers that I eventually rotated with (Epstein-Barr virus and Alzheimer's/gene therapy/lentiviral vectors). There were plenty of differences between them which I will discuss below.

If you have questions, use the comments section below! 

A couple initial factors to consider:
  • Age - Age can be very important. Younger faculty are typically not going to be tenured, they are going to have a lot to prove. This can manifest itself in a positive way where the mentor works hard, is responsible, is very active in their field applying for grants, publishing, attending meetings, and generally trying to establish themselves. It can also manifest itself negatively when they loose all sense of balance, take everything too seriously, and develop a inferiority complex. Guess which one is more common? Older faculty can suffer from a plethora of issues as well. Not staying current with the research field, or the current big names. Older faculty sometimes get so far down their own rabbit hole that they lose sight of the field of research as a whole. They can be far less compassionate (e.g. "back in my day we did everything by hand and stayed overnight to run PCR and only went home once every three days and it was over a mountain guarded by trolls and it was usually snowing...") Often times older faculty will be more stable, and predictable which can be at the very least adjusted for.
    • My best advice is to aim for the middle if you can.
      • Find someone established in the field, not too established (30+ years is probably a little on the long side), but someone who has either already obtained tenure, or is very close.
      • Someone who is well published and connected to or at least knows some of the big names in the field. This will be helpful for collaborations, reagents, and if eventually you decide to do a postdoc it will give you some good options. 
      • Someone who hasn't had so many graduate students and postdocs already that they won't even remember your name, but also has experience and won't make all their management/mentor mistakes on you
  • Advisor status within the field - This can be important for further development, if you want to do a postdoc, or if you plan on staying in the field. However, I think the more important effect of advisor status is during your PhD. Think about how much easier it makes research, development, reagent procurement, publishing, grant getting, etc. if your advisor has some pull. It is almost inevitable that you are going to need advice, or reagents from outside your lab, and it helps to have a good relationship with the people that have them. Does your advisor go to/encourage attendance at meetings? Does your advisor act as an editor for a major journal? Does your advisor sit on funding boards? Does your advisor have a media (social or otherwise) presence?   
  • Gender of advisor - I have worked for two females and two males (two females during undergrad, a male for my MS, and a male for my PhD. I intend this point to be more of a self-analysis point to consider. Do you work better with men or women? Does it matter? I personally don't think that I work better or worse with a specific gender. Some things are different, but I have had success with supervisors of both genders. Understanding and communication is key. 
  • Ethnicity of advisor - This is yet another question you should be asking yourself. I would argue that ethnicity doesn't matter, but understanding and acceptance of differences do. What I mean by that, is if you have an advisor of a different ethnicity and they are unaccepting of your cultural traditions, that can result in problems. Many different cultures and ethnicities have different holidays, belief systems, and without understanding, can result in large differences between people. Unfortunately, many faculty aren't the most understanding. One of the other students in my PhD class once told me, her mother had told her not to work for a woman, or an Indian. She was both a woman, and an Indian. Everyone has an opinion, and I firmly believe it has more to do with acceptance and understanding, however, not everyone is accepting and understanding. So I think it is worth considering these situations.
  • Makeup of lab group - It isn't just your advisor that can make your life hell (or great?), the makeup of the lab is also very important. Is it just you in the lab? Is it a diverse group of techs, postdocs, and other graduate students? Is it homogeneous and you don't fit in? Is it angry? Is it collegiate? These are things that hopefully you can figure out while you are doing your rotations. The lab I worked in while doing my MS in Pittsburgh had an established technician, and three PhDs at different levels in their careers. My PhD lab was me, one technician (three different people during the five years I was there) and toward the end of my PhD, an incredibly inexperienced postdoc. I won't say that one situation was better or worse, because most of the reasons would be subjective. However, from a productivity standpoint, having to be the go-to-guy when it comes to new assay development, training all new staff and personnel, at times having to fill the technician position, or to be your own technician can be stressful and result in a drag on your research. Be careful! The other thing to be very wary of is personalities. If you do work in a lab with multiple people, then be wary of multiple personalities. Many words have been written on this subject (e.g. here and here). I won't discuss it any further in this post, but if people are interested I can cover it at a later time.
  • Tenure status of advisor - Imagine you have the choice between two jobs. The first job is one where you could be fired at any given time (you would be given at least six months notice) based on your perceived productivity. The other job is one where (from what I have observed) you can do and say just about anything you want (or as little as you want) and still continue to keep your position. This is the difference tenure makes. Imagine knowing that your job is safe and enjoying the freedom that comes with security
    • Tenure is a hard topic for me. On one hand, I understand how hard it is to be a young scientist, fighting for grant funding, struggling to publish, with the tenure board hanging over your head at all times. On the other hand, too many tenured faculty I have interacted with are absolutely worthless. I wouldn't want a few bad apples I have observed to justify getting rid of tenure, but the fact remains, there are too many tenured faculty who are not contributing.
  • Funding status of advisor - This one is pretty easy. The more funding, the better. Ideally, the funding will outlast your time as a PhD. Ideally, the funding is coming from multiple sources, for multiple projects. This is a question you definitely want to ask before you join a lab though. Or even before that, before you decided to matriculate to a school or department. 
  • Publications of advisor - There can be a case made for "the more the better", but I don't entirely believe that to be true. Quality is equally as important as quantity. What qualifies as quality is very subjective. But, when I look at a researcher that only publishes in one specific journal (e.g. publishing entirely in Virology, PLoS, etc.), I question how good the research actually is. However, faculty that don't publish very often, but only shoot for Nature, Science, etc. are high risk. A mix of high-impact factor, open-source, and focused journal publications should be the goal.
  • Work schedule and expectations - One of the faculty members in the microbiology department at RFUMS worked at a minimum, 12 hour days during the weekday. He would arrive usually between 9-10am and was usually in his office until 10-11pm. He didn't keep quite those hours on the weekend, but he was usually in at least a small portion of the weekend. Was he more productive than other researchers? No. Were his students and staff more productive? No. Were they expected to be in the lab when he was? Absolutely. This is a huge issue when it comes to advisor/student relations; schedule and time commitment. Inevitably, both you and your advisor think you know the best use of your time. Make sure to work out very early what the expectations are, what your advisor's work schedule is like, expectations they have for you, etc. On the opposite end of the spectrum from the above story, I also knew a faculty member in the neuroscience department at RFUMS that would come in on the weekend to do his students cell culture. Ugh...
Alright, so I think that wraps up the section on advisors. There are a lot of variables to consider, and some carry more weight than others. But let's talk about it! 

If you have questions, use the comments section below! 

Briefly, I want to close out by discussing department chairs. As I mentioned above, I feel like most "graduate school self help" is geared toward relationships with your advisor, but fails to address the chair of your department. If your advisor is stressed, more than likely, you are going to be stressed.

I have noticed over my 12 year stay in higher education, that the department has a personality, and that personality is most often dictated by the chair. Ask any management or administrative person and they will tell you that stress, anxiety, anger, all trickle down to subordinates. I have seen department chairs that are caring, and do extremely well at managing faculty and students. I have also seen some that have massive inferiority complexes, micromanage everyone around them, and throw tantrums when the food and beverage isn't correct for a meeting. Imagine being a faculty member working for someone like that? It would be extremely stressful (as if it wasn't a stressful career already). So if the faculty are that stressed, it is going to more often than not, trickle down to you as a student or postdoc.

My PhD advisor would leave early sometimes (he had small children, family obligations, etc.) and he would leave his computer and lights on, office door open, and would just tell me to shut everything off and close the door when I left. He did that specifically because he didn't want to deal with the abuse from the chair for leaving early. I have a lot of stories like that, faculty, postdocs, and other students in the department all had stories of dealing with the chair. Keep in mind, it isn't just your advisor that can make things better or worse.

I encourage everyone to use the comments section below! 
  • Lance D. Presser has a PhD in microbiology and immunology and is a public health laboratorian.
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
  • Follow Lance @ldpsci

Tuesday, April 1, 2014

Post #3 What to Look for in a School-Program-Department-Advisor - My PhD Process: How I Survived a PhD in the Biological Sciences and Succeeded Afterward

One of the most important things I tell aspiring MS or PhD students is to be extremely aware of the school, program, department, and advisor that you choose. I guess this sort of holds up for undergraduates, or law students, or med students to some extent as well, but let's focus here!

Me, Lance Presser discussing something important (of course).
As I was finishing my undergraduate at North Dakota State University (NDSU), I had a fairly high opinion of my abilities, having spent a lot of time in a research lab, double-majoring in biotechnology and microbiology, and having a pretty good idea of what I wanted to do with my life.

I applied to some of the top infectious disease MPH programs in the country (University of Pittsburgh, Emory, Boston University, and Tulane) and was well received by all of them. Eventually I chose the University of Pittsburgh. Why? Well let's look at what they did right.
  1. Outstanding program. Obviously, if the program has a reputation for being great, your PR people don't have to work quite as hard. Pitt has the benefit of lineage. Jonas Salk, Patrick Moore and Yuan Chang, the Multicenter AIDS Cohort Study, etc. A tradition of excellence is hard to beat.
  2. Student outreach. As special as I might have thought I was at the time, I really wasn't a rock star student or researcher. However, the people in charge of recruiting sure treated me that way. The administrative staff, the faculty that I met, even the students who took me out to lunch when I went for a visit (especially Leah and Alicia), everyone treated me like they wanted me there. And for the most part, the students seemed happy (at least happier than other PhD students I have known). Maybe it was just better times.
  3. Outstanding curriculum. Curriculum can be tricky. Sometimes it looks better or worse on paper than it actually is. Pitt had a nice variety, and I appreciated that even though I wasn't getting an MPH (I ended up in the MS program), I had the opportunity to take many of their classes.
  4. Departmental culture. This one is also tricky to gauge. The best advice I can give to people is that a department typically takes on the attitude of the chair. At NDSU the microbiology department chair seemed very uninvolved and lazy. Therefore, the department for the most part stagnated. At Pitt, the department chair seemed very concerned with finances, rankings, and putting out a lot of impactful research (he was also one of my committee members). Therefore, people thought he was a bit impersonal, but the department was very successful at obtaining funding, and publications. At Rosalind Franklin University of Medicine and Science (RFUMS) the microbiology department chair told students things like, "Now that you are here, best put your balls in a freezer. Graduate school is no time for relationships." or, "You should consider yourself lucky you can attend your grandparents funeral. I didn't even go home for my own fathers." You can easily extrapolate what kind of person (person is generous) would say those types of things to students, and being the chair, you can easily extrapolate what the culture of the department was like (hint: anger and fear).
Once at Pittsburgh, we as MS students had the opportunity to rotate with two faculty members before choosing our permanent lab. I had interacted with Todd Reinhart ScD before matriculating, he was from Minnesota, had got his ScD from Harvard, he was doing great research, and an all-around super person. He was my first choice for a rotation, and I really liked it, but the project was too molecular for my taste at the time. I just wasn't ready for that kind of project

My next choice was Frank Jenkins PhD who had an interesting project that involved immunohistochemistry and other staining techniques, looking for what tissues, organs, and systems Kaposi's sarcoma associated herpes virus (KSHV) infected in men who had died with AIDS.
Cathedral of Learning - University of Pittsburgh, PA
I liked the lab, I liked the project, I liked the people. It was a great experience. The mistake I made at Pittsburgh (similar to the one I made during my undergraduate) was, I didn't focus on getting my name on papers.

As a MS student, I should have volunteered to help the PhD students in the lab more, with the hopes of getting a middle authorship out of the deal (there were three PhD students in the lab at the time which meant at least three opportunities for middle author papers). I also (and this is debatable because, who knows how these things turn out) should have considered another lab, or pushed harder in Dr. Jenkins' lab to get a first-author paper out of the work. Another possibility would have been to put out a review article. I was doing a lot of reading for my thesis and there were multiple "name-brand" KSHV researchers at Pitt. A review article would have at least shown I knew what was going on in the field and had the ability to write and think critically.

As my time at Pittsburgh was drawing to an end, I knew the next step was a PhD. I was impressed and inspired by the faculty and PhD students at Pittsburgh and the career path(s) I saw myself on required a PhD. I could have stayed at Pitt. There were faculty that would have taken me. I had a good run at Pittsburgh, I had won scholarships and awards for my thesis, I had a good reputation among the faculty, students, and administration. However, I felt it was time to leave. Whether that was the right decision...I don't know, but I do periodically ask, "What if?"

At Pitt, I encountered a lot of stellar faculty from other universities who came to give talks, I presented at the American Society for Virology conference in Madison, WI, I had read a lot of papers. I was starting to know things, and I assembled a very nice list of people I was interested in doing a PhD with at a variety of different universities. I set my sights high, universities like Harvard, Univ. of Washington, Univ. of Texas Galveston, Northwestern. I also set them not-so-high when I applied to Rosalind Franklin University of Medicine and Science.

At each of these schools I specifically emailed faculty I was interested in doing a PhD with. Most of the faculty I emailed were great. They were very honest about their ability to take students, due to space or funding issues. I had one faculty say she would love to take me but she was retiring, most said they would take me but I had to get accepted to the program first. Unfortunately, in most cases, I didn't. This is a key step! With interdisciplinary programs becoming increasingly popular, and funding continuing to decrease, making sure the faculty you are interested in have space and funding BEFORE you decide to matriculate to a graduate program is vital!

If you have questions, use the comments section below! 
Rosalind Franklin University of Medicine and Science - North Chicago, IL
I eventually was accepted to RFUMS and started there in the fall of 2007. Let's look at pros and cons, pros first.
  1. I was accepted. This may seem obvious, but if you are absolutely set on getting a MS or PhD, and you only are accepted into one school, sometimes you just have to suck it up and do it. We all make sacrifices, if yours is going to a sub-standard school, or a weak department, that might just have to be the case. You can still be successful, you might have to get a little lucky, or work a lot harder.
  2. Geographical fit. I am a Midwesterner. I had friends and family in ND, MN, WI so being in North Chicago for a few years was a comfortable idea. It is also close to Chicago and Milwaukee (two major cities), and very close to large biotech including Abbott (plus Abbvie), Takeda, Baxter, and Hospira.
  3. Interdisciplinary program. I am not entirely sure that this falls in the positive category. I think when done properly it is a very good thing. I think when done poorly, it can be very detrimental to developing graduate students.
  4. Young faculty. I rotated with three faculty members at RFUMS; Robert Marr, David Everly, and Gulam Waris. All three had been hired within the last year.
  1. No recruiting. Anyone reading this blog heard of Rosalind Franklin University of Medicine and Science? No? I didn't think so. RFUMS is located in North Chicago and people living in North Chicago haven't even heard of it. The medical school has a modicum of recognition as does the podiatry school, but both of them are known as something different (Chicago Medical School and Scholl College of Podiatric Medicine). When both of your somewhat well-known programs call themselves something different (in order to distance themselves from the umbrella RFUMS name) maybe there is a problem that needs to be addressed. In the hotbed of Big-10 schools, and no recruiting is done for the graduate school. RFUMS is not attracting the best graduate students and that is a problem.
  2. No alumni association. When asking the administration if they think they have been successful in training graduate students their answer is 100% yes. What is this answer based off of? Nothing. Zero data. There is no alumni association for the graduate school. 30+ years of graduate students and what do we know about them? Nothing. RFUMS doesn't know where they are, RFUMS doesn't know what they are doing. It is one of the most basic programs that a school is responsible for. It helps networking. It helps you understand and track the training you as a school offer. It helps you fund raise. There are so many important aspects of an organized alumni association, and it isn't an especially difficult task.
  3. Limited interaction with local universities. Northwestern University, University of Chicago, Loyola, Rush, all within 30 miles of RFUMS. How much did we interact with these world class institutions? Maybe once a year at a seminar. Some professors in some departments had small collaborations, which is great. However, most did not even acknowledge that those other universities existed. Most professors were very content in their ivory tower at RFUMS, even though it wasn't an especially nice ivory tower.
  4. Limited teaching opportunities. I can't say there were no opportunities. The neuroscience and pharmacology departments had some teaching assistant-type opportunities. I think physiology might have had some TA opportunities. Microbiology technically had TA duties, but it consisted of monitoring the medical students while they took exams, and handing out workbooks four times a year in some of the medical students problem based learning sessions. There are local colleges, both private four-year and community. I was able to get an adjunct teaching position at a community college, as was another graduate student a year my junior. However, both of us had to hide it from our bosses, and when hers found out, she tried to get her committee to make her quit, even though the graduate student's ultimate goal was to teach, following her PhD. It was very obvious in these situations that certain PhD advisors didn't care what their graduate students wanted for a career.
  5. Limited interaction with local biotech and pharma companies. Geographically, RFUMS was located within a hotbed of large pharma activity. Ideologically, they couldn't have been farther away. There was very little interaction between the graduate school at RFUMS and those pharma companies. In the five years I was at RFUMS and in the couple of years since, I am unaware of anyone (PhD or Postdoc) that got a job at one of those companies. I know a few of the technicians that took jobs at Abbott, and with it, usually they doubled their salaries. The fact that no PhD or Postdoc was able to break into one of those companies from RFUMS is pathetic. It is just another issue that speaks to how little the administration and faculty cared about students, and how little the RFUMS name meant, even on the local level.
  6. Small homogeneous department. When the chair of a department takes an overwhelming majority of one ethnicity of students, postdocs of the same ethnicity, promotes faculty within the department from those postdocs, after awhile "inbreeding" develops. It can very quickly develop into a stagnant, toxic environment.
  7. History of administrative failure. At RFUMS, the medical school has been put on probation by accreditation committees twice in the past ten years. The graduate school has had a history of incredibly poor deans, and recently RFUMS split the dean position into two (promoting both positions from within). The Peter Principle is alive and well within RFUMS.
  8. Interdisciplinary program. Normally, if run properly, I am in favor of interdisciplinary programs. RFUMS traditionally puts together a list of faculty that can "potentially" take students. Every year the list is garbage. Half of the names just stay on the list in the hopes that they will get funding (hint, they never do). With an interdisciplinary program communication, honestly, and openness are key. You absolutely cannot convince students to come to your school, only to switch or limit the faculty they can work with. 
  9. Young faculty. Again, typically a good thing. However, administration failed to notice the trend of decreased federal funding and went through a very large "young faculty hiring phase" around 2006-2007. This has led to a large glut of underfunded, young faculty who are struggling to survive. 
If you have questions, use the comments section below! 

Below are lists that I have compiled in no particular order. The are based off of my experience and many of the other graduate students that I have been around over the years. Obviously, there will be some subjectivity, but hopefully this will give you a better idea of some of the things you should be looking for when considering graduate programs, etc.

Top five things to look for in a graduate school
  1. Size and scope - Can you succeed at a small graduate school? Sure. Does having access to more resources, faculty, and options help? Absolutely. It is amazing how at a larger school like Pittsburgh you take for granted things like journal access. Then you get to a small school like RFUMS and have access to so few journals that it hinders your research and writing. 
  2. Name - Can you succeed attending an unknown school? Sure. Is it easier to network, get jobs, and get ahead when you attend schools like Harvard, Yale, Pittsburgh, Colorado, Michigan, North Carolina, Wisconsin, Berkeley etc.? Absolutely.
  3. Location - I never would have thought this was important, but like a lot of non science jobs, there are certain cities or states that have a critical mass of smart people. Pitt was like that, with Carnegie Mellon right next door. RFUMS was even like that, it just didn't realize it. NDSU was not like that. It was very isolated, which was fine at the time, but I would have hated to be a graduate student there.
  4. Amenities - Sports teams, fitness centers, surrounding bars and restaurants, a beach, running trails, etc. maybe none of those are important to you, but they generally affect everyone's well being.
  5. Trending - This might be a little subjective, but certain colleges just tend to get hot every now and then. It doesn't hurt to ride the wave.
Top five things to look for in a graduate program/department
  1. Culture - The culture of the program and department are probably the most important things to consider. If the culture of either of these is toxic, lethargic, or apathetic, you are more than likely in for a rough time. This can be hard to determine, but if you can find a few 4th or 5th year PhD students and ask, they will generally fill you in. Some advisors and professors will be better at shielding you from this then others, but if the graduate program has a bad culture, you are going to have some of it rub off on you. The best way to determine this at the department level is to look at what the department chair's personality is like. Also, ask around. Most of the time someone will be honest with you.
  2. Name recognition and repute - Lineage still means something in science, as does being a standout in your specific field (we can argue about whether or not that is a good thing). There is a reason certain labs always publish in Science and Nature vs. lesser impact factor journals. Even if you are a great research if your program, department, or mentor aren't cooperative, or supportive, your talent can go to unrecognized or be wasted.
  3. Student success - This needs to be monitored and if the graduate program is not paying attention to what happens to its students after they graduate, it means they don't care. Make sure to look for programs that are involved in their students success, nurture their students with resources, have alumni and other networks that are open and accessible. At Pitt, I got the impression that most of the faculty honestly cared about what their students did after graduating, and helped them achieve their goals. Obviously, there is going to be some give and take because as a student, you are there to get work done and advance yours, as well as your mentor's careers. At RFUMS, it wasn't an impression, it was a firm "You are here to do what we say and if you want to do anything else...don't." The microbiology department at RFUMS was notoriously stubborn, and unless you wanted to do a postdoc, you were wrong. Teaching, public health, consulting, policy, etc. were not options. As a graduate student, your number one job was advancing your mentors career, typically while sacrificing your own interests.The number of careers in academia is rapidly shrinking with no end in sight. Non academic careers are becoming more and more popular, although there is push back from many faculty. Departments and programs need to recognize that there is more than one way to be successful during your PhD as well as after.
  4. Time to graduate - This is becoming less of an issue as funding is becoming more problematic. However, there are certain schools that still have a penchant for keeping graduate students as long as eight to ten years. If you can't finish your PhD in five to six years, either you or your advisor are doing something wrong. Taking ten years out of your life to do a PhD is not a good investment.
  5. Flexibility - This is directly related to the above "student success". Many PhD students now days are not interested in "traditional" academic careers. Most of this has to do with the lack of them, and the competition for the few remaining ones. It just isn't worth it anymore. However, there is a larger (growing) group of PhD students that never had any interest in academia in the first place. Industry, writing, teaching, biotech startup, public health, all are viable options that more students are considering, and most graduate programs are failing to adapt.

Top six things to look for in a graduate advisor
  1. Funding - If they don't have it, they aren't going to be able to support you. Usually they won't take you as a student, but there are some out there that will take you and then once the funding runs dry, not support you. Young professors usually have startup funds that they can use for this purpose, but I think it is probably best to find a middle-career professor who has ample funding.
  2. Network - What do you want to do during and after graduate school? Can your boss help connect you to the right people and places? If not, you are going to have to either do it yourself through cold calls and emails, or rely on other people to help you. Also, there is a very legitimate chance that if your boss isn't in a certain world, (e.g. consulting, teaching, industry) then they might not approve of your decision, and will potentially hold those things against you.
  3. Considers your future and career plans - Related to the thought above, maybe you want to be a microbial photographer. Maybe your advisor has no idea on how to do that, or no connection to any other microbial photographers. But, let's say that you are a good worker, you get your lab stuff done on time and you do it well, you follow instructions, write papers, and are generally productive in the lab. There is no reason that you advisor shouldn't reciprocate and try to help you as much as possible with the next stage of your career. The dirty little secret is, most of them won't help. Either they can't, or they won't, but most of the time, you will be on your own. There are good advisors out there that will try their best to help, and they are worth their weight in gold.
  4. Sane - If this seems like it should be obvious, you might not have hung around with any faculty members, postdocs or graduate students lately. Climbing the ladder in academia requires a certain personality. It does not encourage sanity. This is obviously pretty subjective, but make sure that your sanity and your advisors sanity match up.
  5. Publishes, and advocates for you - It isn't all about them and it isn't all about you. However, both you and your advisor should accept that you are on the same team, and a team works together to be mutually beneficial. Publishing, helping you with your career, are things that a faculty member should be doing to help their students. Sometimes, one side of the team fails to recognize that fact. Guess who usually loses (hint: it isn't the faculty member).
  6. Established lab - Make it easy on yourself (or easier I guess) and find a lab that has a postdoc or technician that will teach you techniques. Most advisors don't have time for that type of hands-on learning. 
I encourage everyone to use the comments section below! 
  • Lance D. Presser has a PhD in Microbiology and Immunology and currently is a Public Health Laboratorian.
  • Follow Lance @ldpsci
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
  • Science Macrocosm Forum