Welcome to Jason's Grad School Blog!

Hi All, and Welcome to my Grad School Blog!

I had been intending to keep a blog of my experiences at grad school as a means to keep in touch with all of my friends and professors. While visiting Ithaca at the end of August, Susan Swensen, current chair of Biology Dept, mentioned that my blog might be a cool resource for undergrads who are considering grad school in the sciences. While this wasn't my original plan for the blog, I really liked the idea, so I am going to focus my blog towards an audience that has some background in science and might be interested in grad school.

To that end, I'm going be writing up two different types of posts. The pieces with titles on them (like this one) are going to be longer, essay style entries where I will talk in depth about a particular topic. For example, today's topic is going to be how the graduate school education is structured, how it's different/similar to the undergrad set-up, etc.

In addition, there will be diary/journal style entries titled "Grad Diary" followed by the date; here I might make a little comment about something funny or interesting that happened during the day, a "progress report" update, a cool show I went to, whatever. These will generally be shorter and are meant to offer a glimpse into the day to day.

Still, since this is going at a rather PUBLIC audience, I will probably not be giving a whole lot about my personal life. On the one hand, I want to give you an idea of what life is like as a grad student, but on the other hand I don't think I need to burden you all with every little detail about my life.

As a word of caution, I can't promise that this won't be science heavy - there's just no way for me to talk about my experiences without being somewhat technical. I'm going to try to keep my language so that an undergrad who has some experience in biology and chemistry can follow along (ex: I will not explain what transcription or translation are, or what an agarose gel is used for, etc). However, I also realize that even people with a scientific background may be a bit fuzzy on what homologous recombination entails, what nucleosomes are, etc, so I'm going to hyperlink terms you should know but I'm not going to explain. They will be linking to a wikipedia page describing the phenomenon, technique, etc. While wikipedia is not the greatest resource out there, most of the science articles aren't too bad, so you should be just fine. Nothing replaces a good refresher in a reference text or, better yet, consulting the resident expert on the topic.

Finally, I want any and all readers out there who are thinking about grad school, or even about undergrad, to feel free to contact me with questions. I will be happy to offer my thoughts, advice, and opinions, and direct you to people who can help you more than I can.

With all that being said, let me explain what my grad school experience is going to entail. While this is going to be focused on how the Biomedical Graduate group at Penn works, most of this is widely applicable to pursuing a PhD in general in the basic sciences.

Research Structure
I think that it might be helpful to understand how research is done at universities like Penn, because it will help to explain the whole education and financing process. Each lab is headed by a faculty member, who is called the "Primary Investigator," or PI. The PI directs the research projects in his/her lab, and spends a very large amount of time writing proposals for new grants or presenting results. Research is funded largely through grants from outside institutions (more on that below) so grant writing is a very important part of a PI's job. Depending on the size of the lab, the PI may or may not spend a lot of time at the bench actually doing research. Generally, the larger the lab, the more likely that grant writing and publications will take up the PI's time. In smaller labs, the PI is doing more of the research at the bench - this is especially true for staff seeking tenure (where publications are directly tied to tenure decisions).

Under the PI are technical staff (lab techs), who are full-time employees who work directly for the PI. They are often people who have a bachelor's or master's degree, and are comfortable just being at the bench. Lab tech's generally do the grunt work of the lab, liking making up reagents, ordering equipment/supplies, perhaps cleaning dishware. They are often the most knowledgeable person in the lab as far how to actually do science.

In addition to lab techs there are post-doctoral researchers, or postdocs. A postdoc is a two year position (generally) granted to someone who has finished his/her PhD. A postdoc experience is generally to help hone a researcher's skills more rigorously and on a particularly specific system - say HIV viral entry specifically instead of virology generally. It is often the case that your postdoc experience defines your future research much more than your PhD experience. People who stay in research generally do one or two postdoc experiences before finding a position in academia, industry, or other research organizations like the Centers for Disease Control or the National Institutes of Health. The PostDoc(s) are often seen as the PI's "lieutenants," and are generally focused on a specific project within the lab. In large labs, it is often the case that a PhD student will get assigned to a Postdoc and refer to them for their research and not have a lot of contact with the PI.

There may also be a senior research assistant, who is like a post doc except that s/he is staying with the PI for a long-time engagement. A senior researcher is often the PI's right hand (wo)man, though this is not always the case. A senior researcer is often very knowledgeable about the questions being pursued in the lab, and like lab techs, are a great resource.

Finally, under the lab techs and postdocs are the PhD thesis students, who are working full time towards their theses. You generally begin working in your advisor's lab during year two, and begin your thesis in year three, and work until you finish.

Publications are the lifeblood of research. Papers always go to a peer-reviewed journal where they are reviewed by other experts in your field before being put into publication. If you look closely at the list of authors, generally the first author is the person who actually did most of the research, followed by other students or lab techs and collaborators who worked on various aspects of the project in descending order of contribution, and finally the primary investigator's name is always last, which indicates whose lab the research came from. A lab that is not producing publications is a lab that is not doing well.

Generally, the PI can be seen as the CEO of the lab, and his/her name is attributed to every publication that comes out of his/her lab, regardless of whether s/he actually did any of the research. They generally focus on securing funding for their projects, presenting the results and findings, and overseeing the overall direction of the research. It is the postdocs, lab techs and grad students who actually do the work (mostly).

Finances
Pursuing a PhD in the sciences is, generally speaking, a very economical choice. In basically all PhD programs, the institution will pay for your tuition, and in addition pay you a yearly stipend with some health benefits. In Penn's case, my stipend will be $28,500 plus basic health insurance. This means that pursuing a PhD does not represent any cost to you outside of living expenses (which is definitely a concern in areas like Boston and NYC). In addition, I am able to freeze my payments on my undergraduate student loans while in grad school, which is immensely helpful.

This seems too good to be true, right? Let me explain how it works. Generally, for masters programs and for other advanced schooling it is an added expense, but most of these fields are "professional," i.e. corporate related fields where an advanced degree isn't necessarily needed to succeed(though it certainly helps). If you want to do research, however, an advanced degree is essential, because these degress entail what are basically apprenticeships in doing science - they are experiential. With an undergraduate degree, the best you can be is working at the bench for someone else. Especially now, if you don't have a PhD in science, you are not seen as a fully trained researcher. For this reason, most people who go into research don't get their masters - that's only if you want to do something outside of research, like consulting, marketing, etc, though that is not always the case.

The real reason that it is so economical, though, is that funding for research is largely from public money. Depending on what your field is, you may apply for funding from a different agency, but it's pretty much the same. Since my field is direclty related to health (i.e. "biomedical science") most of my funding comes from the National Institutes of Health (NIH), a research and funding agency set up by the federal government. All of the research that goes on at Penn is funded from outside the university. These grants usually apply for about 5 years, which means that investigators are constantly writing new grants to keep their projects funded.

So how does this work for the student? Well, the specifics vary by instiution. Generally, for the first year students are supported by the university. By the second year, the student should have already selected his/her thesis advisor, and have begun working in their lab. For most programs, the student's stipends and tuition are paid for by the thesis advisor out of the PI's grant money. After the second year, in most institutions the student is supported solely by the thesis advisor. In return, the thesis advisor gets another researcher in his/her lab to actually do the work and produce results that will guarantee more funding in the future.

Often the university will employ you as a teaching assistant for undergraduate classes and labs, or possibly graduate classes when you are older. In many schools, these TA jobs are the direct source of your income, so you may have to teach more than you would like. None of the programs I applied to required you to teach, mainly because there is so much money in the health sector that you don't really need to TA to supplement your stipend. Other programs may require you to teach more.

At Penn it's a bit modified to the advantage of the thesis advisor (and no real disadvantage to the student). As far as the student is concerned, the tution and stipend are guarenteed up to six years. For those interested in the details: Penn covers the tution for up to six years. The stipend is paid for by the university for the first year. For the second and third years, the students apply for an NIH Training grant, which is a grant specifically designed for student researchers that covers two years of income; if the student is not awarded a training grant, Penn will still pay for your 2nd and third year. At this time I will have chosen a thesis advisor, and s/he will have to pay almost nothing to cover my stipend, though I will have begun working in his/her lab already. Then, beginning year 4 or so, my adviser will take full responsibility of my stipend until I successfully graduate. In addition, Penn does not require you to TA any classes, and actually only lets you TA two or three times (probably because they want you to focus on research and don't want to pay you more than they have to). This money will be a small addition to my yearly stipend.

I want to emphasize here that while much of this is true for most programs, it is by no means true for all of them. A lot of factors play into how funding is handled, and it is not necessarily done the same within an institution. What I've described is true only for the Biomedical graduate group at Penn. The Chemistry Department, as an example, requires a lot more teaching assistantships to support their students. If you are looking at different schools, be sure to thoroughly reseaerch your funding situation.

Taxes are a complicated topic which I still don't fully understand yet. Look back here during tax season for a run down.

Grad Student Education
Now we get to the good stuff. This is my projected academic timeline for the next few years. Based on this and what I've written above, it should be clear that pursuing a PhD is a full time job, and then some; we definitely earn our stipend (in dividends).

During the first year I will have the heaviest class load, designed to bring everyone up to speed on the current knowledge in the field. My program is divided into three tiers of organization. Generally, I am within the Biomedical Graduate Studies group, which is distinct from other graduate programs like physics, chemistry, engineering, etc. Anything related to health and biology is lumped here. The BGS is housed within the School of Medicine. Within this extremely large group of 700 grad students are 7 interdisciplinary groups - I am within the Cell and Molecular Biology Group (CAMB), distinct from other groups within BGS like Biochemistry and Molecular Biophysics, Immunology, Epidemiology and Biostatistics, Genomics and Computation Biology, etc. CAMB is the major group that I will be associated with.

Within CAMB there are six divisions: Cell Biology and Physiology, Cancer Biology, Developmental Biology, Genetics and Gene Regulation, Gene Therapy and Vaccines, and finally Microbiology, Virology, and Parasitology (MVP). This last group is the division I will be working under. I will generally be referring to CAMB as the umbrella group, and MVP as my specific area of study.

My first year I will be taking a general Cell Biology which all CAMB students have to take, a gene regulation course, and an immunology course designed for the CAMB department. In addition, I am to complete three 10-12 week lab rotations during my first year. These lab rotations are to help locate a thesis advisor, and a lab that you are interested in working in. If you can't decide on an advisor based on these three, you are allowed a fourth rotation. During the rotations, students are not generally expected to produce incredible results; rather, they are expected to learn the techniques used in the lab, get to know the projects, and get a feel for the personalities and style of the lab. During the first year, it is expected that when you are not in class you are in lab working. Students often come in on the weekends to finish experiments off or whatever for a couple of hours. And when you aren't in class or in lab, you are studying (or trying to maintain your sanity).

During the first summer, you might take one class or two and maybe another rotation. During the summer you are to have chosen your thesis advisor, who will basically be your mentor and lifeline for the rest of your educational experience. At this point I will be paid through a combination of my PI's grants and NIH training grant which I will have to apply for. During the second year, I am expected to work in my advisor's lab full time, as well as attend one or two MVP specific and elective courses each semester (Virology, Bacteriology, etc). The second year is very similar to the first, except that there is more time in the lab, and you are working specifically in the lab that you will be doing your thesis research in (and hopefully getting some preliminary data). At the end of the second year, you take qualifying exams which include an oral and written component; the exams will test us on anything and everything that has been covered in our classes. Upon successfully passing the examination, I am allowed to begin my thesis research. The proposal for the thesis is due sometime before qualifying exams. After your proposal has been accepted, you spend the rest of your time in the lab working on your project, and maybe taking one or two electives every year. In addition, you will meet at least once a year with your thesis committee to have a progress report.

Once you are in your third year onward, you can basically focus exclusively on your own research, hopefully get a few papers out and attend some conferences, etc. Most people take about three years to finish their research, at which point they give their thesis defense and write up a report. For MVP, the average length of time from start to finish is 5.3 years.

Throughout the entire process, we do get a few holidays off (a few days for Thanksgiving, Christmas/New Years, memorial day, etc) and in addition we are entitled to two weeks of vacation, which you generally will have to negotiate with your thesis advisor.

It's a full time job.

In addition to what I've mentioned above, I will be doing a "certificate program" in translational research (HHMI Med Into Grad Scholars Program). This program is designed to provide PhD students in the biomedical sciences a background in clinical research, disease pathology, and how basic research and clinical research intersect. I am drawn to doing things that blend different specialities and backgrounds, and as someone interested in viruses I am also interested in disease and health, so this program seemed perfect for me. The requirements include a couple of other classes that cover the topics I've already mentioned as well as a clinical clerkship, where I spend a summer in a clinical lab, and shadowing an MD.

Research Interest
As a brief conclusion, if you want to know what it is I am actually studying, I want to study how viruses infect cells and use cellular machinery to "reproduce" and infect other cells. I'm especially interested in viral gene regulation and latency strategies. This invloves a combination of cell biology, molecular biology, and virology, or "molecular virology" as I like to call it. Penn has one of the largest number of dedicated virologists on the East Coast, if not the US, so I should be pretty set to go in that department.

If you want to learn more about the program(s) I'm in follow these links:

Biomedical Graduate Studies at Penn
Cell and Molecular Biology
Microbiology, Virology, and Parasitology
HHMI Med Into Grad Scholars Certificate Program