Flexibility in Research

For the past few weeks I've been working on the figures for my next paper. It's been very crazy, we thought we knew the topic, but the more we uncovered about the dynamics the more it changed the story. But we finally got the foothold and produced the story.

That's just how science is. Some people become so attached to their original ideas that they lose sight of the point of all this: to allow the process to inform us, not just confirm what we already know. That is a dangerous mindset to have in research, the whole point of doing experiments and testing different things isn't there to confirm what you already know, it's to find a new way of looking at the world, find a new explanation for what happens, or to find knowledge previously unknown. Believing that you know the field you are studying absolutely hampers the scientific method, deadens the mind to novel hypotheses. Or as Isaac Asimov put it, "The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but 'That's funny...'"

On the other hand there are those who spend all their time in the shadows, focusing on minute. Sure, they can crank out publications, but many of them are meaningless. They become so enamored with the small details of whatever system they're studying that they lose their place in the big picture. I recently heard a seminar that had this sort of mindset. The speaker couldn't answer a big picture question afterwards because they interpreted it as a technically detailed inquiry. Coming to science with the mind of a technician just produces technical results.

Well, I've got my new story put together in figures and notes, and now it's time to get writing!

Manuscript Submitted!

Sorry for the delay on this update. This is academia, after all!

The reason why I’ve been waiting on this particular post was I wanted to put up something exciting that’s been brewing for a while. After a year of working on this project, we have submitted my manuscript on Two-Component Signaling to Proceedings of the National Academy of Sciences! This has been a very exciting project to have worked on, especially considering we do a bit of real bioinformatics in gathering data to support our theories. We presented this work both as a poster presentation and a contributed talk this year at q-bio, where it was well received. Now to keep fingers crossed as we wait to hear back from them to see if we get triaged or get sent to review.

The delay comes from the game itself: the great Game of Academia. Some professors don’t like that term, as one’s career should never be a game. But politics are everywhere. Can you imagine how much time the President’s speechwriters spend making sure that each word chosen, the structure of every sentence set so that it conveys exactly what the administration wants to say? It’s the same in academia. You have to write your articles so that it is engaging, tells a story. But you have to make sure that you do not suggest much more than what you can show when presenting results. The best scientists are amongst the greatest communicators as what good is your science if you cannot communicate it to others?

So we had to play the game. Make sure the discussion isn’t redundant, but doesn’t overstep and become too hypothetical. Make sure the math supports the text. Make sure we use the same terminology as the leaders in the field so we don’t look like we don’t belong. Even the cover letter has to be worded well: you have to grab the editor’s attention immediately and make the case for why their journal should publish your work. And it gets difficult saying the same thing over and over again without sounding redundant or without wearing out key phrases.

Now that this manuscript is submitted there is not much we can do for it for the time being. We have to wait and see what happens. But rather than twiddle my thumbs, it’s on to the next project. During the editing process I already established a strong head start. I know the story, and it comes down to the figures. Yet another form of the game, but this time you have to make sure that the graphs you show support your story while being easy enough to read. I’ve encountered my share of articles with mind-bogglingly complicated plots, some of which I still don’t understand. Complexity and large amounts of data do not make one a great scientist if others cannot just pick it up, glance at it, and understand what point you’re trying to make by including it. Once I can finish up these figures I can get on to writing the next manuscript!

Anyway, to sum it all up: take the time to make sure your text says what you want, your story is captivating, and your figures make sense!

Keep calm and research on!

What does the next step look like?

Yesterday I went into the University Career Center for an appointment with a career coach, Kelsey. This was a first meeting, so we went over a lot of information fairly quickly. I went over my professional/academic career so far, detailing how I went from a physics major to mathematics then biology, how I spent 6 years in the same lab in UNC, my time so far here at KU, and my programming in my free time. I keep pretty busy!

I also brought along my resume and CV to get a fresh pair of eyes on it. Turns out my experience is enough to warrant going to 2 pages, which is small but just feels exciting. Most people in the past have told me to stick to 1 page, which required some creative formatting. With 2 pages I could add some whitespace to break it up, and get more descriptive of what I've achieved. Luckily I already was wondering that, so yesterday morning I reformatted it to 2 pages. It was good to get a fresh look at it, she caught several things that could be expanded or added.

We also talked about where exactly is the next step. This is where things get difficult. I know I don't want to go into academia. I've seen what that does to people. The constant stress, the long hours, all the grant applications and paperwork. Plus I'd have to spend several more years as a post-doc before I could get a faculty job, perhaps more. There's generally been a shortage of faculty positions opening up, a shortage of grant money, and an oversupply of post-docs trying to get both. No thanks, I'd much rather spend my time on something with a higher probability of working.

So that leaves the corporate/private sector. Now I could easily fit in with a biological lab, I've got over 10 years experience researching biological phenomena. There are a few companies in the KC area where I'd fit in well. But I could also go down the programming road. Good programmers seem to be in demand nowadays, and I'd like to think I've become a good programmer. I've got lots to explore here.

Finally, there's the level at which I'd be entering. I'm no longer an entry-level worker, that much is clear. I have an abundance of experience in the workplace, not to mention my experience with training and supervising others. Kelsey agreed yesterday, stating that it sounds like I'd be a better fit for a more managerial position. Now the question is what does that look like? What does someone with a strong research and programming background do in a "manager" position?

Start of Fall Semester

A bit of an introduction: I'm Michael and I'm starting my 5th year of working towards my Ph.D. in Bioinformatics. My advisor and I are expecting for me defend sometime in the Spring semester. As such I've begun networking, trying to get my name out there for the upcoming job search. Additionally, I've got my first kid on the way, with her appearance coming in mid-November. And on top of that I thought it'd be a good idea to start a blog on my experiences as I approach the end of my academic career and the beginning of my professional career.

Bioinformatics, what is that? Well, it's essentially biology with a computer. Before starting grad school I worked as a research tech in a biochemistry lab. That meant working with living cells, various chemicals, and all sorts of interesting devices, some of which were older than I am. But I've always been attracted to mathematics and programming. Throughout my Ph.D. I've focused on working with computers to explain biological phenomena. My first paper systematically analyzed simple intracellular signaling systems to show how substrates competing for different enzymes could influence each other (Preprint PDF). Since then I've expanded this work to other biological systems.

We're now gearing up for the beginning of the Fall semester; classes start next Monday. The summer has been pretty busy. The bulk of it was grant-writing season for my advisor, Eric. As such I kept out of the way, working on my projects. But the highlight of it, academically, was the q-bio conference in Santa Fe, NM (q-bio stands for "quantitative biology"). That was August 7th-10th. Just before heading down we were rushing around trying to finish up our posters and various travel details. The lab had 3 accepted posters, including mine, and a contributed talk from Eric on my work this year. 

Sangre de Cristo Mountains, the view from St. John's College, where q-bio was held.

Since this was my second time at this conference, I was far more relaxed this year when it came to interacting with others there. I made it a point to sit around people I did not know, introduce myself confidently, and talk science. I met lots of interesting people, such as a physics professor who wrote a mathematics textbook for his graduate students to use and a guy who was interested in doing a post-doc in our department. 

I was scheduled to present my poster on the first night. What made it interesting, as it did last year, was that night, before the poster session, the lab went out to a New Mexican cafe for dinner. Dinner included a lot of green chile and a strong margarita. Tequila and the thinner air of Santa Fe made me kind of warm when the posters began. But once I got into explaining my work I got clear-headed quickly. It was a non-stop science-athon. As soon as I finished explaining my project to one person, which takes quite awhile, I'd get another to step up. After 3+ hours of that I was exhausted.

Me at my poster. And, yes, bowties are cool.

The next day was just as busy. Eric gave his talk on my work that morning. The coolest thing happened immediately after: another professor turned around and told me that my work explained one phenomenon he noticed and he was going to cite my paper in his talk and manuscript. That was exciting. That night Eric and Zaikun, one of my lab mates, gave their posters. I spent much of the time talking with other professors, listening to them talk about their work, and in turn talking about my work and future plans. The rest of the conference got kind of blurry due to exhaustion: there is only so much science I can focus on, and the conference is like drinking from a fire hydrant.

Since getting back, Eric and I have been working hard at getting the paper for this paper put together so we can submit it for publishing. I've also spent some time organizing a dinner for the department so we can meet the new students and our new faculty member. It's becoming more and more of a tradition; Eric started it his first year with a pizza party, and last year we all met at Free State Brewery for dinner. This year we're heading to The Burger Stand, and it looks like we'll have a good complement of students there, plus all of the faculty will probably be there as well. 

But here's the to the start of the new semester and new school year!