Exactly how independent should your research be?

Anna Mueller, Ph.D.

Anna Mueller, Ph.D., changing study systems

The significance of a Ph.D. degree is that you can do much more than excellent research. You can also think of what questions to ask. You know how to push at the most important unknowns. You can read the literature of a field and see not just what is there, but also what is missing. You can tell which missing pieces are important and which are details. You also have a sense of what is feasible and what is not. If there is a new tool developed in this or another discipline, you are quickly able to apply it in new ways to answer things that were previously unanswerable. You are amazing, at least for that brief well-read time when you are embarking on a specific project, before your days are filled with censusing, pipetting, counting, or whatever other routine tedium comes with actually testing hypotheses.

So how can you become amazing if you do a project handed to you by someone else? If you never need to sink or swim according to what your own intellect has discovered, how can you own a field? If you are a cog in someone else’s research machine, even if you get out all the papers, even if you learn well how to do a complex project, have you really learned what it takes for a degree called Doctor of Philosophy, literally from the Latin, philosophiae doctor? I think not, but it depends on the details.

Jennie Kudzdal-Fick, Ph.D. and glory!

Jennie Kudzdal-Fick, Ph.D. and glory!

What is the optimum balance between independence and guidance? The answer is less clear than you might think. At one extreme you might be a nearly completely independent agent, working in a place, on an organism, and on a question separate from your mentor. He might work on grasshoppers, or butterflies, or even Drosophila, asking questions of speciation, crypsis, or population genetics in South Africa, Costa Rica, or Hawaii while you work on Texas wasps with questions of social behavior. Why would you do this? How will you be gently guided between better and worse approaches? How will you learn new techniques or even know what they might be for your field? How will you fund your research? Honestly, this extreme level of independence makes no sense to me.

Yet a few decades ago it was practically the norm in ecology and evolution. I suppose it was only possible because the techniques were few and cheap and science was booming. Yet this system left a lot of people floundering, often leaving the program before finishing, though I can’t say I have any numbers to indicate that this has changed. Some people still adhere to this extreme independence idea, perhaps to justify their own hands-off mentoring, perhaps because it worked for them.

Owen and Larry Gilbert, Ph.D.s several decades apart.

Owen and Larry Gilbert, Ph.D.s several decades apart.

The other extreme is to be given a project that is very specific. It might be one of the aims of a research proposal an adviser wrote. It might be a gap in what the rest of the lab is doing. It might even be heavy on technique development. Is this a terrible thing? Will it keep you from being a Ph.D. in the full sense of the word? I think it depends on how independently you then approach the question. This kind of project can be excellent. It might be the only kind expensive work in a difficult system allows. After all, you might take three years learning some complex cell biology techniques and approaches. If it is your problem, you can learn what it takes.

So, in my opinion, the problem comes in if you are micro-managed, or not allowed to explore your own solutions to the system, even a very specific one. But too close a project assignment has a risk. The risk is that it might not feel like your own. It might not mesh well with your ever evolving interests. Even if you own it, if you don’t love it, it won’t be optimal.

Where does the balance lie? I like to think it is best to do a project in the general area of your mentor’s interests and expertise. What I like to do is to give a new student our papers and our funded grant proposals and suggest that they find in this rich soil something that entrances. It does not have to be something that we directly proposed, though that would be fine. But it should be directly relevant to our general area of expertise and what the rest of the lab is doing. That way help, sympathy, and collaboration are more likely. If someone wants, we are always happy to suggest two or three things to do for a first project. Then the student can soar on their own, having shepherded a project all the way through.

Once we had a student working on stingless bees, on a project central to our interests for which we had funding. Her work went exceptionally well. She published a series of important papers. But the rest of the lab were working on either wasps or social amoebae, so she did not have a team helping her think about bees. I know she felt a bit isolated, though leaving bees was never what she wanted.

So think hard about the program you choose for graduate school. You need to learn a lot to own a field. Mentors can help, but only if they are neither too restricting nor too hands off. It might seem like a delicate balance, but it is one that is often successfully achieved.

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Choosing a graduate program: only three things matter

It is that wonderful time of year when you have heard where you have been accepted.  You will be told about the hundreds of advantages of the program that is trying to recruit you. Your offer letters most likely have information on how you will be assisted in paying for graduate school, though the points I make here also apply to undergraduate colleges and professional programs. How do you choose? Only three things really matter.

First is finances. You should avoid putting yourself into debt if at all possible. Debt will taint your opportunities once you are done studying. Debt is a burden. Debt is staying up at night wondering how you will afford to take the next step when the previous step is weighing you down. Debt cripples your choices. What exactly did you expect to get with that expensive degree? Was that program really better than the one that offered you funding you could live on? The point of this stage is not to profit from studying, just not to have it  hijack the rest of your life. So choose a program that offers clear funding, unless you are one of the very rare for whom money is not an issue.

Second most important is to surround yourself with smart people. Programs with smart people will have you thinking in ways you could hardly imagine before. There are lots of ways of being smart and lots of programs with smart people. In these programs questioning will be encouraged. Exploration will be a team process, with “what if” being an exciting challenge. Smart people are interested in ideas and will talk about the papers they just read, or the talks they heard. I was formed by the smart people, faculty and students, at my own universities, Michigan in Ann Arbor and Texas in Austin. I continued to learn and discover from smart people at meetings from all over the world and at the universities where I have been employed, Rice and Washington University.

Seek out the smart people wherever you are, for they will delight and challenge, though also sometimes annoy. There are smart people in every university and college, but they are more concentrated and more free to discover in some places than others. If you wonder whether your prospective program has smart people, look at their funding. It should be from curiosity driven funding agencies like NSF or NIH in large part. The funding should not be from outfits demanding very specific answers to small problems. It should not be mostly contracts. This is advice my own undergraduate adviser gave me many years ago when I was choosing a graduate program.

There is probably a level above which smartness no longer is a variable that has an impact. I would guess the top 50 or so programs in any field have plenty of smart people to challenge you. They will vary more in the third important component important for your decision.

Third most important is that you should choose a program that reflects your interests. At this level it is not true that all programs do all things. The world experts in something you love may not be at the program that is top rated by US News and World Report, or by any other rating program. At this level the name of the university has little bearing on whether it is a good fit for you. Even if your interests are not very well defined, they are likely to be defined enough for you to see that some universities are much stronger than others in the area of your interests.

That’s it, funding, smart people, and a program that is a good fit. If your offers differ in these variables, your choice should be easy. If they do not vary in these, then other things might influence you. Probably tops for these are collegiality and productivity. Smart people all around do no good to you if there is no time to talk to them, if all are holed up and on their own desperate paths to glory. Your ability to take the next step will be influenced by your productivity in papers and grants, so you should find a program where publishing and grant writing by graduate students is encouraged, assisted, and viewed as normal.

You’re about to embark on a wonderful phase of life, the Ph.D., 3 year or 7 year, or something in between. It is a time when ideas are important, when experiments enthrall, and you’ll make friends for life. Choose and enjoy.


Posted in Graduate school, Undergraduates | Tagged , , | 1 Comment

No, you can’t acknowledge me in your paper without asking!

Most scientific papers have a brief acknowledgements section where people who helped in some small way with the study are mentioned. It used to be the place where the technicians, often female, who might have done all the work were credited. Now these people get authorship.

Perhaps the most usual kind of assistance is reading the paper after it is complete and making comments that improve the paper. A key suggestion or help with a technique might also get someone a mention in the acknowledgements section.

No unauthorized acknowledgements!


The acknowledgements section is also a place to credit funding sources.

Some journals require that everyone mentioned in the acknowledgements section authorize the mention. Even without that requirement, most authors check with the people they are going to mention.

So imagine my surprise when a friend told me I was acknowledged in a recent paper in Nature by Jonathan Pruitt and Charles Goodnight. I said no, it could not be. I had not even read that paper yet and certainly had not seen it before it was published. Moreover, I had seen both authors recently and neither one mentioned it.

But of course my friend was right. This is what the paper says: “J. E. Strassmann and W. P. Carson were invaluable in aiding in the submission of this paper.” What does that even mean? It kind of sounds like I have the secret password to Nature, or that I greased the wheels somehow. I didn’t. Am I being acknowledged for some random conversation about publishing, or for something in this blog? Is putting my name in the acknowledgements some indication that I had an opinion on the paper? I might, but not before I read it, or even know of its existence. I have no idea how W. P. Carson contributed either.

No unauthorized acknowledgements!

I don’t understand why anyone would do this, but it is a really bad idea. Check with the people you acknowledge and be sure they are all right with it. Only acknowledge people who actually have helped with the work.


Posted in Publishing your work, Scientific community, Writing | 13 Comments

Why you won’t learn to write from Steven Pinker’s The sense of style

I think Pinker is just the best. I love his writing. I love his perspective. I love the way he takes on complex and often controversial topics and finds convincing clarity. I think I’ve read all his books. So when I saw he had a new one, The Sense of Style, I bought it. Maybe I could learn to write as effectively as he does if I read it carefully.

It sat on my night table for a few weeks, so I got it on Audible to listen to instead.  I got through a lot of it on a long drive to Fayetteville Arkansas. I loved it.

The first three chapters should be required reading for everyone. The first two make a  case for clear writing. They also show what’s clear and simple and what’s complex and confusing. They poke a bit of fun at the writing bible too, Strunk and White’s The Elements of Style. In many ways they are Pinker at his best. He is strong and opinionated but never pedantic. He points to authority as a reason to do things, except when he disagrees. These are themes throughout the book, especially in the more technical later chapters.

The third chapter is something I could just kiss, if I still relied on the paper copy. My reaction to it was similar to that of my then five year old when I told him I was reading a book called “Bad guys don’t have birthdays.” I could have written it myself, if only I could write as well as Pinker does. In this chapter Pinker begs us to think about what our readers know. Give us some background, don’t just launch into a story as if we lived like little parasites inside your brain. Don’t be like the three year old I met decades ago who told me we could play together when I got to his house, the white one in Illinois.

The chapter is called “The curse of knowledge,” and is subtitled “The main cause of incomprehensible prose is the difficulty of imagining what it is like for someone else not to know what you know.” How true. I wish there were a magic drug I could give all my students that would make them step back after writing and think about what they can add to frame the piece. This could be small things like putting their last name first in the file name, so the professor doesn’t get a pile of papers named “Assignment 1.” Or it could be as complicated as an introductory paragraph on what big question their experiment is addressing and what progress they have previously made. But really, taking a reader’s perspective should permeate writing. It should impact every sentence.

These first three chapters are worth the price of the book, but this is no reason to stop reading on page 76. The last chapter is a lot of fun too. I just listened to a read version of Pinker’s long table on incorrect interpretations of words, the place where he says he gets to be a purist. I agree with Pinker on nearly everything. I guess that means we are both Americans of a certain age who probably like to read similar kinds of books. Or maybe it means something more, that this is really the best way to write clearly if you want to reach an educated audience.

If I so love this book, why don’t I think it will teach you to write more clearly? It is because you can’t learn to write by learning a bunch of rules, or memorizing correct usage of words. Why, you can’t even seem to learn to correct certain consistent writing errors when I correct them directly on your paper. Next time you write for me, there they are again, cropping up like lamb’s quarters in a recently tilled garden. If my comments right on your paper make no difference, how could Pinker’s necessarily much more general book ever reach you? I don’t think it can, unless you are nearly there already and just use it to firm up things you already knew.

Does this mean there is no hope for either teaching writing or learning to write more clearly? No. It just means that the only way to learn to write is to write. And read. Play with your words. Try out different sentences that say the same thing. See what is simple and what is hard. Read your writing out loud. Read everything you can get your hands on. Write every day. Even just half an hour can help.

I suppose if it were Daniel Kahneman writing about writing, he would say that system 1 is largely in charge of writing, while comments on writing address system 2. System 1 is that innate system, the spontaneous response to things we call auto pilot, or knee jerk reactions. We do it without thinking. System 2 is much harder, covers reasoned responses and shuts down when we are tired or stressed. Writing is essentially speech and we just can’t think out every sentence without going crazy.

So the challenge of writing well is to get it into system 1. I think the only way to do that is to write a lot, to read a lot, to have correct language be your default. Reading Pinker should be part of that reading.

Posted in Writing | Tagged , , , , , , , | 1 Comment

Don’t you hate Blackboard for managing courses?

Last September in the same email we got told both that our university had just signed a three-year contract with Blackboard and we got asked what we thought of Blackboard. Doesn’t that seem backward to you? Clearly they don’t really care about our opinion since they signed the contract first.

Frankly, I hate Blackboard. It is clunky, old fashioned, difficult  to manage, and screws up a lot of things really easily. Lots of other universities are switching to a platform called Canvas, which looks a lot more intuitive and easy to use. Why even our own medical campus is trying it out. University of Texas announced the transition to Canvas a couple of years ago. I haven’t tried it, so I don’t know, but I do know Blackboard is a pain.

So why has Wash U stuck with Blackboard, even signing a three year contract as Blackboard falls off the cliff of market share at the best universities? Is there someone at Wash U that wants to force us to stick with it? Some group that has invested in it in some way? I don’t know, but this is really frustrating. Why just look at all these instructions for students to use specific things on Blackboard! Isn’t there something easier?

I would venture to say that any time you get asked your opinion about something they have already signed a three year contract on, you can guess they don’t actually care about your opinion if it is negative. Maybe they are post hoc searching for support. What other old-fashioned ways of doing things are we being forced to stick to without even realizing it?

Posted in Politics, Teaching | Tagged , , , | 2 Comments

Let need, not ego, matter for allocating research space

Remember your first bench? Was it a place to dump field gear? Was it 6 feet of black magic with shelves above for carefully labeled and dated orange-capped bottles? Did you line up your vortexer with your pipetteman rack? Did you paper it over, or leave it gleaming? When you became a PI how many of those benches did you get in your new space? Did you share? How does space get allocated anyway?

A friend moved his research lab three times in about ten years at the same institution. The moves were to different floors of a huge building and brought him into contact with new neighbors. This intellectual stirring might have its own advantages, but what about the disruptive costs? I recall him telling of some experiments that took months to work after a move. We had similar issues with the more drastic move two states away.

Why did my friend have to move so often? It was because he is in a medical school where space was allocated strictly by grant dollars. Instead of shredding his space into tiny disjunct labs, like a farmer with too many heirs, they moved the whole thing as his funding soared. But dollars per square foot is not the only way to determine space.

Number of people makes a lot of sense as a determiner of space. After all, doesn’t each person need their own bench? Our own department is asking about people as we plan for expanding numbers but not space. But even this is not an unambiguous metric. What if you are at the bench only 20% of your work week? Could you share then?

Some research takes more space. In our lab, for example, we often have every surface covered with Petri plates because stacking them more than three or four changes their characteristics. There are certainly other solutions to this problem, but some research really does take up more space even for a given number of dollars or people.

We could allocate space according to age, or according to power or fame. After all, don’t younger people need more space because they have growing careers and have not yet learned to be efficient? But however we allocate benches and walls, us status sensitive humans will interpret it as an indication of rank. How much less space could we make do with if we could somehow break its connection to power?

If we break the tie between space and status, then we don’t need to worry so much about exactly how it is assigned, because it isn’t handed out at all. One popular solution is the open laboratory, with multiple group leaders sharing contiguous space, adding or subtracting fluidly. This can work if the people working in the shared space are not slobs. It can also be a disaster.

I will be controversial if I say most people can probably do with less space, even much less space. After all, many of our tools are miniature versions of their former selves. We share many core facilities also. Where we think, write, and read should not be in the research lab because that space may be hazardous and is certainly more expensive. Just try to remember that your space is not an indicator of your worth. Innovate by being small, not large!

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How to transform research in your field – does Rockefeller University have the answer?

Imagine you have a decade or so to transform research in your field. What would you do? Would you stop doing whatever you are doing to do things differently? What is a transformation anyway? I am thinking about this because apparently a transformation is what Rockefeller University expects of its faculty. It is a 12 year requirement for junior faculty to become permanent, or so I was told.

I like the idea of a goal like this because it is big and will require that you think hard about central questions, but most of all I like it because it recognizes the social nature of science. If you and your work doesn’t change what other people do, then it is simply not transformative. So don’t find a little niche and work in it if it doesn’t have more general implications. Change the field. Ideas, techniques, and discoveries can change fields. Behavioral ecology was transformed by the discovery of how common it was for monogamous looking songbirds to mate with strangers. Social insect studies were transformed by inclusive fitness theory and by measures of genetic relatedness. Behavioral studies have not been transformed as much as they should have been by the increasing understanding of how much parasites and diseases control behavior. Transformations from techniques are everywhere, from new microscopy to genomes, to better statistics. Well, I could go on about big ideas that entrance me, but the question is how can you do this?

Reading and fiddling around with something you like are great ways to start. There is a feedback between doing something, whether it be in the lab or field, or even with pencil and paper, and reading what others have done. Take advantage of this, even if the fiddling seems to lead nowhere and the reading is overwhelming. Then pick something ambitious and stick with it. Don’t flit from one thing to another, rounding out corners or plucking the elusive low hanging fruit.

How to do these big things is not so mysterious. Take the theory from one area and apply it to another. Become the world expert on one group of organisms, testing all theories that are important to them. Tweak a known technique and scale it up to reach new insights. Collaborate. Develop something new even if it takes years.

Then sell your work. Don’t wait for others to discover it. Write reviews. Give talks. Take on collaborators and help others. Be flexible and change if needed, but always push for the big ideas.

What have I done that is so important? I suppose I began by getting to know two species of wasps extremely well, so I could test theories derived from kin selection. I found a great life-long collaborator which made everything easier and more fun. We did a lot of work with DNA microsatellites to estimate genetic relatedness in wasps and stingless bees. I succeeded in finding lots of variable microsatellite loci because I learned this new technique and scaled up to work with hundreds of loci, easily discarding the difficult ones because I had others. More recently we brought theories of social evolution to the cell and molecular biologists working on social amoebae, particularly Dictyostelium discoideum. Now we are developing this as a lovely and tiny system for studying mutualism, farming, and eukaryote-bacteria interactions. We are redefining what an organism really is. At every step we have had a great set of collaborators. Well, you get the idea. What does your list look like?

The people we met with at Rockefeller University clearly get the transformational challenge. Daniel Kronauer has taken one of the genetically odd ant species that are clonal and yet have key features like other army ants of activity and stasis. He has geared up to  collect data on hundreds of colonies in completely automated ways. Along with new genetic systems and experiments, this could be come the system to look at ant cooperation.

Fernando Nottebohm  is writing about the very biggest ideas and discoveries, a step above his specific work on bird song and why some bird species can always learn new songs and others fixate on the songs of their youth.

Joel Cohen told us about Taylor’s law and how he was curious about how it behaved in mid range, discovering that it had a singularity, not a simple relationship. Interestingly, this could only be seen in simulations if the populations were very large, something an early referee missed.

Winrich Freiwald pulled out his computer and showed us how neurons in the brain fired for faces and not other things, some for frontal, others for profiles. I wonder how long it will be before we know what every neuron in the brain does, just as we know the origin of every cell in some nematodes.

Alexander Tomasz flattered us by printing out our CVs and searching for common ground, finding it most strongly in a paper he wrote nearly 50 years ago on the importance of bacterial cell concentration and cell competence (their ability to take up DNA from the environment). I was also interested in his more recent work on infectivity of specific cells in a lineage.

Last in our line up was Cori Bargmann who enticed us by asking for help designing an experiment. It was no surprise she knew exactly what she was doing, though she considered the experiment outside her main area.

Many of these people had nice views of the East River, not really a river, of course. Was it Winrich or Joel that pointed out that the direction of flow was about to change with the tide?

The group was clearly enriched for multinationality and for left-handedness, but these are not the only ways to get to creative fearlessness. We met with grad students and post-docs, talking more about the process of science than their specific results. Be brave and outrageous, I told them, imagining that they are the best of the best, with no need to worry so much about dismal hiring rates. After all, I imagine this innovative place, lacking the petty divisions of departments, will help them blossom into coveted young professors.

So think big, be transformative, and keep your eyes open for the unspecified area job ads for positions at Rockefeller.

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