Google Scholar and the literature glut

November 12, 2011

From Clive Thompson of Wired Magazine

We’re often told that young people tend to be the most tech-savvy among us. But just how savvy are they? A group of researchers led by College of Charleston business professor Bing Pan tried to find out. Specifically, Pan wanted to know how skillful young folks are at online search. His team gathered a group of college students and asked them to look up the answers to a handful of questions. Perhaps not surprisingly, the students generally relied on the web pages at the top of Google’s results list.

But Pan pulled a trick: He changed the order of the results for some students. More often than not, those kids went for the bait and also used the (falsely) top-ranked pages. Pan grimly concluded that students aren’t assessing information sources on their own merit—they’re putting too much trust in the machine.

Now I’m a *huge* fan of Google Scholar. When I am writing a paper or grant, Google Scholar, my university library’s page, and my second brain DevonThink  all stand at the ready. This is because I do much of my reading while in the process of writing. Writing exposes the holes in my understanding. So when I go to Google Scholar to find out what’s what, and I get the inevitable list of 3000 entries for, say, “thermal ecology ants”, which ones do I pay attention to?  Read the rest of this entry »


Honestly, it’s not me, it’s you

September 2, 2011

In the “trying a little too hard to become a citation classic” category of title-crafting, it’s hard to surpass Martin Schwartz’s “The importance of stupidity in scientific research“. Regardless, this is a gripping short essay for the grad student feeling just a wee bit overwhelmed. Some key points:

I’d like to suggest that our Ph.D. programs often do students a disservice in two ways. First, I don’t think students are made to understand how hard it is to do research. And how very, very hard it is to do important research.

Yes, very, very, very, hard indeed with the occasional redeeming bits of dizzying fun, yawping pride, and profound satisfaction.

…we don’t do a good enough job of teaching our students how to be productively stupid – that is, if we don’t feel stupid it means we’re not really trying. I’m not talking about ‘relative stupidity’, in which the other students in the class actually read the material, think about it and ace the exam, whereas you don’t. I’m also not talking about bright people who might be working in areas that don’t match their talents. Science involves confronting our ‘absolute stupidity’. That kind of stupidity is an existential fact, inherent in our efforts to push our way into the unknown.

All good points. We must humbly seek out the great unknown, and be prepared to feel a mite confused for years on end.  However just as I would eschew phrases like “comfortably numb” and “passively agressive”, “productively stupid” should at most be a state of mind but not an item from the mission statement of your CV.

But the capper is the best rationalization for the hazing that grad students go through at the hands of the inquisitorial boards we ominously call “your committee”…

Preliminary and thesis exams have the right idea when the faculty committee pushes until the student starts getting the answers wrong or gives up and says, ‘I don’t know’. The point of the exam isn’t to see if the student gets all the answers right. If they do, it’s the faculty who failed the exam. The point is to identify the student’s weaknesses, partly to see where they need to invest some effort and partly to see whether the student’s knowledge fails at a sufficiently high level that they are ready to take on a research project.

Yes, we reduce you to a mass of quivering jelly because we care…too much.

Definitely worth a read.

Why we do science–lamprey repellants

August 27, 2011

Nobody forgets their first gander at the business end of a sea lamprey.  Petromyzon marinus  is a fish that attaches to another fish, rasps out a hole, and sucks out its prey’s  precious bodily fluids. It is impossible not to have mixed feelings when contemplating the sea lamprey.  When you finish admiring the frankly gorgeous, utilitarian design of its mouthparts (Steve Jobs likely holds the patent) it is perfectly natural to give way to a second, more emotional,  “gaaaaaaaaaaaaaaaaahhhhhhhhhh!”.

The sea lamprey is also an invasive species, with nasty consequences for the fisheries of North America’s great lakes.

Thus it was a pleasant surprise this morning, over my second cup of coffee, to discover the following video on Boing Boing. I save Boing Boing–one of the great cultural websites that also likes the odd science story–for my Saturday mornings. Michael Wagner, at Michigan State university, recognizing that aquatic organisms tend to avoid chemicals that convey the message “someone I know was recently eaten here”, created his own “eau de lamprey mort”, and was the subject of the aptly titled MSU press release “Sea lampreys fear the smell of death“.  Enjoy.

On the Five Stages of Proposal Writing

May 24, 2008

I’m preparing to dust off a proposal that was rejected six months ago. It’s a resubmission to the National Science Foundation. In such cases the word submission is particularly apt. When NSF is funding less than 10% of the proposals it receives, one is pretty much resigned to one or more rewrites before you have a chance at funding. And since you often have only one or two chances a year to submit a proposal for 3-5 years of work, well, one doesn’t have to be a whiz on the quantitative side to see proposal writing as a lovely lesson in the brevity of all things mortal.

But I digress.

While dwelling on such things existential it was great to come across FemaleScienceProfessor‘s take on the the process of writing a grant proposal. What emerges is the notion that successful grants have to be in some way transformative, that their writing is not linear but aggregative, that much of it has to do with juggling budgets and filling out forms, and that, when it’s all over (after months of nurturing the baby that you then unceremoniously kick out of the nest), well….I’ll let her do the honors…

And then.. someone in the grants office pushes a button and the proposal is gone. I get an automated email. I am relieved, but there is also a melancholy feeling of emptiness at the departure of the proposal out of my intellectual grasp. What will I do next? I contemplate cleaning my office, but I don’t actually do it.

FSP is a worthwhile blog. Check it out.

See also:

10 steps toward better grant writing

5 ways of dealing with that rejected manuscript

Another GTDA haiku

Five chunks of career advice from Dan Pink

May 3, 2008

Daniel Pink is a keen observer of the changing workplace and its implications for the way we think about, and train for, our careers. His A Whole New Mind describes the challenges and opportunities in the transition from an “information age”-based economy to a “conceptual age”-based economy.

Now, in The Adventures of Johnny Bunko Pink has created a comic full of advice for college graduates as they prepare to enter the world of business. It is a joy to read. The manga illustrations of Rob Ten Pas give one a new appreciation of this art form. It is also meant to be digested in one sitting, and there is enough good stuff that, upon completion, you feel as if you’ve just eaten a tasty bag of nacho cheese Doritos, only to discover they are 0-fat and full of protein.

Get yourself a copy and pass it among your colleagues. It ought to spur some healthy conversation. Below the fold, I translate some of Johnny Bunko’s life lessons to the world of grad school, with a wee bit of commentary. Read the rest of this entry »

One project: one project log

March 26, 2008


Lab scientists are all over the concept of keeping a laboratory notebook. This is your one-stop summary of a given project, from near-conception through publication. We field biologists, not trained at the lab bench (which tends to be conveniently flat and relatively protected from rainstorms, mud, and leeches) often find ourselves compiling the notes and assorted detritus associated with a given project in computer folders, desk drawers, and refrigerators.

Which is not to say that, at the very least, a logbook, or diary, isn’t extraordinarily useful when you find yourself juggling a variety of projects.

My protocol is to open a new file, named “_Log_projectname” in Word or (now) Omni Outliner–any program that allows you to timestamp a given entry.  The “_” at the beginning of the name is an old trick to make sure this file sits at the top of the folder, along with the manuscript files, figures, data files, etc.

Then, whenever you do something substantive on that project, you make a dated entry describing what you did. My rule of thumb?  If you open up the manuscript, work on a figure, add new data, or perform some analysis, that deserves an entry.

As an added bonus, at the end of that entry,  type out a few of the next steps you foresee in turning that project into published manuscript.

Once you have this habit down–opening up, and adding to, a “_Log” file for every project–you can confidently set it aside for a short time to work on something else. When you return, just read the “_Log” file from beginning to end to get yourself back up to speed.

Just don’t wait too long…


5 ways to exercise your analytical chops

February 16, 2008

Creativity is a about freely generating new ideas and culling 99% of them. The end product of creativity is thus new, useful ideas.

One’s quality as a scientist is a product of these two abilities.

Some folks are so hyper-critical of any new idea that nothing leaves their notebook. Even writing a paragraph becomes an excruciating ordeal, as any abstraction is ruthlessly worried and excised.

Some folks fill their notebooks with idea after idea, but end up swallowed up in the thicket unable to commit to any one idea for long (sort of an intellectual ADHD). Consider this post a dose of analytical Ritalin, prescribed by the good Dr. Tufte.

Edward Tufte is someone every beginning scientist should get to know. His Visual Display of Quantitative Information is the best introduction to the theory and practice of effective graphics. His website includes a bulletin board on all topics analytical, graphical, aesthetic, and concrete. The site’s only downside is that it can swallow Friday afternoons whole if you let it.

In short, Tufte is the paragon of GTDA’s guiding principle:

Quality = great content*great design.

Here is the opening salvo (plus my commentary) from his “Advice for effective analytical reasoning.”

Read the rest of this entry »

Will you earn your Ph. D.?

January 20, 2008

images-3.jpegAn interesting post from the political science blog The Monkey Cage. Some folks at Syracuse University looked for the best predictors of graduate student success in their Economics program, using as data the records of their past students.

The upshot: the best predictor of passing comps: your GRE scores, having an M. A. degree, and having an economics major.

However, the best predictors of completing the Ph. D. program were different. They combined something very concrete–a student’s preparation in mathematics, with something far more intangible–the strength of their research motivation, as gleaned from the personal statements in their application to grad school.

My take, for what’s it worth.

In most programs, your written and oral comprehensive exam tests your mastery of a set of material, and, indirectly, the work habits that allow you to teach yourself.

But there is a reason grad school is often described as a process of transformation from someone who reads to someone who is read.

Because the second hurdle is the ability to design, and analyze novel research. This takes a mastery of logic (and mathematics is, at its heart, logical calisthenics) and a stubborn drive to see a project through. Those students who work on mastering the literature, but avoid the often lonely process of designing, collecting, and cranking methodically through data and manuscripts, risk the scarlet ABD of academia–All But Dissertation.

We’ll be spending some time in the upcoming posts working on your analytical chops. But in the meantime, don’t skimp on math. Even if your dissertation never requires matrix algebra or integration and differentiation, studying math trains your mind to think clearly.

On leaving MS Word for cleaner pastures

January 9, 2008

My mini-rant against Microsoft Word prompted reader Sasha to suggest looking into Scrivener. Now wouldn’t you know it, Virginia Heffernen has a nice article on cheesey little website about her move away from the Redmond empire.  It links to a nice essay by Steven Poole on the same topic.

The upshot of both: the process of creative, synthetic writing is largely divorced from the process of formatting mass-produced documents. Our job as academic scientists is not to write memos, but manuscripts. Why not find software that gently removes the distractions, and lets you, and your words, flow?  Read the rest of this entry »

Flowcharts, how do I love thee?

February 25, 2007


I haven’t used flowcharts much in my teaching or research, but this may change soon. First, there is this marvelous mashup of flowcharts with web pages to teach copyright law. Biologists have long used keys to simplify identifying critters, but I can easily imagine using flowcharts to teach, for example, the experimental results that would allow you to identify different kinds of population regulation.

Perhaps the real utility of flowcharts for graduate students may lie in the underused but powerful practice of Strong Inference. SI endorses building a logic tree when planning your research so that each experiment tests as many different hypotheses as possible. The end result is that each experiment produced maximum bang for your research buck. I am seeing more and more flowcharts in the NSF grants I review.

How would you flowchart your dissertation research?

Finally, flowcharts are effective ways of detecting patterns in otherwise seemingly inscrutable behavior.

Read the rest of this entry »