Saturday, December 25, 2010

The iPad for a Professor- Why I Love It

It's been interesting to watch FaceBook today- MANY of my FaceBook friends got iPads for Christmas, and a decent number got somewhat similar items (e.g., Kindles, Nooks). Not too surprising given the iPad was originally released in April of this year. I got my iPad in early October. Even though I don't use a Mac, I love it- not just as the "new techy trendy toy" (which I fully acknowledge it is that too!) but as a functional part of my work and play. Let me say upfront- I don't think iPads are for everyone. It's neither a laptop replacement nor a smartphone replacement, and yes, no one "needs" to have one- we all got by last year without them. But here's how I use mine and why I like it, primarily in the context of my job.


I use my iPad for many kinds of presentations, ranging from classes to invited talks, and it works fine (just need that ~$30 VGA adapter). If you want full animations like from a laptop's PowerPoint, the "Keynote" app works pretty well and can import PowerPoint files created on your computer. A few graphics or word sizes may need minor tweaks after importing, but the tweaks are fast, and the iPad is far lighter and subtler (literally looks like a leather-covered notebook in the folder I use) to carry to your talk than a laptop.

Personally, I favor the "2Screens" app over Keynote. This app leverages something that's harder to do on a laptop: you can actually use the tablet nature of your iPad. It will present PowerPoint, Keynote, or pdf files as well (albeit without animation), but you can also "draw" directly on your presentation (using finger or stylus). So, when presenting a Punnett's square, your original file can be just the blank square, and you can manually draw in various combinations during the talk, like from an overhead projector. Or you can temporarily make a blank screen for drawing and come back to where you left off in your PowerPoint. Plus, you can save right then and there what you drew. These are features I intend to use a lot when teaching genetics next year. Further, if you want to show something off a webpage, the "Expedition VGA browser" app works great, and you can switch between it and 2Screens in under a second.


I take my iPad to seminars I attend to take notes, just like a lot of people do with paper pads/ notebooks. One advantage I have is that I can insert things into my notes wherever I want- something that wasn't clear may become clear later in the talk, and I can edit what I wrote earlier on the spot (rather than scribbling in tiny writing in the margins). Here's the bigger advantage for me- if I have a question, I sometimes Google it right there in the seminar and find the answer (or find why the question isn't even appropriate, saving myself from looking dumb). Sure, you could do all that with a laptop, but few people take laptops to seminars since they're clunky and the typing is noisier.

If using the "Notes" app, you can have it sync with your GMail, and it automatically saves everything in a GMail folder called "Notes." Months or years later, you can search your account to find which seminar talked about X topic that you vaguely remember- something not possible with a paper pad.


I take my iPad to all sorts of committee meetings- student committees, university committees, etc. For student meetings, I save the student's progress report in the "GoodReader" app right when they e-mail it to me. The night before the meeting, sometimes while reclining in bed, I'll read the committee report, make notes (you can add notes, highlight, whatever, and if you want, export the pdf), etc. Then, at the meeting, I have the document sitting there with my comments in the iPad. If a question comes up at the meeting, or someone vaguely remembers a relevant figure from a publication, we can pull the publication up right then and there in the meeting using "Safari" (the default web browser).

For university committees, documents tend to be saved in Blackboard, and the "Blackboard" app (finally upgraded this month to be allowed to run in the background) is very fast and efficient. Again, I tend to take notes in the "Notes" app.

Somedays, I find that the only time I have to deal with some urgent work-related e-mails is while walking between meetings (or in the 2 minute break between consecutive meetings), and the iPad gives me a reasonable platform with which to do this using "Mail" or the "GMail" apps.


I have learned to read pdfs of publications now using "GoodReader", as mentioned before for committee reports. I don't tend to keep these files permanently (since I can always download them again), but I like going through them on GoodReader, annotating them, and keeping them on the iPad through the "journal club" or whatever other discussion. If I did want to keep the files longer-term, it'd be trivial to e-mail or download them (yes, with annotations) to save on my actual computer.

But life isn't all work. Often, in the evenings, my wife and I will watch a TV episode on the "ABC Player" app, or stream something from "Netflix." Yes, we could do this on a laptop, but laptops are hot and bulky to keep with us while reclining in bed. At mealtimes, I've looked up recipes on "AllRecipes"- even some slightly more obscure things (tonight I looked up "eggplant with garlic sauce") are in there. If I'm bored, I'll read the news on the "CNN", "BBC News", or "NPR" apps, or weather on the "The Weather Channel MAX" app, all of which are really slick on the iPad.


Keep in mind that the iPad will run all the iPhone apps, too, including thousands of games and utilities. Personally, I use "Alarm Clock", "Skype", "WorldMate", etc. when traveling, and I occasionally pull up "DukeMobile" here in Durham to check bus routes, balance on my DukeCard, or whatnot. I meet with people in my research team every week, and our meeting agendas are in Google Docs, which is super-easy to pull up, view, and edit on an iPad (either from Safari or directly from the "Google Mobile" app). If you're helping someone remotely (like a parent) troubleshoot problems on their computer, "TeamViewer" will allow you to see what's on their screen and help them fix it (though they have to install it, too, but it's free for you and for them).

And, of course, it's also a giant iPod, so save your music, movies, podcasts, etc., to watch/ listen.


The iPad is not a laptop or desktop computer replacement. You can buy the "Pages" word processor and edit Word-style documents, but it'll not be as quick/ comfortable as doing so on your computer. You won't want to do any significant table editing or statistics on your iPad either.

Nor is the iPad a smartphone replacement. I can't imagine carrying that big thing while walking around a town and trying to use the "Map" app to find where to go. I wouldn't want to use the many coupon apps on it, since again, it's big and bulky, whereas my iPhone fits in my pocket or holster really nicely. And I definitely wouldn't want to pay a data plan for it.

It doesn't have flash. Yes, I wish it did. But it's no tragedy that it doesn't for my uses. It just slightly limits the videos I can watch from the web on it, all of which I can see on my desktop or laptop anyway. Nor does it have a camera, but again, my smartphone does. The iPad doesn't do "everything".

And there are "competitor" products. Personally, I think none of the ones out right now are serious competition given the number and quality of apps available for the iPad. That may change in 1-2 years, but this was not meant to be a purchase to last forever. Computers are often nearly obsolete in under 4 years, and I expect similar for devices like the iPad.


Still, the iPad is lighter than most laptops but with a bigger screen/ keypad than a smartphone, and does a lot of the functions of both along with a few of its own. It's extraordinarily simple to use. The battery is great- lasts far, far longer than my laptop battery. It boots up from off in under 30 seconds or from standby in 2 seconds. It switches very quickly and easily from "portrait" to "landscape" view. It doesn't get very hot when running even for a very long time (though that may be the leather case insulating it).

Although people made fun of the name a lot when it first came out, for me, the only thing it totally replaced is a "pad" of paper that I would carry around (though I do now use my laptop less, too).

Do I "need" an iPad? No. I got by fine before I had one. However, does it enhance my ability to work and play more efficiently (or with greater enjoyment)? Weigh that question against the cost, and you can decide for yourself. For me, the answer was, and still is, yes.

PS- And no, I didn't write this blog entry on my iPad. :-)

Thursday, December 23, 2010

Is our grant peer-review system the "best of all evils"?

'Tis the season. No, not that one- like every year at this time (and two other times each year- once in May and once in September), many of us get a stack of grant proposals to review. I just got my stack yesterday and haven't glanced at them yet. For those of you outside the science research community, researchers spend months preparing these proposals (12-15 pages in length, plus several more pages of budget, resume, and other nuances). They agonize over minutia like whether to cite X or Y paper, whether to talk about contingency plans in detail or to present an air of confidence in the approach, whether to present the fine experimental details or save space for more justification on the value of the study to the field, etc.

After these months of work, three or more other anonymous scientists ("reviewers"/ "panelists") read over the proposals- rarely spending more than a few hours on any one in particular (and frighteningly sometimes less). They write a critique- strengths and weaknesses of the work (kudos to NIH for forcing reviewers to actually mention the strengths). The work is discussed in a meeting with ~20 other scientists who have not read the proposal. And finally, it's given a score. Then, in large part using that score, the funding agency decides whether to fund the research or not. Odds of funding are around 10% (don't nitpick- this is close enough).

Most of the ones I read are from people like me- university professors. So, my question is this- is this really a good use of our time? And if not, is there a viable alternative, or is this "the best of all evils"? Let's think of how many person-hours are used in proposal preparation and proposal review. Some of it is definitely worthwhile- forcing the scientist to carefully plan his/ her research and think of what would be the highest impact rather than status quo. The presentations often help guide the subsequent publications in thoughtful ways. Similarly, reviewers benefit by getting a broader view of the field and what kinds of research people are doing.

But there are downsides, even beyond the time commitments of all the parties involved. We all know a few outstanding scientists who seem incapable of writing decent proposals for many different reasons. We also all know that there are some who are great "salespeople" but may be lacking on scientific follow-through or rigor. The present system strongly favors the latter over the former. There's also a general "risk aversion" that comes across in peer review, despite extensive efforts by funding agencies to prevent this. But, if only ~10% of proposed research will be funded (for reference, in a two-day grant review meeting, this may be ~6 proposals), reviewers sometimes have a hard time suggesting that something that "would be very cool but might not work" get funded over something that "would be kind-of cool but will for-sure work." Peer review is also far from perfect- many good proposals get sunk because a reviewer misunderstood something or had a different perspective on what is useful than the proposer. Finally, and frighteningly, university promotion and tenure decisions often seriously consider funding success- seeing it as a quick surrogate to how the community views one's research.

Scientific publishing has gone through major revolutions in the past decade, first with a push for "open-access", and more recently a decision that the merits of science should be sometimes judged historically (the essence of PLoS One): all work that is scientifically valid should be published and history will decide what was most useful. Obviously, public funds (remember- the public funds all this with taxes!) are more precious than whether something is published or not, so a direct analogy is not possible. But is there another way? Or is this really the best of all evils?

Wednesday, December 8, 2010

What's the next "big thing" in evolution?

This is the type of question people ask all the time. Indeed, our Monday seminar speaker asked my opinion on this question in our one-on-one meeting. I'd be curious what some of you folks think. I gave a talk on this, specifically with respect to speciation (my research focus), at the Linnean Society of London last September.

Immature subfields thrive on dichotomies, and then they mature with realization that there are always exceptions to the "rules" (if "rules" even existed). For my evolution colleagues, think about these classic or even recent dichotomies- classical or balanced school? Does natural selection or genetic drift shape DNA sequence variation? Did species evolve via sympatric speciation or allopatric speciation? Is divergence driven by regulatory changes or amino acid coding changes? Case studies always come up to show "at least one" case of the putatively rarer type.

We then grow a little bit to ask about "relative frequencies." The question is sometimes then reworded slightly to "which is more important", but even that's a can of worms- is "rare" equivalent to "unimportant"? Surely not. Does it really make us rethink things if one happens 80% of the time vs. 20%? Or even 95% vs 5%? (I might concede 99.99% vs. 0.01%.)

Further maturation sometimes goes to, "What are the conditions that favor X over Y?" or "In what species/ types of genes/ networks/ whatever do we see X being more abundant than Y, and what does that tell us about their differences or trajectory?" thus changing the discussion from pattern-based to process-based. However, although these questions are more mature, they rarely grace the top "magazines" (Science and Nature) in which we often strive to publish. Instead, the magazines favor the primitive dichotomies, especially when the underdog theory can be demonstrated. A few years ago, an editor from Science magazine asked me what she should seek out. My answer was, "I don't know, but please DON'T publish another marginally stronger proposed case of sympatric speciation." (They actually did, the next year.)

Obviously, I'm overgeneralizing. There have been many very interesting observations in evolutionary biology that didn't fall into the dichotomization trap or follow the path I described. Elegant models have been developed and later strongly supported or conclusively falsified. And Nature and Science do sometimes publish "mature" results. But what IS the next big thing? Personally, I am skeptical it would be "an extended synthesis", as some have argued. I also doubt it's obvious in other recent "buzz-topics", like "evolutionary medicine" (which is useful but I don't see it as a paradigm change).

So, what is it? Thoughts?

Thursday, December 2, 2010

Science and the public

On the one hand, I'm fuming over the Majority Leader-Elect's website asking for "citizen review"of National Science Foundation grants based on the abstracts online. Presumably this will be used as an excuse to cut NSF funding by a commensurate amount. All researchers like myself who work on topics to which the public can be uninformedly "reactive" (e.g., evolution, sexual reproduction, species formation) are obviously shocked and worried.

On the other, while not dwelling on the obvious deficiencies (being generous) of this idea, let me put out a thought for comment/ discussion. Do we, as scientists, do enough to inform the broader public about the importance of our research, or scientific research in general? The NSF and NIH ask that we have a short "public relevance" statement in our grant proposals, but I know that many of us put little or no energy on this statement (and frequently leave it as a few sentences packed with impenetrable jargon, possibly ending with "including humans"). Obviously, scientists are not a uniform group- some spend a ton of time speaking in public forums and are otherwise engaged with their local or national communities. However, my uninformed guess is that such scientists are in the minority- many of us rarely escape the ivory tower, and some even get resentful at having to justify "valuable basic research" to the "lay public" or even to colleagues doing applied research.

Similarly, we often complain bitterly when school board members take stances against ideas we know to be true. But how often do we present those facts "we know to be true" to the broader public, hence educating well-intentioned but misguided school board members? Heck, how often do we even vote in school board elections, except when reacting to a crisis?

We know science. We know it darn well. Politicians and school board members don't know it nearly as well, and it's unreasonable to think that they would. We can say they should just leave us alone, but they won't (and shouldn't)- their, and everyone's, tax dollars fund the science that we do. It's incumbent on us, those who know science, to make the impact of science far more clear to the public. We can do this through: 1) taking those "public relevance" statements in our grant proposals far more seriously, 2) maintaining websites that actually explain what we do and why anyone should care, 3) being pro-active in reaching out to schools and public presentation forums to provide resources & lectures, 4) becoming engaged in our community through informed voting and writing to politicians, and 5) many, many more possibilities. Yes, our time is limited, and academic scientists often work 50-60 hour weeks already. But we have to do it, and there are resources to help us (here's the plug for our university science writer, especially if as great as ours here at Duke!). Irrespective, we can expect a lot more misguided (again, being very generous) proposals like this one to cut funding to research. Let's just put some effort at minimizing their impact.

Thoughts? Comments?

Monday, November 29, 2010

Crazy idea for revamping the PhD program...

We still run Biology PhD programs basically the same way people did 20-30 years ago. Professors offer graduate classes in their areas of specialty, often formatted not terribly different from advanced undergraduate classes. Students very often struggle to find graduate classes in which they're interested either to fulfill a requirement or to learn SOMETHING besides what they're doing in lab. The efficacy of these classes, especially those "concept-centered", is often low... the students "learn" a lot the same way they did in undergrad, where a ton is covered of which very little is directly relevant to them, and the portion that was relevant would have been picked up anyway through independent reading. Meanwhile, we largely fail to train PhD students at skills or concepts they will actually need: 1) grant-writing (there's an exception with one class here at Duke), 2) what it really takes to run a lab, 3) developing and giving lectures in a class, 4) outreach and speaking to the public, 5) career options besides becoming a clone of their PhD advisor.

Why? Because we (faculty) are lazy is why- if it worked for us, it's "good enough." I'm currently floating a proposal with various folks in Duke Biology for a three year "PhD roadmap" that I'd love to get feedback on. Here's the outline. The objectives were to come up with a roadmap that would do all this while not being overly onerous or annoying to the students or faculty. In this vision, all pieces could be "optional", but this overall plan would be laid out as a suggested roadmap- with the exception of the year 1 spring class (for which we'd need the full cohort to participate for it to work).

Year 1-

Fall: A) Take "tools" coursework (e.g., statistics, programming, Matlab)

B) Take “tutorial” course(s) based on interests rather than the usual concept-courses. We'd ask in-residence faculty to set aside time to do a course or two wherein they just meet with 2-5 students every week (or every 2 weeks) for an hour or two to talk about papers in an area of mutual agreement. Basically, PhD students take the initiative to tell faculty what they want to learn/ cover, identify faculty with that expertise, and then
meet with them in small groups to cover that material informally through directed readings and discussions (NOT PowerPoint lectures!). Ideally, it would be mutually beneficial, as the faculty member could use it as impetus to read some of the papers in a stack on their desk (or virtual stack in their RSS feed reader)

C) Take Bio307 Grad School 101 course (half-semester, 1 hr/ week).

Spring: A) Student-driven journal club/ presentations (presentation dates organized in fall). This course would meet twice a week: Tuesdays are class-like presentation by student on a contentious topic of their choosing (graded by peers on clarity, comprehensiveness, etc., of their presentation
), and Thursdays, students read and discuss a recent paper relevant to Tuesday's class. The student's temporary advisor would attend to give feedback, answer questions which the student doesn't know, etc., but the student is giving the presentations.
The purposes of this class are: have students intensely research something IN WHICH THEY'RE INTERESTED and then present it (no better way to know a subject); real lecture-style presentation experience; NSF pre-doctoral fellowship preparation before year 2; increasing self-sufficiency.
It'd be required, but very low effort except that which hopefully they're very interested. There'd be no tests- if it's not your presentation week, you just show up, listen, and provide feedback/ discuss.

B) Can also take more tutorial courses based on interest.

Year 2-

Fall: A) outreach activity on topic of interest: must reach people outside college/ university setting (K-12 activity/ presentation, or public presentation, or something else). Use creativity, and present something in a way people not in the field (e.g., your grandmother) will understand.

B) Can also take more tutorial courses based on interest.

Spring: grant-preparation class, like that currently offered in UPGG? Good timing for DDIG or NRSA prep, since due in fall of year 3.

Year 3- Fall and Spring: A) Each semester, student identifies a "mentor" besides their advisor and meets with them for an hour every other week to talk about the job and maybe "witness" parts. This type of mentorship currently happens in J Reynolds' class on college teaching. Preferably, one of two semesters, student identifies someone NOT in the department to take on this role (med school, teaching position, industry, government, etc).

B) Take Bio308 course on career options (good place to find people who could be mentors, half-semester, 1 hr/ week)

What's with this whole blogging thing?

So, I post all the time on Yelp about local restaurants. I occasionally post on other blogs about science or academic procedures (e.g., in various PLoS sites). Is there interest in a merger of the two, and is there more generally benefit or interest in having such a blog? I'll play with this for a while and see if there's interest, cross-posting on FaceBook since there's already a group seeing what's there. Comments/ thoughts/ suggestions from bloggers or blog-watchers welcome!!! (Especially as to whether to do this such that it can be seen by the >250 students in my class next semester...)