Functional genomics in the classroom

I’m currently attending the ASM General Meeting in San Diego, and the first session I attended this morning was titled “Functional Genomics in the Classroom,” which focused on a few case studies aimed at educating “New Biologists” – the next generation of biologists who, among other things, are more specialized in their area of expertise and must consequently excel at collaboration.  These efforts all incorporated actual research into the course design by allowing the students to choose experiments to attempt and working together to execute and interpret.  It seems that functional genomics is especially suited for uniting teaching and research because it is very versatile and can be largely data driven.  This drives costs per student pretty low in comparison to traditional molecular biology studies.

If you’re interested, I’m experimenting with using twitter during the conference, so you can follow my tweets here. Also check out the hashtag for the conference: #asmgm


My experience with wikis for collaboration and teaching: OpenWetWare

It’s been a while since we actually discussed the use of wikis and other collaborative software in teaching, but I thought I’d give a review of my own experience with the format for anyone who’s interested.  A little more than a year ago, our lab began using some of the tools provided by OpenWetWare, an open-access wiki which aims

“to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering. OWW provides a place for labs, individuals, and groups to organize their own information and collaborate with others easily and efficiently. In the process, we hope that OWW will not only lead to greater collaboration between member groups, but also provide a useful information portal to our colleagues, and ultimately the rest of the world.”

Our lab has a page in this system that any of our members can edit that serves as a repository of information for internal use, as well as a resource for anyone else interested in what we do and how we do it.  Overall, the tool is extremely versatile, and we don’t take advantage of everything available, but here’s an overview of the more common uses and my thoughts on how it stacks up for each.

  • Lab webpage – OWW provides a very simple, no-HTML-knowledge-needed interface and hosting service for labs in this field, and allows all members of the lab to be involved in maintaining a public front.  This makes it relatively easy for current research projects to be updated regularly, which means a lot to potential graduate students (at least it did to me).  This also gets everyone in the lab involved in shaping the goals and image of the lab, which joins us as a team and helps our individual development as scientists.
  • Online protocols – Protocols on OWW can be either lab-specific (like these used by our lab) or consensus (like this excellent protocol for Ethanol precipitation of nucleic acids). The consensus protocols are the resource that brought me to OWW in the first place, and the quality of the entries is indeed very good, better in many cases than those on or other similar resources.  From a personal development standpoint, I found it to be a tremendous exercise to post the protocols I use regularly because the threat of peer review causes me to be that much more thorough and to closely consider every step I take for it’s purpose and validity.
  • Course webpages / Teaching – I have a friend in the lab who keeps course materials from a few courses he’s developed under his user page on OWW.  This space serves not only as a public repository for syllabus information, but also as a space for discussions of shared readings and project brainstorming and planning. There is some – although not insurmountable  – technical barrier to entry, and the courses here were relatively small and the students were more tech-savvy than many.  We have both found that, in other cases where users are less comfortable with the medium, there is some hesitation to try it out, and it can be difficult to get students to participate.
  • Open Lab Notebooks – One of the most interesting features on OWW is the Lab Notebook, which does what you’d think, except online and open.  I can’t use this personally because of IP issues, but I love the idea of a similar system on a private server if necessary, if only out of the convenience of having easy organized access to my collaborators’ and my own notes, protocols, and progress readily available and searchable. Aside from this, I think it could be fantastic as a teaching tool.  Online lab notebooks could replace or enhance lab reports in teaching labs where individuals or groups link to that for their grade.  The notebooks can be organized by project, and summaries of each project and the results could replace the traditional lab report.  Because the wiki tracks changes, it would be relatively simple to monitor distribution of work among a group, and the talk page for each project could be a forum for feedback from the instructor or TA.  What I’m describing is essentially what is done by each team as part of iGEM, the undergraduate synthetic biology competition that VCU participated in for the first time last summer.  I’ll have more on this experience and its good and bad in a follow-up post.  In any case, I highly recommend looking over some of the recent notebook entries found on the Lab Notebook link above for ideas about how they are used and organized.

Like any other technology, wikis are not a magic bullet for Instant Student Learning, but it is a pretty powerful medium for online collaboration of all types, and, in the right hands, it could greatly enhance student engagement and encourage meta-level thinking about the content they are presenting to the world.

Is Google to blame for my misconceptions?

We had an interesting discussion last week about how individuals can evaluate the reliability of information on the ever-fluid internet.  After all, if anyone can edit Wikipedia, it might be wrong!

The truth is, though, that every human throughout history has held ultimate responsibility for what they call “True.”  For a long time, we outsourced this decision making to the experts who wrote encyclopedias and newspapers, and, of course, we still often pass on our duty to think for ourselves.  We call this “peer review.”

Of course I’m being facetious, as there’s no way anyone could dedicate the time required to truly investigate every claim they encountered.  At some point you have to trust someone. Still, it’s nothing new that I have to think for myself.  Now, I just have much more information at hand with which I can make a decision.

fictional jimbo wales, you old charmer!

The web-citizen’s new role

In class last week, we discussed some of the implications of the ever-growing abundance of information made available by the internet. In many ways my thoughts echo those of StatGuy and probably countless others who have been asked to memorize pages of information that is a click away.

When information is scarce, it has value, and this is the basis of hundreds of professions throughout history.  Electricians, for example, have been able to charge for their services because they know a great deal more than the average person about how appliances should be wired, what gauge wires are necessary, and which types of switches are appropriate for a given job.  Many educators have taught and continue to teach as if this knowledge is the end goal.  I find this view to be especially prominent in the sciences, where so many lectures are structured like this: “Here is how the circulatory system works; memorize the names of these arteries.”  This is useful information (especially, of course, if you happen to be a medical professional), but, in itself, it’s useful in a very limited way.  If I become an electrician, or a store manager, or an economist, or most any citizen who doesn’t have regular direct contact with the circulatory system, I can forget everything about this lesson, so long as I remember that the information exists, and I can recall enough detail to Google the rest.  With this kind of instant access to information, mere awareness of a concept is almost always enough to “get by”.

Real value in this environment is not derived from the information itself.  The value is derived from the connectivity between concepts.  It’s emergent.  If everyone has instant access to wiring diagrams, online tutorials, and DIY kits from online stores, the electrician stays relevant by staying aware of all of the options available and instantly making the connection between the job at hand and the best and fastest solution.  Likewise, educators can no longer hope to remain relevant by distributing information in tidy packets.  They must be able to efficiently integrate an understanding of the content with pedagogical knowledge.   Furthermore, the content needs to change to reflect this shift in order to prepare students for this new type of role. It’s not enough for them to “know things,” as current testing might have them believe.  They must have the ability to synthesize connections between concepts in order to understand, interpret, and create.

Web presence up in this piece

Jeff’s emphasis in class today on managing your online presence reminded me of a tool I saw recently for aggregating your web identity elegantly and easily.  From Lifehacker: is intended to act as a splash page for your virtual identity, routing viewers towards the aspects of your online persona you want to share. You can pull from over a dozen services including Facebook, Twitter, Flickr, LinkedIn, Tumbl.r, and more.

Click through to Lifehacker’s coverage to see a video of how easy it is to set up, or see some examples of how people are using it at the directory section. Most current users seem to be graphic designers, artists, or consultants of some type, and you could argue that it may not be appropriate for an academic presence, but since the design and layout is up to you, I don’t see why it couldn’t be useful for the more “serious” types.

On the other hand, academia honors and even requires publication of all types, but companies competing for very thin margins in a global economy are less likely to value the benefits of putting lots of information out there.   This is part of the reason why I haven’t used this service or others, and why I’m still deciding whether this blog will develop beyond the scope of GRAD 602.  I’m still exploring the balance between the democratic ideals of open access science and the capitalistic constraints on intellectual property.

The freedom of design

Understand by Design (or UbD, if you’re pressed for time) is an exciting, if somewhat intuitive, approach to course and curriculum design in which planning does not begin until clear goals for understanding are defined.  It seems obvious that this is how teaching and everything else Should Be Done; life and semesters are too short to waste any time without a clear direction.  But this, of course, is missed by all of us at some point.  Things get too busy, responsibilities pile on, and at some point, we have to just do something whether it’s the right thing for our goals or not.    When we are actually able to get it together, it’s amazing how pervasive the benefits of good planning can be:
That’s what I find so exciting about this process: it is so much better for me and the students to be in the middle of a UbD. Everything seems so relaxed, I’m more confident, and the students are very excited. They seem to sense something more at the core of what we’re doing. I suppose they sense the goal: the goal is usually not revealed as completelyand clearly. I know what my students know, I know what they don’tknow, and I know what I need to do. How liberating.
—A teacher reflecting on using UbD [emphasis mine]
The quote above is from the introduction to the book Understanding by Design, which is available for free in e-book format to VCU students through the library catalogue. My wife will gladly tell anyone who will listen that I am not a planner.  I tend to let things roll how they will and run with it, so “freedom” is not something I naturally associate with this kind of structure.  On the other hand I have felt both the regret of time wasted without direction, as well as the freedom that can develop from the confidence that I’ve “done my homework.”  I’m excited to have an opportunity to develop course goals and a suitable curriculum to meet those goals now, as a grad student, before I am faced with additional pressures associated with a new faculty position.

What’s the classroom good for, anyway?

Many in the class seem to agree that the classroom provides some value over entirely remote learning approaches, and many stated advantages are in the area of how well the teacher is able to monitor student engagement (e.g. catch a sleeping or slacking student, detect the end of an attention span, etc.)

In a hypothetical environment where students are more mature – or at least more motivated – and are able to reliably self-police their engagement, to what extent does the value of a classroom meeting diminish?  Some students thrive in personal face-to-face conversation, and this should be encouraged, but video chat and video conference technologies are getting to be remarkably smooth and reliable, and study sessions with other students and the professor or teaching assistants may be more use of time spent together.  Additionally, the internet has made a ton of information available for interested students of any topic.  Wikipedia has a Wikiversity branch in which volunteers put together lesson plans and reading on topics ranging from religion to engineering.  Admittedly, the content currently available is pretty limited, but it is sure to grow, and there are myriad other similarly open resources. I think that a suitably motivated student could self educate to a remarkable level of understanding simply by consuming existing online material, participating in online forums, and even jumping into contributing to wikipedia pages. Oh, if only I could reach such hypothetical maturity! :)

I’m not saying the classroom isn’t valuable.  After all, even internet nerds see the value in meeting often for conferences and symposia.  It’s thrilling to experience the amount of learning that can happen in such a short span when lots of motivated individuals get together in person, but I think it’s a mistake to rest on the classroom as mostly a tool for policing lazy students.