Bench Press

Because many science bloggers are practicing scientists or experts in their field, they can provide a unique educational bridge between academia and the public and distill important experimental findings into an accessible, interactive format. Yet academic institutions have been slow to appreciate blogs as valuable mediums for facilitating scholarly discussion, illustrated by the lack of institutional blogs or blogs by established academics. It is true that few quality-control or vetting mechanisms exist to help readers evaluate a blog, which typically earns its reputation based on the blogger’s credentials and reader feedback. Yet both academic institutions and blogs aim to engage and educate the public and advance scientific knowledge and discussion. By combining the credibility of institutions—trusted gate-keepers for scientific truth—with the immediacy and networking infrastructure of blogs, we believe that these shared goals can be better served with benefits to both partners.

An excerpt from a nice paper by Shelley Batts, Nick Anthis, and Tara C. Smith over at PLoS Biology discussing blogging’s potential in academia.

The Internet is not the first thing people think of when they think of a technological improvement that has dramatically changed science. This is because most people think of the ‘net in terms of the services that it provides (e.g. “I found a cool science video on YouTube” or “I found my soulmate on MySpace”), the true impact of the Internet on science is a lot deeper than that, for two reasons:

1. The Internet lets scientists access information from anywhere quickly and cheaply. Before the ‘net, you would have to make expensive long-distance phone calls/faxes or wait ridiculously long times for “snail mail” to get access to the latest scientific findings or to engage in a meaningful scientific discussion with your peers. Today, pretty much everyone has access to Google and Wikipedia (among other resources), letting scientists from all over the world quickly (and cheaply) draw upon the thinking of other scientists, regardless of their location.
2. The Internet lets more people drive scientific discussion. With the Internet, the core of intellectual discussion no longer need be in the printed letters sections of Science or Nature, not when every scientist can have his or her own blog, Twitter account, and/or Facebook profile. Can’t find people to discuss an obscure article from Blood? Blog about it! Find the scientist who published the journal and write a comment on his Facebook wall or his blog, follow his Twitter feed, or, if you’re more old-fashioned, write him or her an email.

But, despite the great potential of the Internet for radically shifting and improving the way scientific discourse is done, many scientists are choosing not to actively participate in #2, whether it be because of a lack of familiarity with these new technologies or because of a fear of being scooped. And that is a shame. The Internet is a uniquely collaborative and social tool — meaning that it’s value comes from people being willing to both use and contribute.

Chances are if you’re reading this blog, you already understand and embrace the power of the Internet for changing how science is done and discussed. This post (and this blog) is preaching to the choir to those of you guys and gals. But, even so, we all have to endeavor to:

• encourage scientists to blog, whether it be to help educate the public about things like vaccine safety, evolution, and global warming or to help drive discussion about exciting or informative research (e.g. with ResearchBlogging.org)
• leave meaningful comments on science blogs — blogging when nobody seems to care is painful and not inspiring. Blogging when the only people who seem to care leave flames or spam is even more painful. Leave smart comments that push the discussion forward. It’s more interesting for the blogger, for you, and for the legions of people too shy to comment.
• teach your fellow scientists about Twitter and social networking, because nothing helps foster a real sense of community then using tools designed to link people with one another
• develop a Wiki for your lab — it’s easy, helps to spread information within your lab (something I’m sure your PI would love to see more of), and is a good jumping off point for demonstrating why the Internet is a powerful tool which is made only more powerful by collaboration
• reach out to new science bloggers and Tweet-ers; it’s always difficult to try something new, and it’s even harder if you’re trying something and everyone is immediately hostile or unfriendly
• use the power of the social Web — drink the Kool-Aid; use the blogosphere to help yourself find potential collaborators, new insights, or even new sources of information. Use Twitter to meet up with scientists with similar interests (and they don’t even have to be scientific interests — they could just be hobbies!)

My hope is that as the power of the Web becomes further developed and better established in the minds of the scientific establishment, the Internet will grow into something which dramatically improves the quality of scientific discussion and thinking rather than be relegated to the realm of those scientists who just happen to be tech geeks.

edit: per Ander’s comment, replaced “more and more” with “many”  (brain fart)

Cameron Neylon wrote a great post about the difference between recording and presenting data in an online lab notebook. The whole post provides a great analysis of the differences he sees between LaBLog, the UsefulChem wiki and the basic philosophies behind their use.

The end of Cameron’s post really got me thinking about the possibilities that a “presentation layer” could have in an online lab notebook. I envision a presentation layer that leverages recent innovations in webapp technology to automatically generate a flowchart-like view of all posts/data/experiments contained within one’s notebook. This graphic would be interactive, customizable, and could be coupled with methodology excerpts in order to provide a complete view of experiments over time.

Much like the grouping of messages by conversation in Gmail provides an innovative and more intuitive organization of e-mail, I feel that a graphic of this sort would be an intuitive manner to deal with the somewhat fragmented nature of online lab notebooks without too much editing after the fact. It would make it easy to visualize branches in experimental thought or dead ends. While also consolidating experiments for viewing by people with access to your online notebook. Ideally providing an accurate representation of work flow and thought process.

I suspect coding something like this wouldn’t be the simplest task and there’s definitely a fair amount of kinks that I’m sure would have to be worked out. Regardless I’m excited to be able to think about the possibilities that online lab notebooks will bring to science over the coming years.

I’ve been told biologists are just haters, but who needs to know why things have mass when we can find the Darwin particle!

A depiction of what the silicon nanowires look like. This array of nanowire detectors is able to detect single proteins in the bloodstream. Each nanowire corresponds to a different antibody. Credit: Vista Therapeutics

I can see it now. Season 43 of House M.D. House asks his team of fellows to determine the concentration of a certain protein in a patient’s bloodstream. Instead of taking multiple blood samples and performing several tests, including purifying the samples, marking the designated proteins, and using imaging technology to check for the labeled proteins, the fellows simply use special nanowire sensors to accomplish in five minutes what originally took 90 minutes. Although House may not be around for 43 seasons, the scene just described may be commonplace in hospitals all over the world. This ground-breaking technology is currently being researched by Vista Therapeutics, as they aim to provide the “ultimate sensitivity” with this new product.

Here is a description provided by the MIT Technology Review:

To make the detectors, Vista Therapeutics has licensed nanowire sensing technologies developed by Harvard University chemist Charles Lieber. Silicon nanowires, semiconducting wires as thin as two nanometers, have what Lieber calls the “ultimate sensitivity,” even with completely unprocessed samples such as blood. When a single protein binds to an antibody along the wire, the current flowing through the wire changes. Arrays of hundreds of nanowires, each designed to detect a different molecule in the same sample, can be arranged on tiny, inexpensive chips. The changes can be monitored continuously as molecules bind and unbind, making it possible to detect subtle trends over time, without requiring multiple blood draws.

The standard protein-detection technique, ELISA, is very sensitive but, Farr says, takes 90 minutes to perform. It starts with a blood draw that must be extensively processed–first to purify the proteins, then to label them with fluorescent dyes–and then tested with expensive imaging equipment in a hospital lab. “ELISA is a powerful technology for one-time measurements,” says Farr, “but there’s no existing technology for continuous biomarker measurement.”

With the ability to perform extremely precise, continuous monitoring of unprocessed blood samples, who knows what the future holds in store for nanowire detectors. You can be sure that I’ll be waiting for its debut on House.

Helpings hands? This metal-and-polymer gripper, triggered chemically, could usher in a new era of minimally invasive surgery. Credit: Timothy Leong/JHU

The other day I happened upon this article and I couldn’t help but be impressed. Today minimally invasive surgery implies smaller incisions, but incisions nonetheless. How would you like minimally invasive to mean zero incisions?  If Dr. Gracias and his colleagues have their way that may soon become a reality.

From the MIT Technology Review:

The new technology is a step toward surgical tools that move more freely inside the human body. “We want to make mobile surgical tools,” says David Gracias, a biomolecular- and chemical-engineering professor at Johns Hopkins University, who led the development of the new gripper. “The ultimate goal is to have a machine that you can swallow, or [to] inject small structures that move and can do things [on their own].”

A gripper based on the current design could respond autonomously to chemical cues in the body. For example, it might react to the biochemicals released by infected tissue by closing around the tissue, so that pieces can be removed for analysis.

Gracias and his colleagues presented the microgripper at the American Chemical Society meeting earlier this month. To demonstrate the device, they used it to grasp and maneuver tiny beads and clumps of cells in a petri dish. They have also used the device in the laboratory to perform an in vitro biopsy on a cow’s bladder. “This is the first mobile micromachine that has been shown convincingly to do very useful things,” Gracias says. “And it does not require electric power for operation.”

In it’s current iteration the gripper is maneuvered by magnets thereby removing the need for any incisions. As a scientist I can’t help but wonder when this remarkable device can be made available for laboratory use. Being able to manipulate items at a microscopic level based on chemical features could be very useful. In the meantime I look forward to a future of incision free biopsies!

Neil Saunders recently wrote about the the difficulty some people find in keeping an electronic notebook; over the past year, during my rotations, I’ve used both paper and electronic notebooks, and I’ve come to one conclusion: whatever you can make electronic, make it so. Trust me, it’s worth the effort.

First, a bit of context. I’m an experimental biologist, not a computational biologist (at least, not primarily computational), so I have to deal with the fact that not everything in my research can be “electronified.” I’ve got samples in the freezer, vials of things in the fridge, cultures going in the incubators, and so on. Thus, I’m not looking for a notebook where I can keep every single bit of my research; maybe when the Matrix Google finally digitizes all of reality, I can finally just plug into my computer and never leave my desk.

On the other hand, though I’m not a computational biologist, I am pretty comfortable with computers. I program, I know HTML, and I can use Photoshop pretty quickly. I’m fine with cobbling together my own electronic lab notebook of sorts from the tools I can find on the internet (such as making a wiki); others (such as some in my lab) might find even formatting a wiki post to be an intimidating prospect. So what I do might not work for you.

Right now, my lab has an internal wiki using the MediaWiki engine, and I’ve been using my wiki space as my lab notebook. The wiki is backed up regularly, is password-protected, lets me view and edit the wiki from any internet-connected computer, has full-text search built-in, and has an editing format lets me put in cross-references to other entries; this is all I generally need for a lab notebook.

How do I manage the offline stuff, like gel pictures, data sheets, and so on? Well, I can put a surprising number of things on the wiki (for example, the lab next door lets me use their UV transilluminator, which has a CCD camera that I use to save TIFF images of my gels onto my network account), but basically I keep everything in a giant binder, numbered in order by date, and then put a reference to it in the online notebook. That way, I can easily find a result; just search the wiki for the entry I’m looking for, look up the reference number, and then find it in my binder of results. I do something similar with my experimental samples; my initials, followed by an experiment number, and then a vial number (such as “EJS-109-10″).

Unlike some people, my note-taking philosophy is that the lab notebook shouldn’t necessarily be a dirty log of absolutely everything that I do or think about while I’m in the lab; I don’t put in routine calculations or procedures, such as cell culture maintenance, making common reagents, and so on. The whole point of a lab notebook is so that I can keep track of what I did, so if I, or someone else, needs to look up what I did, or what’s in a vial in the freezer, I don’t have to spend hours trying to remember what I meant with “RfMQ2-3a-4-5-07″ on a tiny tube cap.

Sure, it’s sometimes nice to have everything in one lab notebook, gels pasted in and so on, but frankly, I find that even just the organizational benefits of being able to read my own handwriting and being able to search and cross-reference my posts to be worth giving up the all-in-one solution. When I kept a paper notebook, I spent so much time flipping back and forth between pages trying to remember where I’d written the concentration for the vial in my hand. Now, I just search for the vial number and voila!

Not only that, but I like to organize my lab notebook by project, rather than chronologically, because I generally have more than one thing going on at the same time. Organizing that way is doable on paper if you use a binder and loose-leaf paper, but still quite a hassle, especially since some experiments don’t always fit cleanly in one project or another, making it hard to find later (“Did I file it under this project or the other one?”). I prefer the electronic notebook, which lets me organize by both time and project, and lets me put experiments under more than one lab notebook by simply putting a link to it from both project pages. Not only that, but if I’m repeating an experiment with slightly different conditions, I can simply copy-and-paste a previous experiment and change just a few things.

Paper just doesn’t cut it for me anymore. If I were keeping a paper notebook, I’d basically be doing all the same things as I do on my electronic notebook: a loose-leaf notebook organized by projects, numbered experiments, separate binder of raw data, cross-referencing based on page numbers or experiment numbers, and so on. My online notebook does all this and adds remote access, readability, copy-and-paste, and searching to boot.

Not only that, but because my lab notebook is online, if I’m writing a paper or making slides for a presentation, I can be lazy and work from home. Win for the web!