Bench Press

Having spent the past couple weeks helping pack up and move the lab. I noticed my lab had an abundance of ancient data storage devices. Various floppy/zip disks and future museum pieces (Macintosh LC anybody?) were found hiding in all manner of locations. While I’m certain that we have paper copies of any data that could be found in those disks and computers archiving or even simply accessing the data on many of them might be impossible today.

An article from Physorg.com discusses the potential of a “digital dark age” resulting from an unintended consequence of continued technological innovation. Much like the inaccessible data that I found during my lab’s move, society’s rapid digital advancement has rendered it vulnerable to what Jerome P. McDonough, assistant professor in the Graduate School of Library and Information Science at the University of Illinois at Urbana-Champaign terms a “digital dark age”. The whole article is fascinating as it details several potential data black holes. A few interesting examples:

Magnetic tape, which stores most of the world’s computer backups, can degrade within a decade. According to the National Archives Web site by the mid-1970s, only two machines could read the data from the 1960 U.S. Census: One was in Japan, the other in the Smithsonian Institution. Some of the data collected from NASA’s 1976 Viking landing on Mars is unreadable and lost forever.

It’s a shame that valuable data from, not only a historic event, but also one of such exploratory significance is now lost forever. McDonough goes on to talk about the potential loss of political and popular culture due to data obsolescence and closed platforms.

McDonough also cited Obama’s political advertising inside the latest editions of the popular videogames “Burnout Paradise” and “NBA Live” as an example of something that ought to be preserved for future generations but could possibly be lost because of the proprietary nature of videogames and videogame platforms.

“It’s not a matter of just preserving the game itself. There are whole parts of popular and political culture that we won’t be able to preserve if we can’t preserve what’s going on inside the gaming world.”

McDonough’s discussion of videogames is only the tip of the iceberg. The enormous amount of user generated content that currently provides so much amusement (youtube, failblog, etc…) is a large part of modern culture and it’d be a shame if measures aren’t taken to ensure that future generations have access to it. Hopefully we’ll heed the warnings of information scientists like McDonough and begin making progress towards protecting our digital information by attempting to future proof as best as possible.

Personally after sorting through and moving the “digital archives” of my lab I’m ready to start taking some steps to future proof my digital existence.

Steps that I plan on taking:

• Reducing my reliance on proprietary file formats (bye bye Word).
• Duplicating my backups onto various media periodically.
• Migrating to new storage technologies, such as “the cloud” (Google engineers can figure out how to keep my data safe, right?)
• Make sure this blog’s future proof =).

Any suggestions on other steps I could take?

A completed magnetometer.

The age old dilemma of magnetic resonsance imaging: do you sacrifice precision for size, or size for precision?

Generally, behemoth MR machines are required to produce images of great detail. The downside? Price, immobility, and an inability to take the device to the field. The tradeoff of using their smaller, less expensive counterparts, however, is their lackluster resolving power. This could all change with John Kitching’s new developments in MR technology. Kitching, a physicist at the National Institute of Standards and Technology, is working on smaller, less expensive MR machines with resolutions that rival their larger cousins. Taking a new spin on an old idea, Kitching has adapted the procedure of producing atomic magnetometers and taken it to a significantly smaller scale.

The result: highly sensitive magnetic sensors about the size of a grain of rice. Kitching believes that mass production is not too far off in the horizon, and with an army of tiny magnetic sensors, the possibilites are endless. Pocket-sized MRIs, anyone?

In the spirit of Thanksgiving I’d like to give thanks to the many things science, tech, or otherwise that have provided me with a sense of wonderment, a moment of joy, a chuckle, or a LOL over the past year.

• I’m thankful for the rapid development of internet technologies which allow me easy access to a wealth of media (a.k.a distractions) from awesome experimental data to cultural gems like this.
• I’m thankful for the reference books, papers, and tools available on Pubmed, without which hours of toil may have turned into weeks or months.
• I’d like to give thanks to the many science blogs that populate my Google Reader. The science blogosphere is something I’ve found and come to love over the past year. From Aetiology to Mystery Rays from Outer Space (and everyone else in the blog roll!) the content, breadth and discussion continue to impress me day in and day out.
• I’m thankful that many scientists defy the stereotype of being resistant to change by actively taking a role in the adoption of internet technologies not only to alter the way they work or store data, but to advocate a revolution in the way science is communicated. Discussions about Open Notebook Science can only help the scientific process.
• I’m very thankful to those making use of their knowledge and experience to encourage future scientists and dispel myths in order to help educate the public.

Last but not least I’m thankful for my family and friends, especially my blog mates here at Bench Press and I’d like to wish everyone a happy Thanksgiving!

Been on a blogging hiatus thanks to various lab issues that have cropped up over the past month. It’s amazing how much stuff one has to do to move a lab that hasn’t moved in 12 years… Anyway, here’s a few science tidbits that caught my eye over the past few weeks.

• Developing more efficient green technologies ftw.
• DARPA awards $1.95 million contract for developing “a ‘fieldable’ in-theather, culture-manufacturing system” for “blood pharming”.
• Having worked on drug discovery for HIV and now working on gene therapy vectors, this story in the WSJ about a bone marrow transplant curing a 42-year old of AIDS is remarkable and heartening.
• A troubling legal ruling about liability for generic drugs.

Inspiring students to be interested in (or at least to value and respect) science is something which the scientific community has unfortunately passed on to under-prepared teachers. This has serious consequences. When leading US politicians can pander to the public by asserting that vaccines can cause autism or that fruit fly research is pointless, I would like to think that the scientific community would be scrambling to find ways to reach out to more properly educate people about why and how to think about science.

Allyson, over at the Systems Biology & Bioinformatics blog, recently wrote an interesting post about her volunteering experiences with the Teacher-Scientist Network which pairs teachers and scientists in an attempt to help educate children about science. The post is fascinating, but I think her tips for scientists reaching out to students are especially useful:

1. My method of using no text on the vast majority of the slides really worked. It was especially useful as it meant I could stop anywhere in my slides if I was running out of time, and the littlest ones were not distracted by trying to read the words rather than listening to me.
2. Pictures of fluffy, pretty, cute, or “gross” animals were very, very popular. The number of “Awwwws” I got when showing pictures of cats was astounding. Equally, all the older ones wanted to see my pictures of the newborn mice (pretty gross with no hair!), and all ages enjoyed trying to figure out what the photo of e.coli was.
3. As soon as you ask a question, they all raise their hands to answer it. Not sure when this stops, but I know that by the time I was in high school the teachers had a hard time prying any answers out of the majority of us! However, on Monday I was at a school where the eldest was 11, and they all wanted to contribute. So, ask them questions. I found there were two types: the question where I wanted to get an answer (such as “What traits make a good horse?” or “What do you think makes these two cats different?”) and the type where I just wanted them to feel included in the talk, and just wanted a show of hands (such as “How many of you have a cat?” or “Who has heard of diabetes?”).
4. Introduce some ethics, and show how scientists think very carefully before doing research. We talked about genes a lot, and how putting new genes in bugs like e.coli can help us, e.g. the human insulin gene into e.coli to help with diabetes. I told all the older kids that it wasn’t the tool that is a problem: a tool is neither good nor evil. It’s how that tool is used, and people need to make a fresh decision, and think about the benefits and downsides each time that tool is used. I said genetic modification is like a knife: it is neither good nor bad, and that scientists try very hard to make sure that it is used for the right reasons, and in a safe way.
5. Visually-arresting analogies: Even though DNA is a double-helix and not a spiral staircase, I found it a very useful analogy, especially for the younger ones.
6. My partnered teacher had prepared some slides to show the kids prior to my arrival. They dealt with Mr. Green Genes, the GFP-glowing cat. Some of the other teachers also talked to their kids about inheriting some of your traits from your mom, and some from your dad, and used the labradoodle as a visual aid. This prepped them for my talk, which I think was really helpful.
7. Make your talk inclusive. It keeps their interest, I think. When I showed pictures of cats, I included one picture of my own cat, and told them a little about her. I often asked them questions about if they had pets, or scientists in the family, or liked the look of a picture, or knew what something was.

I think Allyson makes a lot of great points. But, in keeping with the theme of this blog to talk about technology, I think we can add a few suggestions to her list:

• Put up a science website - The best learning happens outside of the classroom. Now, I don’t advocate scientists to turn their labs over to 8-year-olds, but I do think that giving students a resource to look at outside of class.
• Edit wiki’s - It’s astounding how many people use Google and/or Wikipedia to find information about science and medicine. This represents an incredible opportunity for the scientific community to properly inform the public — fail, and let vaccine fear-mongers, Creationists, global warming deniers, and their kind guide the public discussion.
• Put up online video - A few years ago, online videos were clunky and difficult to use. So you had an excuse back then to not put up videos on your website. Today? Different story. When YouTube is a household name, there is no excuse for people not to put up engaging demo videos — because people who don’t know what they’re talking about are.
• Use feeds - Twitter. Flickr. Del.icio.us. RSS. These are becoming increasingly more mainstream, especially among students, so scientists should learn to use them. Who knows, your picture of GFP-tagged Neurons may be what inspires the discoverer of the cure for Alzheimers?
• Interactive applications - Show the public what you’re researching in a way which actually speaks to them. No, don’t show them your NSF grant application, show them a Google Earth layer highlighting your research on Ancient Rome, the impact of global sea levels rising, or the beautiful nebula that you’re telescopes are pointing at. Present an applet which shows the beauty of a Lorentz attractor, or examples of simple machines in your household.

I was going to write a long essay about how web technologies have advanced to the point where science can be shared and discussed and shown in sophisticated ways through the web.

But, rather than bore you with those trivial details, why not just show you.

Before the Web: Read (Science 15 August 2008: Vol. 321. no. 5891, pp. 970 - 974) and its tiny paper figures and hope that you can visualize what’s going on.

After the Web: Read the paper online, Read a blog post on said paper (from science blog Mystery Rays from Outer Space). Watch this video of neutrophils (a type of white blood cell responsible for attacking infection, tagged Green) infiltrating a mouse ear that has just been injected with beads (tagged Blue) and Leishmania major (a bacteria, tagged Red).

4-dimensional image series from the ear pinna of a LYS-eGFP mouse in which blue fluorescent beads and L. major had been deposited adjacent to one another in the skin of the same ear. eGFP-expressing cells are shown in green, L. major-RFP is shown in red, and beads are shown in blue. Playback speed is 1200x. Scale bar, 200?m

Comment on blog post and ask blog author question about how neutrophils are attracted to the beads. Get a response. Make my own blog post about the discovery. Reflect on the impact of the Web on science.

The future of blogging...humans not included

I was taking a look at Engadget earlier today and happened upon this post. That tiny little robot featured next to the laptop is not just a trendy desk accessory, but a full time blogging machine. The NetTansorWeb is Wi-Fi enabled, contains a small camera in its head with which to scout the human race’s weaknesses take pictures of its surroundings and post to a blog with short comments!

At my previous job my department worked with high-throughput machines in a variety of experiments, speeding up compound screening and assay development. Now if only someone could transfer some of the “smarts” the NetTansorWeb seems to have to my qPCR machine. I certainly wouldn’t mind some short comments along with my results. Until then I look forward to seeing what these robots will be blogging about… maybe we can add one to the payroll.

Read more at Bouncing Red Ball.

I always find it fascinating how fast technology moves; in this case, “seam carving”, which is a clever algorithm for removing or replicating low-content spaces in images, is now going to be in Photoshop CS4 as “content aware scaling”! Pretty awesome for an algorithm that only got presented last year.

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)