Bench Press

The always thoughtful Deepak Singh brings up a great point in a recent post on his personal blog:

Not all data should be published via a peer-reviewed publication. Not every protocol needs to be. But making the data available via wikis, open data resources is pretty much a no-brainer and not just for the future. You enrich currently available data, and have the ability to leverage an additional layer of resources.

Deepak isn’t the only guy to think this, Derek Lowe from In the Pipeline raised a similar point:

Perhaps there should be a way to dump chemical data directly into some archives, the way X-ray data goes into the Protein Data Bank. That wouldn’t count for much, but it would capture things for future use. Having it not count much would decrease the incentive for anyone to fill it full of fakery, too, since there would be even less point than usual. And before anyone objects to having a big pile of non-peer-reviewed chemical data like this, keep in mind that we already have one: it’s called the patent literature, and it can be quite worthwhile.

(all emphases mine)

I think they both have a very good point. Some form of centralized data repository, even if non-peer reviewed, could help tackle the problem that everyone hears about but nobody ever tries to solve of not having a central place to share negative results and protocols (akin to what this blog proposed previously for bio/pharma companies).

It could also help us re-prioritize publication and peer review efforts away from sheer data collation which, while extremely important, is distinct from experimental/study design, data analyses, and drawing conclusions where peer-review is more valuable (there’s only so much peer-review can do to when looking at a data collection effort in isolation).

With modern internet technologies being as fast and as scalable as they are now, there’s simply no reason to use the traditional journal to chronicle every single discovery or achievement. Better to collect most of it in API-accessible/index-able repositories so that others can share in it and curate it and instead focus publications on building analytical insights.

(Image credit)

If you’ve never used Google Earth, I’d recommend trying it out, at least once. For those of you not in the know, its an amazing piece of software which lets you access Google’s wealth of geographical and geological information (although with its layers feature, it also gives you access to the oceans, the moon, the sky, historical sites of interest, and Mars).

The magic of new, cheap and powerful technologies and information sources like Google Earth is that they can also be used to push additional experiments and discoveries. Widely available mathematical analysis tools like Mathematica let a professor figure out what instruments made up the mysterious “twang” at the beginning of the Beatles classic “It’s Been a Hard Day’s Night.” Advances in gaming and graphics technology make it possible for gaming consoles and personal computers to do sophisticated number-crunching. And, Google Earth helped make it possible for a team of students to take pictures from near-space for only $150.

More recently, Google Earth helped a team of researchers led by the University of the Witwatersrand’s Professor Lee Berger to find and unearth new fossil remains, including those of the newly discovered Australopithecus sediba (pictured right) in the Cradle of Humankind World Heritage Site in South Africa.

Berger and his associates used Google Earth to learn how to identify cave sites from satellite imagery and to help supplement on-foot exploration to map out ~500 previously unknown caves and, subsequently, 25 new fossil sites!

This discovery has been especially exciting as some have argued it could potentially be “the point from which the genus Homo [the genus we humans are a part of] arises” and “a good candidate for being the transitional species between the southern African ape-man Australopithecus africanus (like the Taung Child and Mrs. Ples) and either Homo habilis or even a director ancestor of Homo erectus (like Turkana Boy, Java man, or Peking man).”

Check out the University’s web coverage of the discovery as well as the Google blog’s coverage of the event as well as the video celebrating Professor Berger’s find (below):

(Image credit – University of the Witwatersrand website)

Science papers by Berger’s group: (1) and (2)

Here at Bench Press we’re always interested in new initiatives that harness the advantages of the internet. We’ve covered various powerful distributive computing initiatives as well as breakthrough collaborative endeavors in scientific research. So I was intrigued when I saw buzz on Twitter about the Obama administration’s attempt to crowd source suggestions for scientific policy.

Through the American Association for the Advancement of Science (AAAS) and associated non-profit Expert Labs, the Obama administration wants to hear what grand challenges scientists envision taking on.

Expert Labs has a nice video explaining the reasoning behind this grand experiment in policy crowd sourcing.

After a quick search on Twitter I’m a bit curious as to how Expert Labs plans to parse all the data they’re going to get from this call to arms, but I’m optimistic that some interesting insights can be gleaned as to the opinions of Americans on the directions science should be headed in. More data never hurt right? If you’re interested in submitting an idea follow the directions here, you’ve got until April 15th!

Previously at Bench Press we’ve written about the power of distributive computing and it’s ability to pool resources from volunteers over the internet to tackle projects on protein folding and the search for extraterrestrial intelligence. As distributed computing approaches mainstream, numerous projects focusing on a variety of questions have emerged.

One project that caught my eye is the Quake-Catcher Network (QCN). The network is described as

a collaborative initiative for developing the world’s largest, low-cost strong-motion seismic network by utilizing sensors in and attached to internet-connected computers.

The QCN utilizes accelerometers attached to computers to monitor for vibrations. Vibrations detected by the accelerometer are then recorded and compared to readings from other computers in the network. Only when a sufficient number of computers report comparable readings at the same time will the data be reported as an earthquake. Most recently the QCN detected a magnitude 4.4 earthquake in the Los Angeles area yesterday morning. The data generated from QCN participants can be seen here.

The beauty of the QCN is the enormous cost savings their approach can provide in comparison to traditional seismic networks like those run by the USGS. New accelerometers are now much more affordable. Sensors that plug into a USB port can cost less than $50. In addition, an increasingly common feature for laptops is a built in accelerometer to detect sudden movements like drops in order to shut down components to protect them from damage. These accelerometers can be utilized and provide a fairly large potential participant base who merely need to install BOINC and join the QCN project to begin providing data to the network.

As the number of QCN participants grows the heads of the project, Drs. Elizabeth Cochran and Jesse Lawrence, hope the network will provide not only a wealth of data for geologists but potentially a small bit of warning in the event of a large earthquake for those miles away from the epicenter. Currently, Drs. Cochran and Lawrence are working hard to increase the number of participants while also providing educational tools for use in schools to teach about earthquakes and science behind them.

Living in San Diego I think I’m in a prime location to help out so I look forward to contributing some data to the QCN (magnitude 4.0 or less please!).

(Join the Quake-Catcher Network)(Source – LA Times)

I’ve never understood why researchers or authors cheat or plagiarize. Either what you’re lying/cheating on is completely inconsequential, and hence its not worth it to risk your career/reputation over being caught, or its a big deal and sooner or later someone will verify it.

And as Derek Lowe’s blog In the Pipeline points out in a recent post, it’s especially not worth it when someone is extorting you. Apparently a postdoc in Peter Schultz’s renowned group at Scripps named Zhiwen Zhang did a little fudging in some published papers on incorporating glycosylated amino acids into proteins.

Around the time that the Schultz lab was starting to have difficulty replicating Zhang’s work, Zhang apparently began receiving e-mails at his new faculty position at the University of Texas which demanded he send $4000 to an address in San Diego or “you lose job… Texas will fire you before you tenure”

The San Diego police were apparently involved and, although they found a suspect, Zhang did not press charges (presumably to avoid publicizing his fib?). Eventually, though, the extortionist sent an anonymous letter to Scripps, University of Texas, and a number of publications, and Zhang was denied tenure.

Who was our mystery blackmailist? And who knew what and when? I have no idea, but I will say two things:

1. Don’t cheat in a publication. Like I said before, it either doesn’t matter enough to risk your career or it matters a great deal and, in that case, you’ll be caught when someone tries to replicate your work.
2. It’s only in the era of the internet that such a thing gets spread so widely and so quickly.

(Comic credit – CheatATE)

We’ve written a couple of times about the asteroid Apophis which, while unlikely to hit Earth, will make a very near pass of 18,300 miles above the planet’s surface in 2029. NASA’s Jet Propulsion Laboratory just released an excellent animation of just how close Apophis will be when it passes by.

Wow for some reason 18,300 miles doesn’t seem quite as far anymore.
(Video Credit – Wired Science)

What can you do with a 110 foot wide, nine story tall radio telescope that weighs almost a million pounds? Not a question the average person or even educational institution asks themselves. Yet, this was a question Lewis Center founder Rick Piercy contemplated when he convinced NASA to donate a radio telescope being decommissioned that had once been used to communicate with Apollo spacecraft.

Thanks to Rick Piercy’s efforts K-12 students around the world have access to the Goldstone Apple Valley Radio Telescope through the Lewis Center’s GAVRT program which is a partnership with NASA offering a variety of programs exposing students to radio astronomy and cutting edge scientific work. Teachers from all institutions are welcome to join the program and are given a training seminar and visit to the telescope in order to familiarize themselves with the curriculum currently designed around the GAVRT as well as learn how to control the telescope via the internet.

In one of the ongoing projects students have been giving NASA scientists a helping hand track the Lunar CRater Observation and Sensing Satellite (LCROSS) spacecraft with the GAVRT. The LCROSS mission is ongoing and the satellite is scheduled to make impact with the moon in order to look for water on October 9, 2009. One of the beauties of this program is that not only is this a unique learning opportunity for the students, but they also help provide additional data gathering time for NASA scientists as explained by Brian Day of the NASA Ames Research Center,

Because LCROSS has a very steeply inclined orbit, we have only a 2-hour window once every 3 days when we can check out the spacecraft using the Deep Space Network. So we decided to ask GAVRT for help. These kids help us get extra listening time for our spacecraft, and they get an incredible educational experience in return.

Thanks to the internet and some enterprising individuals some lucky students will have a front row seat to some exciting scientific exploration of our nearest celestial neighbor. I look forward to hearing about the results of the LCROSS mission. Congratulations guys!

Read more about GAVRT and the LCROSS mission.

We’ve previously covered the computer modeling solutions being used to model and track the paths of near-earth asteroids (especially those which might treat Earth like a dartboard), but for those of you not content to just sit at home while NASA scientists do all the tracking, the asteroid trackers at NASA’s Jet Propulsion Laboratory have made it now easier to follow what’s going on in the world of near-earth asteroids from the comfort of your own home.

The first little gadget they’ve developed is a computer widget (pictured on the left) which is compatible with the Mac OS and Yahoo widget engines.

What it will show is a list of the next five near-earth asteroid approaches (within ~20x the distance of the moon) and an estimate of their size (including a pictogram depiction of what that size means) as well as their distance. The widget will also make it easy to find more information about the particular asteroids it is identifying (an example is linked here) which will show off a dynamic Java applet map of the asteroid’s orbit through the inner solar system (which you can manipulate so you can see how the orbit looks in 3D) as well as a wide range of data on the asteroid such as the eccentricity of an asteroid’s orbit (in layman’s terms, how oval-like versus how circular), the orbital period (the time it takes for an asteroid to complete one rotation around the sun).

The second thing the brains at NASA’s JPL have put together for researchers and amateur astronomers is a Twitter account (@AsteroidWatch), which accompanies NASA JPL’s main Asteroid Watch site. The feed went live on July 29, 2009 and, although not written in the cutesy voice of the MarsPhoenix twitter account (which followed the exploits of the Phoenix Mars probe NASA launched a while back), the AsteroidWatch feed so far has reported on near-earth asteroids and new reports and articles issued by NASA’s official asteroid tracking team.

You can follow the BenchPress team on Twitter! You can follow us at Anthony (@AnthonyPhan), Ben (@BenjaminTseng), Eric (@EricSuh), and Kevin (@Kevin_Tseng).

As Ben mentioned on Monday, we at Bench Press were disappointed that we were unable to attend the 2009 Science Online London Conference, but we were glad to see the amazing coverage within the blogosphere. One of the panels I was interested in was the first breakout session titled “What is a scientific paper?”. A discussion on the essence of scientific papers could be incredibly enlightening about steps needed to modernize scientific communication and publishing.

Having read through various notes and posts about the panel I have to agree with Cameron Neylon that while the panel’s discussion on methods to modernize papers themselves had some interesting ideas, a key issue with papers was glossed over; their continued publication in antiquated vessels known as journals. As Cameron Neylon writes:

The journal used to play an important role in publication. The publisher still has an important role but we need to step outside the notion of the journal and present different types of content and objects in the best way for that set of objects. The journal as brand may still have a role to play although I think that is increasingly going to be important only at the very top of the market. The idea of the journal is both constraining our thinking about how best to publish different types of research object and distorting the way we do and communicate science. Data publication should be optimized for access to and discoverability of data, software publication should make the software available and useable. Neither are particularly helped by putting “papers” in “journals”. They are helped by creating stable, appropriate publication mechanisms, with appropriate review mechanisms, making them citeable and making them valued. The point at which our response to needing to publish things stops being “well we’d better create a journal for that” then we might just have made it into the 21st century.

Cameron argues effectively that the journal, as used today, does little if anything to optimize access and discovery of data thereby constraining scientific communication and handicapping scientific progress.

While the panel may not have addressed this key issue thoroughly enough, I was happy to see that PLoS has taken a first step to address the limitations of the traditional journal with their new project PLoS Currents: Influenza. As described in their FAQ PLoS Currents: Influenza is

a website for immediate, open communication and discussion of new scientific data, analyses, and ideas in a critical research area. Submissions are screened by a group of leading researchers in the field, and those deemed appropriate are posted immediately and publicly archived at the National Center for Biotechnology Information (NCBI). All content is open access, available under the terms of the Creative Commons Attribution License.

The explicit goal of this project is to provide easy and efficient access to data on Influenza, in hopes that scientific discussion and breakthroughs can be made in a more timely manner. While PLoS still differentiates Currents from Journals, their step out of the typical scientific publishing space with this project is commendable and looks like a great first step at expanding scientific publication. Hopefully this experiment works out and other publishers will begin to experiment as well.

For more coverage on PLoS Currents: Influenza, Bora Zivkovic has a great introductory post.

Here at Bench Press, we’re very interested in how to leverage new internet technologies to help scientists work better, collaborate more effectively, and reach out to the general public in a meaningful way. So, when we found out we wouldn’t be able to make it to the 2009 Science Online London conference (or solo09 as the Twitter-verse seems to be calling it), we were disappointed to say the least (although for some reason it completely escaped our mind that we could’ve attended for a nominal fee via Second Life).

Thankfully, the people who attend a conference dedicated to talking about better ways for scientists to use the internet are also the most likely to live-blog the event. So, thanks to the always-wonderful Allyson Lister over at the Mind Wobbles, the public has access to an avid conference blogger’s account of the conference. And, as a bonus, on each of her posts, she’s also linked to the FriendFeed discussions of each of the panels!

The two sessions I found most interesting (and wished I had been there to see) were:

• The live-demo of the not-yet-public Google Wave by Cameron Neylon, Chris Thorpe, and Ian Mulvany and the discussion of its potential as a means for collaboration (Google, if you’re listening, I’m still waiting for my chance to try it!)
• The discussion on how science communication will be done in 50 years with science fiction author John Gilbey. I’ll be honest, I couldn’t quite tell from Allyson’s notes what exactly happened, but when the notes talk about creating a “University of Rural England where things are not always as they seem” with “machine-enhanced clairvoyance for science quality auditors” and “a temporal portal to allow historic research leaders to be employed on projects”, you know it must’ve been fascinating.