Bench Press

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.

Previously, Ben wrote a post about innovative use of the virtual world Second Life for simulating N-body problems. One of the groups behind the impressive OpenSim mod, the Meta Institute of Computational Astrophysics (MICA), is incredibly unique in that the organization itself is an exploration into the utility of emerging virtual world (VW) technologies (e.g. SecondLife) for scientific and academic work.

A group of scientists from the California Institute of Technology, Princeton, Drexel University, and the Massachusetts Institute of Technology founded MICA in the spring of 2008 in order to explore and take advantage of what they saw as a new frontier in collaboration and information dissemination. MICA’s goals are¹:

• Exploration, development and promotion of VWs and VR technologies for professional research in astronomy and related fields.
• To provide and develop novel social networking venues and mechanisms for scientific collaboration and communications, including professional meetings, effective telepresence, etc.
• Use of VWs and VR technologies for education and public outreach.
• To act as a forum for exchange of ideas and joint efforts with other scientific disciplines in promoting these goals for science and scholarship in general.

In addition to the collaborative research we’ve written about before MICA also “conducts weekly professional seminars, bi-weekly popular lectures, and many other regularly scheduled and occasional professional discussions and public outreach events, all of them in [SecondLife].” A screenshot of one of their astrophysics seminars can been seen below. MICA has also begun experimenting with various teaching formats for undergraduate and graduate level courses.

MICA members attending a weekly astrophysics seminar by Dr. M. Trenti, given in the StellaNova sim in SecondLife.

What really impresses me about MICA however is their belief in the platform.

[W]e wish to lead by example, and demonstrate the utility of VWs and immersive VR environments generally for scientific research in fields other than humanities and social sciences (where we believe the case is already strong). In that process, we hope to define the “best practices” and optimal use of VR tools in research and education, including scholarly communications. This is the kind of activity that we expect will engage a much broader segment of the academic community in exploration and use of VR technologies. Second, we hope to develop new research tools and techniques, and help lay the foundations of the informational environments for the next generation of VR-enabled Web.

Hopefully MICA’s innovative use of SecondLife will prompt other scientists to follow. I definitely want to check out one of the lectures one of these days.

(Exploring Use of Virtual Worlds as a Scientific Research Platform: The Meta-Institute for Computational Astrophysics)

In order to deal with the global outbreak of swine flu effectively, tracking the number of swine flu cases is imperative. Having as much accurate data as possible regarding the epidemic is essential for evaluating what moves the global community ought to start taking to make it through this outbreak. Thus, using quick and accurate tools to evaluate the countless samples  being collected around the world is an absolute necessity. Luckily scientists at the University of Colorado and InDevR, a small biotech in Colorado, may have exactly what the world needs in a microarray chip dubbed the FluChip.

In 2005 Dr. Kathy Rowlen, CEO of InDevR, led a team at the University of Colorado working with the Centers for Disease Control and Prevention (CDC) in developing the FluChip in order to allow labs across the world to quickly distinguish samples between 72 different influenza strains. Her group’s work produced a viable testing platform that produced results in less than 12 hours with impressive accuracy.

Now Dr. Kathy Rowlen and InDevR have licensed the FluChip technology from the University of Colorado. InDevR has arranged to begin testing samples of the swine flu on a M-gene variant of the FluChip while also working on improving the initial design by incorporating new technologies, hopefully making a new assay basic enough that any lab with PCR capabilities will be able to utilize it. Here’s to hoping the FluChip will help us get a better picture of the current state of the swine flu epidemic.

InDevR Press Release:

InDevR, a small biotech company in Boulder, CO, announced today that they have licensed the FluChip technology from the University of Colorado.  The FluChip was invented by a joint team of scientists at the University of Colorado and the Centers for Disease Control and Prevention in an NIH sponsored effort led by Professor Kathy Rowlen.  Rowlen, now the CEO of InDevR, said that InDevR has arranged to test genetic material from the recent swine H1N1 virus on the MChip as well as other versions of the FluChip which are under development.  According to Rowlen “Based on work we conducted a couple of years ago, it appears that the M-gene version of the FluChip will be able to distinguish human H1N1 viruses from the new swine H1N1 virus.  If that proves to be the case, the FluChip will be a much needed and powerful new tool for surveillance since all of the current influenza diagnostics on the market are unable to subtype this virus.” The most popular diagnostic tests for influenza include rapid immunoassays, which are only able to identify the type (A or B) of influenza virus, and reverse-transcriptase polymerase chain reaction assays, which were designed for human-adapted influenza viruses and are not able to identify the swine H1N1 subtype.  State Public Health Laboratories must now send any influenza A viruses that cannot be subtyped using existing diagnostics to the CDC for analysis by genome sequencing or viral isolation.  The CDC must select viruses to analyze since it is not possible to run every sample collected from a large number of Public Health Labs.

The M-gene based FluChip has been demonstrated to delineate human-adapted viruses from non-human viruses, such as the H1N1 virus that caused the 1918 “Spanish Flu”.  “Since the FluChip assay can be conducted within a single day it could be employed in State Public Health Laboratories to greatly enhance influenza surveillance and our ability to track the virus,” Rowlen said.  InDevR will combine the FluChip technology with an innovative detection technology (NESATM), which InDevR also licensed from the University of Colorado and further developed with NIH sponsorship, to make the FluChip assay inexpensive and easy to use in any lab that has basic PCR capabilities.  “Kathy and her team have been engaged with this and similar diagnostic technology for many years,” said Mary Tapolsky, Senior Licensing Manager at the University of Colorado Technology Transfer Office. “CU TTO is excited about this experienced and motivated group developing and commercializing this promising technology.

As genomes have been sequenced over the past few decades scientists have looked for new ways to analyze and interpret the wealth of information. They’ve developed numerous algorithms with goals ranging from organizing evolutionary family trees (inspired by plagiarism detecting software) to aligning genetic sequences. All of this to answer the numerous questions that can now be asked thanks to sequence databases. One of the many things scientists have attempted to study is positive selection in protein-coding genes.

Positive selection of advantageous gene mutation is particularly interesting to scientists as it can provide insight into the function of new genes. However, positive selection is difficult to detect and analyze as neutral and deleterious mutations predominate advantageous mutations in frequency. Initially scientists looked for positive selection by simply comparing the ratio (/omega) of nonsynonymous nucleotide substitutions (d_N) to the number of synonymous nucleotide substitutions (d_S) between homologous protein-coding gene sequences while utilizing Fisher exact tests to accept or reject a null hypothesis of neutral selection¹.

Over the years scientists developed additional statistical analyses to infer positive selection. Two of the most popular methods are the branch-site method (BSM) and site-specific method. The BSM utilizes a likelihood ratio test to detect positive selection within a given phylogenic branch. The site-specific method on the other hand utilizes /omega to look for specific amino acid substitutions that are positively selected. Both of these methods have been utilized in hundreds of papers and seemingly provided a great deal of insight into potential points of positive selection within various genomes. What would you say then when told that both of these methods contain significant flaws which provide an inordinate number of false positives?

Bovine Rhodopsin protein with predicted sites in red and experimentally determined in blue. (Adapted from Yokoyama et al. 2008 PNAS)

That’s exactly what Masatoshi Nei and his group believe to have shown in a recent paper evaluating the reliability of the branch-site and site-specific methods. Nei’s group utilized several controlled computer simulations as well as data collected by Shozo Yokoyama, at Emory University, on dim-light vision opsins in vertebrates² in their studies determining that both the branch-site and site-specific methods yielded far too many false positives. Nei and his group contend:

This low rate of predictability occurs because most of the current statistical methods are designed to identify codon sites with high /omega values, which may not have anything to do with functional changes. The codon sites showing functional changes generally do not show a high /omega value. To understand adaptive evolution, some form of experimental confirmation is necessary.

From this paper it looks like scientists looking for high /omega values may have been chasing ghosts by assuming that amino acid changes result in functional changes indicating proof of positive selection. The potential impact this will have on hundreds of papers is stunning. In the end the take home message is that statistical analyses, no matter how elegant, have their limits and ought to be utilized in conjunction with experimental data as much as possible.

(Sources: 1 – Reliabilities of identifying positive selection by the branch-site and the site-prediction methods , 2 – Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates )

updated: Had to change all the &omega to /omega because WordPress kept changing it into ? for some reason…bah

Thanks to the internet the enterprise of playing practical jokes on the world has become incredibly easy and every year now I look forward to seeing what hilarious items pop up throughout the internet. So here’s a quick list of some of my favorite tech/science April Fools jokes for 2009:

Google masters artificial intelligence. The brilliant people over at Google continue to amaze by creating the world’s first “artificial intelligence tasked-array system” which they’ve dubbed the Cognitive Autoheuristic Distributed-Intelligence Entity (CADIE). Apparently it’s already cranking out changes at Google: “Earlier today, for instance, CADIE deduced from a quick scan of the visual segment of the social web a set of online design principles from which she derived this intriguing homepage.”

Gmail Autopilot. Thanks to CADIE e-mail’s even easier than before. By using the Gmail Autopilot one can set simple sliders to manage all your e-mail without going through the hassle of reading and writing. E-mail will never be the same again. Nigeria may become more wealthy though…

Let Gmail Autopilot handle all your e-mail conversations.

Tiny black hole on Earth created by Large Hadron Collider. CERN admits that the real reason they shut down the LHC was due to the creation of a “tiny black hole” that they have “kept under quarantine” and are monitoring as we speak.

Qualcomm, on the cutting edge of Bioengineering. Qualcomm best known for it’s CDMA technology for wireless networks has delved into cutting edge research to improve wireless network coverage around the world. The video below takes an exclusive look behind the scenes of Qualcomm’s latest work.

Happy April Fools!

Sorry for the late post everyone between lab and March Madness (UCLA ftw!) it’s been a hectic couple days. Despite all that I wanted to write a quick post about a news feature on science journalism over at Nature by Geoff Brumfiel. Brumfiel’s article discusses the rapid decline of science journalism and questions whether science blogging can step in to fill the role.

It’s very well written and brings up several interesting points which are already being discussed all over the blogosphere. One idea in Brumfiel’s article really caught my attention and that is that since science journalism is atrocious to begin with, we’re better off without it. Larry Moran’s comment that “[m]ost of what passes for science journalism is so bad we will be better off without it” is sentiment that’s apparently shared by many bloggers and while I don’t disagree that a lot of what passes as science journalism is poor (thanks to a variety of issues e.g. dwindling budgets, lack of writers with legitimate science backgrounds) I can’t agree with the sentiment that society would be better off without some form of mainstream science journalism. Regardless of their failures, mainstream science journalism at it’s worst raises awareness of scientific endeavors within the general public and at it’s best ought to serve as a legitimate watchdog for scientific misconduct.

Even if hype and marketability play a major role in the presentation of science news stories, the exposure, discussion, and potential inspiration from scientific breakthroughs presented in the mainstream media outweigh much of the typical issues (e.g. inaccuracies, oversimplification, and generalizations) that scientists have with scientific journalism. I became curious about science by getting a taste from mainstream scientific journalism as a young student and I’d hate to see that possibility disappear.

The mainstream media’s science coverage is definitely flawed but that does not provide a necessary and sufficient justification for getting rid of mainstream science journalism in it’s entirety. Improvements can and should be made, however as discussed by Brumfiel’s article this will ultimately require a give and take between journalists and scientists. The editorial introduction to Brumfiel’s article puts it best:

[I]n today’s overstressed media market, scientists must change these attitudes if they want to stay in the public eye. They must recognize the contributions of bloggers and others, and they should encourage any and all experiments that could help science better penetrate the news cycle. Even if they are reluctant to talk to the press themselves, they should encourage colleagues who do so responsibly. Scientists are poised to reach more people than ever, but only if they can embrace the very technology that they have developed.

In the end as Bora Zivkovic astutely states “[s]omebody has to actually be paid to write about things as they come out”. There will always be a need for a “professional” science journalist of some sort and I think scientists can play a large role in helping these journalists be science journalists. The decline of mainstream journalism in it’s current incarnation provides a grand opportunity for scientists to help fix the problems that we currently see. The movement of bloggers into print media and John Timmer’s work at Ars Technica are just two examples of how scientists can begin making an impact on the scientific journalism establishment. Participation in the discussion and providing new ideas will ultimately help more than happily dancing on the grave of that drivvle most scientists view scientific journalism as.

Having read and watched a fair amount of science fiction during my formative years, I’ve always been enamored with the concept of nanobots being used within the human body to help maintain our health. While the reality of microscopic machines moving to normally inaccessible areas of the human body and performing life saving tasks is still decades away, researchers led by Professor James Friend at Australia’s Monash University have demonstrated a proof of concept piezoelectric ultrasonic motor that could be a crucial step in providing locomotion for the nanosurgical robots of tomorrow.

In the abstract of their paper they describe their concept as:

A motor for in vivo microbot propulsion is presented with a stator diameter of 250 µm, demonstrating the potential to directly drive a flagellum for swimming at up to 1295 rpm with a torque of 13 nN m. The motor uses coupled axial-torsional vibration at 652–682 kHz in a helically cut structure excited by a thickness-polarized piezoelectric element.

Piezoelectric ultrasonic motors like the one designed by the team are built to harness special materials that exhibit the piezoelectric effect. Materials like lead zirconate titanate, thanks to the piezoelectric effect, are capable of producing electricity when stress is applied as well as the converse, producing stress when an electrical field is applied. This effect is already used in a variety of everyday applications, such as electric guitar pickups as well as auto-focus in reflex cameras. The motor (seen below), called the Proteus, designed by Friend’s team is made up of three main components: the piezoelectric element, the stator, and the rotor.

The team began to design the Proteus by utilizing computer models (seen below) to produce a novel robust stator design. They determined a helically cut stator would serve best in transferring stress and turning the rotor. The group hopes to improve their model in future work by incorporating further criteria and motor components.

After utilizing computer models to design the stator a prototype was fabricated for physical tests. Various tests were run to ascertain the potential of the Proteus. The group’s tests are promising as they found the “output power [is] on the order of what is necessary to navigate small human arteries.” In addition to the promising power output, the stator design is currently “70% smaller than the smallest design produced so far”.

While the design of a small motor is still just a small first step towards in vivo swimming surgical nanobot I can’t help but think about the possibilities this innovation will lead to. Maybe Professor Friend can contact Dr. Gracias at John Hopkins about working on a swimming microgripper next.

All graphics and quotes from:

B Watson, J Friend and L Yeo 2009. Piezoelectric ultrasonic resonant motor with stator diameter less than 250 µm: the Proteus motor. Journal of Micromechanics and Microengineering.

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!

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)

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