Our brains on music…

25 July, 2011 1 comment

At the 2009 World Science Festival, neuroscientists (Jamshed Barucha and Lawrence Parsons), a psychologist (Daniel Levitin) and musician Bobby McFerrin (yes, of the “Don’t Worry, Be Happy” fame) explore the idea of how our brains accept, react to, and process music.

Bobby McFerrin’s demonstrates  our innate appreciation of the pentatonic scale using the audience as his accompaniment to produce music. Ah, the power of combining science with the arts!!

If this grabs you, you can watch the full program (all 105 min of it, including all the hard core science stuff!) here.

STEM-STEAM is it time? Are we ready?

22 January, 2011 1 comment

STEM to STEAM Conference, hosted by the Rhode Island School of Design, 20-21 January 2011

I have just returned from a truly stimulating conference co-sponsored by RISD (Rhode Island School of Design) and NSF (National Science Foundation). The conference was entitled, “Bridging STEM to STEAM: Developing New Frameworks for Art/Science Pedagogy.” Attendees included everyone from artists and designers as far-flung as Japan, policy-makers and program officers from NSF, National Endowment of the Arts, and AAAS, accomplished academicians/designers from Brown, RISD, MIT… and then there was me… mesmerized, overwhelmed, and thrilled.

I realize this is not truly a direct discussion of biomimetics or bioinspiration, for that matter, but it is directly related. STEAM is simply a reimagining of STEM (Science, Technology, Engineering, and Mathematics) with Art added in, to signify a new initiative to push for direct collaboration and synergy of the STEM fields with the arts. It also creates a clever, catchy, new acronym. My concern is with the question of whether we, as professionals, academics, students, ready for this collaboration, or are we looking instead at the generation of exactly what the new name suggests: hot air? And if we are ready, what can we do to maximize the success of this wonderful collaboration?

My personal hope is that the combination of art with the sciences will inspire and catalyze progress in both fields. To me, the contribution that art/design can make to the sciences is limitless (and thus a motivation for this blog). In the most obvious connection, art can help with maximizing the visualization and communication of our science. In fact, ask Edward Tufte, and he will probably tell you that the best scientists also have an impeccable design flair combining aesthetics with efficient information communication. See, also, the Nature Methods Points of View column by the Broad Institute’s Bang Wong, for monthly commentary demonstrating how basic design principles facilitate data accessibility. I think all us scientists have a lot to learn from our artist counterparts.

Open source software such as Circos can be used to visualize genomic data in a visually pleasing way while simultaneously enhancing communication. Shown here are ChIP-Seq, chr 22 methylation, whole-genome methylation, multi-species comparison, human genome variation and self-similarity and MLL recombinome. (from Circos website)

A more challenging aspect justifying combining arts with the sciences is in identifying how art can actually accelerate scientific progress. An excellent example of this is the use of animation software such as Maya for pushing forward X-ray Reconstruction of Moving Morphology (XROMM) development, an increasingly valuable tool for biomechanical analyses. Art can also inspire new science, as shown in the PBS documentary “Between the Folds“, in which the ancient art of origami is inspiring mathematics, engineering, and product design.

I leave the challenge of identifying how science can help the arts, to the artists, who can speak more directly about why they would want us in their world… and not for the lack of having ideas about how we can help (think prosthetics and ergonomics, for starters!).

The challenge of the STEM to STEAM conference was to discuss how we can increase the collaborations, to identify the similarities and differences among artists and scientists, and to devise strategies on how to go about bridging the gap… priming the machine, so to speak, for a rather revolutionary change in the way we all think about and do our work.

If you are out there reading this, please weigh in. I would love to hear your thoughts about this matter.

And I now leave you with a video of a project co-produced by one of the conference attendees, Jonathan Harris, called, “I Want You To Want Me.” He is only 30 years old, and already very clearly quite a force to contend with.

Evolution and genomics in anti-malware software

16 December, 2010 Leave a comment

While most “normal” people look forward to the cinnamon spices, roasted turkey, and holiday cheer typical of this time of year, starting just before Thanksgiving, I start my mad annual scramble to get posters and/or talks completed, and proposals perfected for early January deadlines. This year has been no different, as I planned in September to have a proposal written by November, and drafts circulating with knowledgeable colleagues throughout December so that I could kick back and enjoy the holidays. Yet now I find myself still drafting the first section with only one month remaining, leaping out of bed early in the morning to catch a few hours of writing before heading to work, and then rushing home in the evenings to continue the mental onslaught on my computer…

I returned last night, ready to spend an evening typing away ferociously; but upon opening my computer, I was greeted with a series of error messages and the following window:

A screenshot of the window created by malware HDDTools, meant to scare users into purchasing software.

Needless to say, this sent me into a flurry of activity. For once, I was actually relieved to discover that my hard drive was not indeed about to implode, and that this was instead the spawn of a rogue app spread by a trojan (the fact that the malware then launches into a system scan is a clue… since if my hard drive was indeed failing, it certainly wouldn’t be able to execute a scan!).

In the hours that ensued as I tried to manually remove all components of this app from my computer and then protect it against further breaches, I discovered Ad-Aware’s Genotype detection system. Here is what CNET (6 December 2010) says about Genotype:

Lavasoft first started changing Ad-Aware’s protection engine more than a year ago in version 8.1, when it introduced Genotype. This heuristics-based technology identified identical snippets of code across multiple threat mutations. In version 9, Genotype receives support from what Lavasoft calls “Dedicated Detection.” This tech looks inside files, analyzes the code, and creates a loose pattern for finding families of related malware. The company touts that a single dedicated detection signature can detect hundreds of thousands of threats. More importantly, Lavasoft expects that dedicated detection will lower false positive rates by creating more points of comparison.

So while traditional detection software worked by matching a threat to a list in a database which needed to be repeatedly updated, Genotype looks for commonalities among the components of an app to determine threat level. What this permits is a sort of almost predictive detection capability that works by evolution of known threats, permitting dynamic detection over the old, static methods. Pretty cool, no?

To read more about this, click here.

Categories: Uncategorized

The Penwald Series

2 December, 2010 Leave a comment

For those of you who loved playing with Spirograph as a child (or an adult), Tony Orrico has transformed himself into a human Spirograph… with scientific inspiration from the National Academy of Science in DC.

Categories: bioinspiration Tags: ,

Bionics in 1999

9 November, 2010 2 comments

The Fly-O-Rama created in the Dickinson Lab to study how flies maneuver during flight, by tethering fruit flies to a metal rod and giving them a virtual world to react to (see photo below for a tethered fly's eye view!).

I was rummaging through my electronic library today and came across a paper had I read over and over again in 1999 as a new graduate student with a nearly insatiable appetite. I am now realizing that it was right around the time this paper was published, that the seed of biomimetics was planted in my head. This article is written by a then faculty member at UC Berkeley (now at Cal Tech), by the name of Michael Dickinson. Even then, as a fairly new professor, it was clear that Dickinson was a rapidly rising star — one with amazing vision and a force to contend with. As the head of a fly neurobiology and flight lab, he was a pioneer in understanding the mechanisms of fly flight using self-created contraptions such as RoboFly and Fly-O-Rama, pictured above. I hope you enjoy and are inspired by this article as much as I was.

Photo courtesy of M Dickinson

The great stone house of Portugal

5 November, 2010 1 comment

Photo by Feliciano Guimarães

On the hillside of the Fafe Mountains in Portugal stands A Casa do Penedo, or “the House of Stone”. This amazing home is constructed among four large boulders with walls made of a concrete mix, created to melt the actual house into the flanking boulders. The windows overlook the mountains of Marão.

Although the home is built to blend into its natural surroundings, it still has the basic characteristics of a traditional home, with windows, doors, and a shingled roof, as well as creature comforts such as a fireplace and swimming pool, carved out of the side of a boulder.

Photo by Feliciano Guimarães

Apparently, the home was built in 1974 as a family retreat. However, with the overwhelming interest it has attracted due to its unusual design, the current owner, Vitor Rodrigues, has had to move to seek greater privacy. Also, as a result of problems with frequent break-ins, the home is now reinforced with bullet-proof windows, steel doors, and window grates. However, it apparently still contains a rather cozy interior, as shown by this video.

What do fish and ears have in common?

20 October, 2010 Leave a comment

I’ve got this great undergraduate student in my lab who is (at least for now) exhibiting all the traits of the ideal student any professor would love to have around: he volunteers ~10+ hours per week here, if no one is around, he finds things to do to teach himself new skills, he reads journal articles on his own accord that are aligned with interests of the lab, AND he’s creative! Lately, he has been trying to tackle a rather substantial challenge I presented to the lab: designing a force plate that can measure forces under granular media.

What?

OK. Here’s the context: I used force plates to measure how hard and in which directions an animal is pushing when it steps on the ground. By combining this with measured movements of the animal that I quantify by analyzing synchronized high-speed video, I can calculate how much power the muscles must produce around each joint in order for the animal to move the way it does. This technology has been commonly used since the mid-1980s or earlier, for locomotion on flat, homogeneously hard surfaces. While we know a lot about how animals move across these types of “lab environment” surfaces, we know far less about movement over natural surfaces that may shift or change squishiness, orientation, etc. with each step.

Granular media, such as sand, therefore, is a particularly interesting material to me, as it actually makes state changes as an animal moves. For example, when sand is sitting undisturbed, it resembles a solid. Yet, when an animal strikes the surface and strokes through it with its foot, the sand actually becomes a fluid for a short while. Any sand that is kicked up during the step is actually acting like a gas! With all this in mind, measuring forces on sand can be a rather challenging conundrum.

In a meeting with my undergraduate student last week, he presented a design to me that involved peppering a surface with a grid of lumps that each could sense fluid movement. Little did he know, what he was showing me was something holding remarkable resemblance to hair cells, sensory receptors that are found in our ears AND in the lateral line system of fishes!

 

A haddock with the lateral line highlighted (black line running the length of the fish).

 

Ever wonder how a school of hundreds of fish manages to… school with such regularity and neat, synchronized prowess? The next time you catch that rainbow trout, sunfish, sailfish, or whatever strikes your fancy, take a close look at the side of their body and  you’ll see a series of dashes and dots that run from the rear side of the gill margin all the down to the base of the tail. These little holes mark the external opening to the lateral line, the pressure-sensing secret for fishes.

 

Detail of a lateral lines (the dots/pores on the scales). Photo by P. Spaans.

 

Within these pores are receptors called neuromasts. Neuromasts look a little like a thimble placed open side down on a table top. Each neuromast is made up of a group of cells called hair cells, named because they (grossly) resemble a Leprocaun troll doll, with different length hair bundles mounted on top.

 

Note the uncanny resemblance between the Leprochaun troll doll's hair and neuromasts!

 

The entire neuromast is covered in a gelatinous glob, forming a cupula. Deflection of these hair bundles due to changes in fluid flow causes the production of a receptor potential. Deflection direction also stimulates the production of different types and magnitudes of potentials, enabling the fish to determine the direction of the flow. Changes in fluid flow direction or pressure can be due to an underwater obstacle, a neighboring fish, or even a predator, enabling a fish to respond seemingly magically while the approaching object is still far away.

 

Anatomy of the fish lateral line, with a neuromast pictured on the right.

 

 

It turns out that my student (I guess not so surprisingly) was not the first person to think of using the neuromast as a biomimetic sensor: a group of scientists at the University of Illinois, Northwestern University, and Institut fur Zoologie have developed nano hair cells they call ALL (for artificial lateral line) that can localize the position of a crayfish placed in a tank. Take a look at their paper, published recently in Bioinspiration and Biomimetics. Call it bias or whatever you want, I am still excited to see where (if anywhere) my student will take this biomimetic idea of his. Let me know if you have any input on how he can potentially use this to invent a new type of force plate technology, and I’ll put you in touch with my student to try to make this a reality!

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