It Takes a Village

I thought this place would have nothing to offer over the summer in terms of festivals and concerts. Who's even here for that? Are there enough people to make it a sizable event? Do businesses even bother coming out during the summer?

The Summer Solstice Fest in downtown Blacksburg proved me wrong: I've seen crowds just as big before at Relay for Life and Gobblerfest(more on that in the fall), among others. The town came alive, galvanized by all the local businesses and musicians coming together to put on a truly unique festival.

Early afternoon at the festival. The event stretched at least three blocks of  Main Street and more.

From a business perspective, Summer Solstice is an effective springboard for small companies or organizations to make themselves known and spread awareness through free stuff, the universal college student attractant, and unusual activities and games. Some showed interesting ideas:

This neighborhood committee set up a sandbox in one of the alleys right outside Starbucks. Kids play, and their parents get the sales pitch. How they cleaned up all this is beyond me.

Cabo must use the same sand guy. A DJ and plenty of lighting provided a great nightlife scene, giving off that bar by the beach feel.

This artist is an engineering professor who has been "doing sketches on the side" for about nine years. He was doing quick caricatures with a comic-book like feel to them (Think early Walking Dead Comics).

Another neighborhood complex set up this water balloon launching game, which was completely free. Never before have I heard such small children talk so much smack.

A Women's Fitness Club offered a water bottle to anyone who could do 20 pushups. If you're wondering, this was pushup #183.

 Some attractions were more legitimate than others. I didn't even know the flea circus was a real thing, but apparently it is. And it was as ridiculous as you can imagine. I learned that Flea Circus ringmasters come from a long sequence of fathers pressuring their sons to take up their flea-covered mantle. He fired a flea from a cannon. He had one wave a flag. He had another swing on bars. I felt bad for the little kids in the front row who bought into all of it. But at least he had a quirky, borderline creepy enthusiasm; I was about to leave due to the overwhelming smell of corn.

If he said "I hope this doesn't BUG you" one more time, I was about to start the Great Blacksburg Riots of 2013.  

Definitely check out The Next Three Days Blacksburg Website if you're in town. The site shows the schedule of restaurant specials, concerts, and other events for, you guessed it, the next three days.

As a dog lover, I appreciate how every local Blacksburg event is dog friendly; the sheer amount of them and their good behavior are impressive. The Solstice Fest had a petting zoo and a dog parade along Main Street. I was too busy  D'awwing to take pictures, and I only ended up getting two. Sorry.

For her talent, she played "Somewhere Over the Rainbow" on ukelele. It's a shame she lost to the  Dachsund that rolled over for ten consecutive hours.

"Hey, my eyes are up here."

Later that night, the concerts got into full swing. For an event like this, I figured the acts would be too few to last til midnight. Wrong again. And these groups weren't campy garage bands, either; you could tell they had put thought and time into their setlists. Clearly, the hosting radio channel brought in the cream of the local crop.

Everyone funneled toward the stage as the night winded down.  While the day was chock full of kids in Angry birds shirts, many more adults came out for the night concerts.

The Alexander Black House is currently under renovation/restoration on Draper road. A model of Victorian architecture, it'll also be a museum and cultural center.

The Alexander Black House should be almost twice the size of what it is now when it's finished. It provided a great backdrop for the festival, and will hopefully become a centerpiece for events in the future.


Cheers,

Ben

Week 3/4: Programming Made (Sort of) Easy

Figuring out wiring and circuitry is only half the battle; these systems need to be told what do, along with all the specifics that go with those actions. We're programming a small robot to perform certain commands, and once we have it down, we'll build a larger one. Here's where the biology comes in: instead of a small microchip giving commands, it'll be bacteria acting as the robot's brain.

For programming, we've been using Arduino, a microcontroller board that acts like a mini-computer with its own power source.

We used the Arduino UNO, but there's also the Leonardo,  Lilypad (a circular platform),  Nano, Yun, and many more. They offer different sizes, power sources, and functionality.

The UNO is about the size of a playing card, and uses its own type of code as a simpler substitute for C++, a notoriously hard code to understand.

I won't go into the nitty gritty specifics of the code, but it's a lot more straightforward. Assign a device (LED, sensor, motor) to a one of thirteen ports, and you can control under what circumstances the devices are powered through the Arduino.

Using a do-it-yourself Arduino kit with next to no instructions, we were able to put together a moving robot with four-wheel drive  and an ultrasonic sensor that could execute various commands as given by the computer; move forward, move backward, turn right and left, rotate the sensor, and record distance via ultrasonic echoes.

All four motors are connected to the Arduino through the breadboard, as is the motor rotating the sensor on the right.

Right now, the motors for the wheels are controlled by the computer; enter a positive value for moving forward, negative for reverse, and two other arbitrary variables for turning. Speed is controlled by the value entered: the higher it is, the faster the wheels move.

The circuit on the breadboard with the black chip is called an H-bridge, which can direct current in either direction. This is what allows the wheels to spin one way or the other.

Our next step is to have the sensor take over this job; much like the bacterial interface we'll install, it will send distance data to the Arduino and eventually the motors to move in a certain direction. Once we figure out the basic skeleton of the code and wiring, it's just a matter of making sure the bacteria fit in.

It's hard to see here, but we've used an H-bridge already built into a breadboard/chip to use less space. If  you take the tape off, the whole thing doesn't fall apart, I promise.

Was that not the most entertaining and interesting post ever? Maybe I'll search for the Holy Grail next week and write about that to make up for it.

Cheers,
Ben

'Burg to 'Burgh: Day 3

Carnegie Mellon University barely touches UPitt, and yet the campus has such a different feel to it. Surrounding by buildings and open quads, you wouldn't know you were in a densely populated city. Of course,  today Pittsburgh was back to its "usual" weather of cloudiness, humidity, and rain. Blacksburg, take notes.

Our workshop was held in Hamerschlag Hall, which sounds more German than Otto von Bismarck eating schnitzel in a fresh pair of lederhosen. The building houses most of the engineering department and its labs, and while getting lost, I came across a huge conference room/lab that looked just like the UN. No shortage of funding here.

Hamerschlag Hall would fit in just fine in D.C. There's also five floors below this one, with windows facing out towards the rest of the city.

We met Dr. Ruder's colleague Lina Gonzalez and several interested CMU undergrads on D floor, four floors below the hall's entrance. This workshop was meant to explain the idea behind soft lithography, an effective method for creating microfluidic devices.

Lithography was originally used in the art world: professional lithographers, sometimes students of famous artists, could effectively recreate a work by laying layer upon layer of ink and other material until the image is completely rendered. These students then sold their work; the better the quality of their re-creation, the higher the buying price.

Now this technique has been adapted to craft microfluidic channels, as seen in "lab on a chips". There's about five steps in the process, and if you're not careful in any step, or leave your material on a hot plate for too long, you have to start over. A warning:

I apologize if I get too technical. But the man who passes the judgment should swing the sword.

The dimensions of the channel itself are sketched out on AutoCAD, sent out to a company with a high-resolution printer, and the transparency is promptly returned. Next, the master template is made on a silicon wafer with SU-8 photoresist, a very viscous polymer. 

A series of UV and hot plate treatments follows, and then a developer solution is added along with several other reagents. Placed in a vacuum,  the photoresist polymer not bound to the silicon wafer is washed away, leaving only the AutoCAD design. The duration of UV and hotplate exposure it critical; the thinner the channel, the shorter the treatment time.

The wafer/photoresist solution in a vacuum.

That's developing solution in hand on the left. It washes away the portion of the photoresist not exposed to the UV light, AKA everything but the master mold.

Next, we added PDMS (Polydimethylsiloxane) to the master mold template and mixed gently. The mixture was then heated to "cure", or harden, the PDMS polymer. The section of the polymer was isolated and the PDMS layer, now with the channel pattern imprinted was peeled from the wafer.

A special kind of needle was used to poke holes at ends of the channels for adding nutrients, treatments, and the like. But the side of the hardened PDMS with the imprinted channel is open to the air. To fix this, the PDMS and a clean glass coverslip were placed in a plasma cleaner, which cuts off a small layer of electrons from the surface. Now, the PDMS and the glass can covalently bond, forming an airtight system. It was impossible to pull apart with sheer force.

The final product. That white circle is a needle insert, and you can see the branching of the channels  as transparent lines.

We got to keep the channel above as a keepsake, it makes a really good . And the CMU crowd were welcoming folks, too. The workshop gave us a great start for how we can re-create and use something like this for our own projects.

Cheers,

Ben

'Burg to 'Burgh: Day 2

We headed into the Steel City early Sunday morning, coming in through the Fort Pitt Tunnel. The mountains surrounding the place bear a resemblance to those around Blacksburg in that you can see them miles ahead, but steep cliffs from the result of blasting dot the Pittsburgh perimeter.

That pointed building ahead is called Fifth Avenue Place, a shopping and office complex. The mast at the top sways  a good three feet in high winds.

 We passed through the University of Pittsburgh several times due to its central location, much like VCU in Richmond. It has more quads and recreational fields of its own though, and its buildings blend in with the cityscape, save for one:

The Cathedral of Learning has 43 floors with public access to the  36th. Despite the name, no religious events are held here.

The first few floors are the equivalent of Tech's Torgersen Bridge, a quiet study area for students, while the higher levels house offices for the Honors Program, Study Abroad, etc. A few students were at work, but we mostly saw visitors like us walking around.

I wonder how that old Headmaster is doing these days. Oh wait...

From the 36th floor. The Carnegie Museums are on the left, with a quad for communications majors on the right.

Our first stop was the Carnegie Museums of Art and Natural History, both located in the same building. We didn't have time to visit the Carnegie Science Center or the Andy Warhol Museum, also in Pittsburgh. I can only appreciate a soup can for so long.

The Natural History Museum progressed in an evolutionary fashion, from dinosaurs all the way up to modern mammals and other cool things that can kill you.

The windows in the back show the museum's library, with over 132,000 volumes.

  Among the displays I recognized a model of a T. rex skeleton  I had seen before: "Jane", which I saw on exhibit when I was 14 at the Burpee Museum in Rockford, Illinois, where my mom's family is from. The actual "Jane" in Rockford is the best preserved and most complete skeleton in existence of a juvenile T. rex. My sister is also named Jane, who is also a cold-blooded reptile (sometimes).

Plenty of other animal exhibits from around the world were on display, such as this one:

A French naturalist and taxidermist witnessed this badass scene and recreated it in the late 1800s, entitled "An Arab Courier Attacked by Lions."  The courier has killed the lioness here with a shot to the head.

It's probably thanks to this guy that Barbary lions are now extinct. And yet, the public and art world of 1898 thought this was so discomforting and unsuitable for display that the Carnegie Museum acquired it for only $50.

The art museum has everything you would expect and then some; a giant statue room, a large atrium with casts of famous buildings and sculptures, and art pieces sorted by style and civilization. Japanese prints, Renaissance art, and Hindu idols were all there.

The modern art section is another story. If you've seen Banksy's documentary "Exit Through the Gift Shop," then you know how confusing modern art can be. It's not supposed to make sense. You're not supposed to piece together a story or find an underlying meaning from it. Scratching your head and wondering what the hell you're looking at is the point.

The first exhibit in the modern art section. I think I did something like this in third grade and got a C+.

Slenderman has really let himself go.

Yes, this is a looped video of a cat drinking milk. And yes, this is in the modern art section.

A more artsy piece called the "Walking Man".  It sold at auction for *Raises pinky  to mouth* $100 million dollars! But this isn't the only one; there are five more models.

After giving up trying to figure out what everything meant, we took a wooden gondola up to Mount Washington, which offers many high-end restaurants and homes along with a great view of the Pittsburgh skyline. Unfortunately, we weren't dressed for the occasion.

The gondola during its 300 foot descent. The red building below is an old train station converted into a shopping and tourist center.

 From the top of Mt. Washington. Heinz field is centered here, home of the Pittsburgh Steelers. Nice try, Bane.

Our workshop at Carnegie Mellon started early the next morning, so we left after eating to rest up and read over some papers. Pittsburgh has a lot to offer, and it can't be covered in a single day. A Pirates/Steelers game in town would definitely make a great second trip.

Cheers,

Ben

'Burg to 'Burgh: Day 1

It's our first weekly lab meeting, intended to discuss our objectives for the next week each Friday. We plan a schedule for working on our project (discussed in a later post) and review the papers we've read. Dr. Ruder mentions an old colleague of his who's "a pro" at creating microfluidic systems via soft lithography and happens to be holding a workshop on the 10th. In other words, her research fits in well with our goals, and learning to recreate what she does will help us better understand our project. Mentioning that her lab is up in Pittsburgh, Ruder then asks us, "Are you free this weekend?"

The next morning I'm on the road with my two co-workers. The drive's five hours, but considering the 18-hour Illinois trips I'm used to, it was nothing. We stayed at my fellow Scieneer Sean Hardy's house in Peters Township, about a half hour's drive from the city. Although the workshop was held on Monday the 10th, we left on the 8th so that we could spend a day exploring the city.

Peters Township is a suburban area with your basic shopping outlets, chain restaurants, and an excellent school system; definitely a good place to raise a family. Sean's dad owns a good deal of property in the area, and judging from his memorabilia and the fact that we caught him right after a game of golf, business is going smoothly.

That's "Mean Joe" Greene's autograph second from the right. I couldn't try on the sweat-covered jersey, though.

We decided to look into a local candy store called Sarris Candies, a small business started up by the late Frank Sarris in nearby Canonsburg. Sarris started the business developing formulas in his basement, before starting up his own store, which to this day refuses to expand, still run by the Sarris family. The interior looks like what you'd expect in a candy store, save for this modern marvel of chocolate engineering (which will probably be offered as a major here at VT in 2016):

I really hope the AC never breaks down in here.

Would I want Head Chocolatier on my resume?
Absolutely.

Sarris's shop has raked in countless small business awards and continues to be a major player in the community, supporting countless local teams and schools. Signatures of countless celebrities and athletes line the walls, some frames picturing Frank Sarris greeting them. It's definitely worth a look if you're in the Canonsburg area, as it's a place that really gives off that "Small Town America" feel.

Oddly enough, the whole place was staffed by  18-20ish-year-old girls. Nice one, Sarris.

Cheers,

Ben

The Local Flavor

I said most of my posts would be about my research in Blacksburg, but I've decided to post about the things I see around town; the festivals, the events, you name it.

There's plenty of shops and eateries around here, but one gem I recently discovered was the Farmer's Market, literally a few steps off campus. Vendors come from all across Virginia (Floyd, Roanoke, Willis, Pearisburg, and more) with all kinds of edibles and antiques.

On a busy day, most vendors can't fit under the wooden awnings.

Plus, there's plenty of people watching to do; for example, take this dapper gentleman below:

The Bagger Vance of Blacksburg makes an appearance.

I talked to one of the head organizers of the market, and asked her about all the oldies posters I kept seeing. They had a early 1900s-old-advertisement-like feel to them. If you've played "Bioshock Infinite," you know what I mean.

Local groups in Blacksburg play at the market every Saturday. Mumford and Sons could come and play that one song with the banjo.

The market organizer told me that a professor in the visual arts department puts the designs together, and they're so popular that they can't put them up around campus because people will steal them. Luckily they were selling old posters at ten bucks a pop, so I had to get one:

They seemed to have a poster for every major event at the Market.  4th of July, Summer Solstice, cook-offs and more had their own unique designs.

And you won't find friendlier vendors anywhere else. Even if you're not looking to buy, all of them are approachable, and don't stand over you expecting you to buy something. I met one woman named Rhonda at her stand called "The Mischievous Carrot Farm" which she operates in Floyd, less than an hour away. 

She lives in a yurt, a portable tent-like structure with felt and wool siding where she makes new and unique products from previously used textiles, among other wares. Check out her site, it's got a lot to offer! 

http://www.mischievouscarrot.com/

A more modern take on the yurt, previously used in the steppes of Central Asia. There's also an oculus in the top's center for stargazing.

There's also homemade tea, coffee, grilled meats, and burgers and other things to raise your cholesterol.  Weekly free concerts are put on in the market square every Wednesday, which I plan on checking out. It's easy for me to forget the culture around here when I'm so consumed with school, and the market's a great little slice of that.

So go if you're here. Talk to people. Ask questions. Threaten some small children with a hand-carved cane. And you might just see me there trying to barter with/for goats or something like that.

Cheers,

Ben

Week 2- Honey, I Shrunk the Lab!

I've been looking over several papers this week, including Dr. Ruder's research proposal to the ONR (which is confidential) and a more general overview of the "lab on a chip" (LOC). Here's what I read/understood:

I was really hoping they'd shrink me down for the day and have me work like this. Put Rick Moranis in the mix too, and we'd have a Disney movie on our hands. But imagine each scientist here and their respective equipment reduced to a minuscule size and placed on a chip several millimeters in length, They could still carry out the same tests and find the same results, albeit on a smaller scale. You also wouldn't be able to hear them complaining the whole time.

Talk about cutting edge. Not only does the miniaturization of a laboratory like this one save cash and resources, but the liquid dynamics (or microfluidics) involved have countless practical uses. For example, the diagram above shows a chip dealing with the Polymerase Chain Reaction, a process that amplifies a desired portion of DNA. The pathway eventually leads to the electrophoresis section, which separates the DNA into bands. Usually, this requires an agarose gel and an specific electric current separate from the PCR reaction, but in the LOC, it's all integrated. You can trace the entire path(s) from start to finish.

 The small amount of liquid required provides numerous benefits: less waste, shorter diffusion distances, and lower cost, among others, allowing for a fast, efficient, compact system. Electric circuits and programming are both involved in making this possible, but from what I've seen, the circuits aren't terribly complex.

Integrating so many functions on one platform reminds me strangely of a eukaryotic cell and its functionality; both have interconnected pathways that make efficient use of space. And although it's cheap to manufacture in large numbers, I feel like I would lose these things all the time. And that's why I never bought an iPod Shuffle.

Several different LOCs mass produced by Agilent Technologies. The colors most likely code for different integrated tests/analyses. 

What first came to mind for me was if we could engineer LOCs to detect disease. Doctors could run diagnostic tests, especially in third world countries, at a quick and hopefully efficient rate without transporting pounds of lab equipment from village to village. If this could be adapted to work in this context, such technology could drastically change the medical environment.

Despite the kinks that scientists claim they need to work out of LOCs, the fact that one small chip can do so much with so little is ridiculous. Analyze unknown DNA? Detect cancerous cells? Diagnose HIV? Play Pokemon games in high definition? It seems to me the LOCs have become a new medium for which previously studied concepts can be applied. I hope to utilize such a platform for my research once it gets underway in the next few weeks.

Cheers,

Ben

Week 1- I've always dreamed of being a [wire] stripper

I had my research orientation on May 28th, which included meeting my research group and many others both familiar and new. Many friends who had stayed here for the summer told me Blacksburg was nothing but a ghost town, but in the auditorium of the Fralin Life Sciences building, it sure didn't look like it.



I was also impressed at how friendly people were. I've had my fair share of awkwardness in large groups that already know each other, but in this setting, someone pressed the reset button. Everyone was on the same unknown page, and it was great to have that opportunity to comfortably meet so many people with a shared interest again.

My first day in the lab started off with a meeting with Dr. Ruder, my project mentor. The guy's one smart cookie with a heck of a resume: B.S. in civil/environmental engineering at MIT, and eventually a Ph.D. in Biomedical Engineering at Carnegie Mellon. During his post-doc years at Boston University he worked with James Collins, considered one of the founders of the field of synthetic biology. He completed his first year here as an associate professor in BSE this year. Did I mention he's only 33?

 He explained to my fellow Scieneer Sean Hardy and me what we would be doing in the ten week span in the context of his research. He said we would be developing unique individual projects, and when he said the job was "more than just pipetting things," I knew I was in the right place.

But since the job was more than just pipetting, it included other concepts unfamiliar to me. But walking into the unknown is part of the experience, too. Dr. Ruder gave us this week to familiarize ourselves with the beginner electronic kits in his lab, so that we could better understand his projects.

One of our final products looked like this:

Nah, I'm just kidding, this is more like it:

It all felt like playing my Lego sets all over again, minus the pain from stepping on them. The manual provided basic information on capacitors, resistors, transistors, and LED lights, and from someone who knew nothing about electronics, I can say I learned something. We made a circuit like the one above, a working loudspeaker, and a few other toys. Other techniques, such as wire tying and stripping, came eventually as well.

Soldering was the hard part, although the most fascinating. It involves the joining of two metals by means of a third metal with a lower melting point. The third metal used to be made of toxic lead, but has been replaced by almost 100% tin material. When heated, the soldering iron instantly melted the tin wire, which we placed between the two wires. When we pulled the iron back, the liquid formed a solid in less than a second. Not only that, but the synthesized joint, when done correctly, could not be pulled apart by force and still conducted an electric current. I would solder myself a suit of armor if I had more time. Either way, soldering has more industrial/mechanical applications than I can count.

Dr. Ruder gave us a few papers to look over, one of which I cannot discuss. We'll be taking  elements from his research to implement in our own projects, mostly in synthetic biology. I'll post again this week once I have a clearer idea of what I'm doing.

Bio

"Opportunity is missed by most people because it is dressed in overalls and looks like work."

         -Thomas Edison


I've written journals before, but never on a consistent basis. I would eventually get tired of trying to keep track of myself and what I had done and felt that day. This blog is for me to share some of my experiences here in Blacksburg over the summer in the hopes that I can keep it going more easily on a computer. Well, that, and the fact that I can make my obsession with Emma Stone-Watson known to the public.

Here's the short version:

I'm a biological sciences major at Virginia Tech, Marching Virginian, avid swimmer/runner, and coffeeholic, to name a few.  With the MVs, I've been to Orlando, Charlotte, New Orleans, and many other ACC schools. Say what you will about our team, but I can't complain about the free trips.

I've lived in Lee Hall for two years as a part of the Da Vinci Biological and Life Sciences Living Community, the second year returning as a mentor. I'm here for the summer working with the scieneering program (an interdisciplinary study of science, engineering, and law).

I'm working for the summer under Dr. Warren Ruder in Biological Systems Engineering on biosynthetics, the explicit details of which I'm not allowed to discuss. Don't worry, we're not making constructing cyborgs to enslave the human race. Yet.

I'll be updating this blog on just about everything: local Blacksburg events, Scieneering/research happenings, what color my pee was this morning (not really), and anything of note that comes to mind.

Cheers,

Ben