Courtesy Mark RyanLast October, I attended the Geological Society of America’s annual meeting held here in Minneapolis. The convention presented plenty of opportunities to hear the latest ideas in geology, paleontology, and planetary science but the highlight for me was being able to join a GSA field trip on Lake Superior aboard the research vessel, the Blue Heron.
Courtesy Mark RyanThe 86-foot vessel is owned by the University of Minnesota-Duluth (UMD) and operated by the Large Lakes Observatory (LLO), an organization created in 1994 for investigating the geochemical and geophysical properties of large lakes, and their global impact. To accomplish this research, the LLO required a worthy vessel for limnological research, and the Blue Heron was purchased just three years later.
The vessel docks at the Corps of Engineers Vessel Yard on Park Point (aka Minnesota Point), a natural sand bar separating Duluth’s harbor basin from Lake Superior. The ten-mile spit was created by the lake’s wave action on material deposited by the St. Louis river, and is supposedly the largest freshwater sand bar in the world. Field trip leaders Doug Ricketts, the marine superintendent at LLO, and Charlie Matsch, professor emeritus of geology at UMD, greeted arriving participants and divided us into two groups. While one group spent the morning on Lake Superior, the other visited geological highlights in the Duluth area with professor Matsch. In the afternoon the groups switched places.
I joined the morning shift on the lake with a dozen geologists made up of GSA attendees from Minnesota, Wisconsin, and City University of New York. Besides Doug Ricketts and the ship’s five crew members, regents professor Tom Johnson, and the director of the LLO, professor Steve Colman, were also on hand to help demonstrate and explain the Blue Heron’s research capabilities.
Courtesy Mark Ryan
Courtesy Mark RyanWe shoved off right on schedule, heading across the harbor toward the Superior entrance on the Wisconsin end of the sand bar. The crew spent this time going over the ship’s safety rules - how to descend ladders, which alarms meant what, how to communicate with the bridge - that sort of thing. We then made a quick tour of the facilities. The Blue Heron is equipped with a wet lab on the open deck and two dry labs inside, and all sorts of data gathering equipment for geophysical, geochemical, and biological sampling. These include multibeam sonar for profiling the lake bottom and sub-bottom, several coring instruments for collecting sediment samples, and water samplers able to collect at various depth levels in the water column while also measuring such things as temperature, depth, pH levels, and conductivity. There’s gear for tracking lake currents, and plankton nets and a trawl for gathering biological data. Inside, both above and below deck, computers record, display and analyze the gathered data. Many of the off-ship instruments can be monitored and controlled on-board from computer consoles.
Courtesy Mark RyanThe R/V Blue Heron is outfitted to carry five crew members and six researchers and can stay on the lake, around the clock, for 21 days between port calls. It’s used mainly on Lake Superior, the largest and least studied of the Great Lakes. Shipboard amenities are sparse (there’s no television or DVD) but include eleven bunks, a full galley for food preparation, dining table, shower, and of course, the "head", or as you landlubbers like to call it, the toilet. Internet service is sometimes available when the vessel is near shore.
Courtesy Mark RyanUpon entering Lake Superior, the crew set to work demonstrating some of the vessel’s science gear, which is pretty much the same kind of instrumentation used in oceanographic research. Just beyond the Superior entrance, the EchoTech CHIRP/sidescan sonar tow fish was lowered from the Blue Heron’s stern. This bright yellow instrument is towed underwater behind the vessel as it makes several passes over the lake bed, and able to gather hydrographic and bathymetric data. One function is to send out an intermittent, low frequency “chirp” pulse that can penetrate the sub-bottom and record changes in its geophysical properties. The sonar data is processed using on-deck computers.The first demonstration was a scan of the underwater channel of the Nemadji River, a Wisconsin tributary to the lake. The mouth of the Nemadji has been drowned by a process called post-glacial rebound or more scientifically, differential isostatic rebound. During the last ice age, a mile thick sheet of ice covered the region and placed enormous pressure on the earth’s crust, depressing it downward. As the glaciers retreated, that enormous weight was gradually removed, and the lake basin began to rebound (a process still going on today). But the northern and eastern ends of Lake Superior basin are rebounding at a faster rate, tilting the water southward and to the west and subsequently flooding those areas of the shoreline.
Courtesy Mark RyanAs the submerged tow fish was doing its stuff, we all gathered at a couple workstations in the lower deck dry lab to watch as images appeared on the computer screens. In one, you could plainly see the distinct profile of the Nemadji’s drowned riverbanks.
Courtesy Mark RyanThe other monitor displayed bathymetric information being picked up by the duel frequency sidescan sonar. Printouts of the lakebed topography, created from a mosaic of stitched-together scans, were laid out on a worktable with several charts and maps.
Courtesy Mark RyanFor the next demonstrations, the Blue Heron moved out several miles onto the big lake. We’d all been warned of the lake’s fickle weather, and told to bring proper attire, just in case. Having been raised in Duluth, I was well acquainted with Superior’s moodiness, especially in autumn, so I brought along rain gear, a jacket, and an extra sweatshirt, expecting the worst. But I was most comfortable in jeans and a t-shirt. Cloud cover was sporadic, and while the water temperature was only around 49 degrees, the air temperature hovered in the mid to upper 70s during the entire excursion. We couldn’t have hoped for a nicer day; a perfect Duluth day, as we used to call them.
While some of the group watched the crew prepare for the next presentation, others enjoyed lunch (sandwich, chips, fruit and a cookie) at the galley dining table. During my lunch break Tom Johnson told me the story of how the university came to own the research vessel. In her previous life, the Blue Heron was known as the Fairtry a commercial fishing trawler that fished the Grand Banks in the northwest Atlantic (like the Andrea Gail in The Perfect Storm). UMD purchased it in 1997 and Tom sailed it from Portland, Maine, through the St. Lawrence Seaway and across the Great Lakes to Duluth. Despite some minor engine problems at the start, he said it was a fantastic two-and-a-half week trip. Over the next winter, the Fairtry was converted into a limnological research vessel and re-christened the Blue Heron.
Courtesy Mark RyanMeanwhile, out on the back deck, the crew was ready to launch the next instrument, a carousel of canisters called Niskin bottles used for sampling the water column.
Courtesy Mark RyanThis device is lowered into the lake and controlled remotely from the deck, and can collect samples at various depths into any one of its dozen canisters. It can also measure temperature, conductivity, pH balance, transparency, dissolved oxygen levels and other tests. After deployment, marine technician, Jason Agnich, sat at a computer workstation just inside the hatch, and easily controlled the carousel with a joystick while monitoring its progress on a couple electronic displays.
Courtesy Mark RyanWe moved a little farther down lake where two coring instruments, a spider-framed multi-corer, and an arrow-like gravity corer were put into action. The first can collect several shallow core samples by lowering it by winch to the lakebed, while the latter is dropped like a giant dart deep into the sub-bottom sediment for one large core.
Courtesy Mark RyanAfter each was raised back to the surface, the collected core samples were removed from their tubing and laid out on the wet lab table for study. We all huddled around the workbench as each core was cut open with a knife so participants could take a closer look. The sediment cores were composed of a densely packed fine-grained mucky silt as brown as milk chocolate, and appeared more appropriate for a scatological study than a geological one, to me anyway. But that didn’t stop some of us from taking home a small plastic bag of it as a souvenir.
Courtesy Mark Ryan
Courtesy Mark RyanAs we made our way back toward the harbor, I stood at the starboard rail and took in the beautiful autumn colors lighting up the lake’s distant North Shore. We were three, maybe four miles offshore but I was able to pick out my old stomping grounds in Duluth’s east end. The old neighborhood – like much of the city - was built up on terraces formed by past shoreline configurations of prehistoric Lake Superior. Duluth’s Skyline Parkway, a boulevard that skirts the hilltop across the length of the city was built on an old gravel beach line of Glacial Lake Duluth when the water surface was nearly five hundred feet above its present level. The bridge over the mouth of the Lester River was just barely discernible from where I stood but it was easy to spot the large swath of dark pine forest that encompassed Lester Park and Amity creek (the western branch of Lester river) where my friends and I used to hang out. It’s also where Charlie Matsch would guide our group later in the afternoon. He brought us there to examine the Deeps, my favorite old swimming hole carved out of the massive basalt flows that extruded from what’s now the center of Lake Superior during the Mid-continental rifting event that took place nearly a billion years ago.
Courtesy Mark RyanWe returned to port through the Duluth entrance, and as we entered the canal captain Mike King announced our arrival with a blast of the Blue Heron’s air horn. Duluth’s landmark Aerial-Lift Bridge, already raised for our return entry, responded in kind with a shrill loud blast of its own. Tourists lining the pier called out and waved as we passed the old lighthouse and rolled toward the harbor. We all waved back and I have to say it was kind of a thrill, for me anyway, after having participated in the same ritual, oh probably a hundred times in the past but always from the pier not from a vessel.
Courtesy Mark RyanThe Blue Heron swung in through the harbor, and soon we were back at port where we started at the Corps of Engineers Vessel Yard. Charlie Matsch was there to greet us and take for the second leg of the field trip.
Charlie took us first up the hillside to the rocky knob near the landmark memorial Enger Tower where he showed us some interesting exposures of gabbro, an intrusive rock common to the geological formation known as the Duluth Complex. Much of the bluffs west of downtown Duluth are composed of this dark, course-grained mafic rock. Now, I admit I enjoy a geological outcrop as much as the next guy (especially when a real geologist is explaining it), but it was the sweeping view from the hilltop that drew my attention.
Courtesy Mark RyanThe lake and harbor and much of the St. Louis river bay stretched out below us in an array of vivid blues contrasting with the bright reds and golds of autumn. On one side of the harbor, bridges, railroads, and structures of industry jutted out on Rice's Point toward Wisconsin, paralleled on the other side by the slender ribbon of Park Point. As I took in this grand vista, a small, barely discernible bluish blur of movement caught my eye. There, cutting through the harbor, the Blue Heron headed southward toward the Superior entrance for another run on the great lake.
Andrew Hessel hopes that an open source approach in pharmacology will produce safe, effective, and individually personalized medicines quickly and inexpensively. Hessel likens the exponential advances in synthetic biology to the boom in the electronics industry.
One big difference, though, is that biological manufacuring does not require expensive refining, huge factories, or expensive tools. Biological organisms are alive and can self assemble complex structures from basic ingredients.
Foundational work, including the standardization of DNA-encoded parts and devices, enables them to be combined to create programs to control cells.
- Cells are being engineered to consume agricultural products and produce liquid fuels.
- Bacteria and yeast can be re-engineered for the low cost production of drugs. (Artemisinin, Lipitor)
- Bacteria and T-cells can be rewired to circulate in the body and identify and treat diseased cells and tissues. BioBricks.org
Eric Fernandez has a blog for do-it-yourself types like 23-year-old Kay Aull who set up a do it yourself DNA lab for genotyping her GFE gene in her closet! Be sure to check the archives for more than a hundred informative DIY Bio posts like this one by Make's, Mac Cowell.
Costs are coming down fast and genetic synthesis or gene fabrication is a cottage industry. Biofabs like GeneArt, Blue Heron, DNA2.0, and Codon Devices can deliver a synthesized product from an e-mailed description almost over night. Synthetic biologists envision writing the DNA code for such products the way computer programmers write software.
The Registry of Standard Biological Parts is a continuously growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems. Founded in 2003 at MIT, the Registry is part of the Synthetic Biology community's efforts to make biology easier to engineer. It provides a resource of available genetic parts to iGEM teams and academic labs.
The International Genetically Engineered Machine competition (iGEM) is the premiere undergraduate Synthetic Biology competition. Teams participating and over 1200 participants will all specify, design, build, and test simple biological systems made from standard, interchangeable biological parts. If you go to this iGEM results page you will find video links for the winning presentations. You can read team abstracts of the iGEM projects here.