Interview with David Thornton, Biodiesel Guru

This is an edited version of a slightly longer interview which I may post later- edited because of size constraints for the Spring 2012 issue of Tigra Scientifica for BioSc 494: Popular Science Journalism.
The Clemson Clean Energy project is pretty neat- check them out here!
 

Danielle- The green energy and the biodiesel and the zymology projects are all interconnected. How many related projects are there?

Thornton- Well, we’re going to have to make a lot more Creative Inquiry sections next year because in Green Energy and Biofuels there’s four different groups. One group- all they care to do is make biodiesel. They just want to master bioprocessing and make biodiesel on the pilot plant, and that’s how the pilot plant program got started. Another group looks at how to produce more oils, and one way was to take cafeteria food waste and process it using black soldier flies that will also produce a protein meal, meanwhile turning the organic food waste into compost that they’ll use at the organic farm. We actually just finished, or we’re in the process of constructing that digester right now.

D- You’ve already done some of the feeding of cafeteria waste to the black soldier flies?

T- We’re building our prototype right now, so we’re doing something that’s a tenth of the scale of the final one, and hopefully we’ll start feeding it next week.

It’s a 12 day loading time, and for every square foot of surface area it can process three pounds a day of food waste. It’s not that much, about two fistfuls. Once it goes through a pulper, and it has a lot of water…  but it’s per square foot, so for each tile on this floor you dump that much food in there and the flies will eat it. They self harvest and they self propagate.

D- Okay. So when you mean self-harvest…?

T- They try to climb up to pupate, and what we do is they train them when they have to pupate so they go through these little channels, and they just jump into our bucket!

D-Well, that’s convenient. What other projects are there?

T- Well, we have one trying to make jet fuel out of sunflower oil, which we have some locally produced sunflower seeds. We pressed them in the press we have over at McAdams, and then we refine that oil and convert it into biodiesel. So basically, we’re trying to make this sample of biodiesel and probably only 25% of it will be these polyunsaturated acids which will be very favorable cold flow. We’ll at least be able to take that fraction and send it off for some testing to see if it’s a good source of blended jet fuel. The remaining 75% will melt down and be good transportation fuel. But it is kind of energy-intensive because we’re using freezing cold temperatures to separate it. Just a start to see how our sunflower will perform.

D- And that started this semester, so it’s kind of a new project?

T- Yep, we have one student who-  I think he’s from mechanical engineering- he’s also a pilot and he’s very interested in how to make jet fuel. The Department of Defense and the military are very interested in jet fuel as well, so it’s a possible source of funding if we get good preliminary results from regional sunflowers. This could be a good way to stimulate that production. And there’s another group…

T- We have another creative inquiry called Coproducts, and they make soap, degreaser, and they kind of overlap feeding yeasts and feeding glycerol to algae. So that’s where the overlap really occurs. I’ve actually got four classes going on right now without me there- they made some degreaser and they’re cleaning our biodiesel processing trailer.

D-Sort of doubles as doing work and cleaning up the lab?

T-Yeah! So they’re taking pictures and documenting, they cleaned it with just warm water, they cleaned it with conventional degreaser, and then they cleaned it with their degreaser, taking pictures of each different form, and comparing their pH and their effectiveness, and how much it costs per volume of cleaning. That’s just kind of a fun one that’s not a really scientific but very practical and applicable. If we could convert all of our glycerol on campus to some of the degreaser to clean the floors in the labs, and the rest of it feed it to algae, it’d be an elimination of our waste stream right now to generate value from the coproduct. Part of biosystems engineering is eliminating the term ‘waste product’. Waste is but a resource misused. That’s why we do all this research on finding uses to support the economics basically of renewable fuel production because they’re not so favorable right now.

D- Yeah. And it sounds like you’re sort of working to self-contain systems, like you mentioned with the ethanol and the algae used to go back into the biodiesel and then take the glycerol waste product from that and use it in these other products and it just cycles.

T-Yeah. And that just ties into what our creative inquiries are going to turn into-we’re trying to do a more integrated research approach on, to create on campus an integrated biorefinery.  It means you’d be producing ethanol and biodiesel, and taking those waste products and then powering the plant with gasification using the waste products- or coproducts from those other things. You’d be producing each of the three mainstream biofuels, which are ethanol, biodiesel, and methane that can come in many forms, either anaerobic digestion, methane gas, or in this case, synthesis gas produced from gasification, which are predominantly methane. They could replace propane or natural gas. Self-contained is the goal. That’s the point of this system.

D- Have you gotten a lot of feedback from campus outside of the biodiesels group, like from Aramark?

T- Yeah, we work closely with Facilities… And Aramark, actually- they were the first company to agree to this because it’s their oil and they’re essentially letting us have it to make biodiesel. We can make probably about 3,000 gallons of biodiesel a year. Last year I think we made somewhere around 2,000 gallons. Some of that oil’s disappeared- I think people were thieving it from the receptacles, so now we have locks on our dumpsters. We’re getting a lot more oil, so we know something was wrong last year. This year we should be getting at least 3,000 gallons from just the oil from Aramark. We’re also picking up from Brioso, the new Sweetgrass restaurant, Crocs… but facilities is supporting us to grow. They want us to get to 10,000 gallons a year, which will be half of the diesel fuel consumed on campus. We’ve been running 20% biodiesel, and this week we’re going to bump that up to 25% biodiesel, and gradually get up to see if we can get some vehicles running on 50% biodiesel during the summer months. We have a few vehicles in our department that we run on 100% biodiesel. The feedback from facilities is positive; we just need a way to make more fuel. Hence, we have this research, right?

The New Fisheye View: The Sea in HD

This appeared in the Spring 2012 edition of Tigra Scientifica for BioSc 494: Popular Science Journalism.

The world as we see it is full of a bewildering number of hues, enhancing life with a spectacular array of shades. What if there’s another layer of information and detail we can’t sense, though? Humans only see a small portion of the electromagnetic spectrum. Unlike us, some animals see polarized light, which enhances their world even more, analogous to adding color to a black and white image. In a study at the University of Bristol published in Current Biology February 2012, Dr. Shelby Temple, Professor Justin Temple, and collaborators have discovered that cuttlefish have the most acute polarized vision of any animal observed so far.

            What makes polarized light different? Polarized light rays vibrate in one plane as opposed to multiple planes like other light rays. For humans, polarized light usually means reducing glare with sunglasses or watching a movie in 3D, some organisms have greater purposes for it. In other animals, polarized light is used for navigation and orientation. In 2006, Savannah sparrows were found to use polarized light to determine where north and south is more accurately. The researchers believe that animals may use polarized light in predator/prey detection and in signaling and communication, especially in cephalopods like octopus, squid, and cuttlefish. The cuttlefish species studied here cannot see what humans consider to be visible color wavelengths, so polarized may substitute as a method of seeing the details of its world.

            So, how do you give a cuttlefish an eye exam? To examine the sensitivity of cuttlefish vision, the researchers took LCD computer monitors and removed the polarizing filter. A video was played for the cuttlefish in which an expanding circle mimicked the appearance of a looming predator.  These circles were shown at different levels of grayscale and different angles of light so they were only visible to creatures with polarized sensitivity. When they detected the movement, cuttlefish responded by changing skin patterns. Cuttlefish responded to differences as small as one degree of polarization, significantly more precise than previous species like octopus and crayfish examined which responded to differences of 10 to 20 degrees. 

The researchers also analyzed low- and high-resolution sight by examining images of aquatic life. Because we can’t see differences in polarization, false colors were substituted, and the team found that while animals disappeared into the background in the low-resolution images, they were visible in the high-resolution analysis. This leads Professor Temple to note that camouflage in the polarization dimension has not been investigated and could be the reason why cuttlefish and other predators may have developed high sensitivity to polarized light. The mesmerizingly detailed patterns cuttlefish flash on their skin may also use polarization for detailed signaling and communication, but more research is needed. This study is a great beginning to investigation of alternative ways to sense the world and could be applicable for finding out how animals and plants signal each other- imagine if there were giant ‘DO NOT EAT ME; I’M POISONOUS’ signs we’re not even aware of in everyday life. Perhaps eventually humans too can tap into this other level of vision for navigation and communication purposes. 

 

http://www.sciencedirect.com/science/article/pii/S0960982212000115

Practice Makes Perfect: Musical Training has Long-term Impact on Neural Responses

This article appeared in The Tiger on February 17th, 2012 and in the Spring 2012 edition of Tigra Scientifica for BioSc 494: Popular Science Journalism. 

While many people have heard of the pseudoscientific “Mozart effect” on learning, what if actually learning to play music has an even greater, biological benefit? Many musicians start learning their instrument from an early age and continue playing for years to come, spending many hours practicing and playing. As people age, neural responses to aural stimulation slows down, and may lead to issues in communication skills. In January, a study by Dr. Parbery-Clarck, Dr. Nina Kraus and, others published in  Neurobiology of Aging shows that musical training may alleviate age-related delays in response to audio stimuli.

            Why might musical training play an important role later in neural response speed?  Musical training requires a musician to learn to recognize differences in pitch, timbre, and timing— how high or low a sound is, the ‘voice’ of a sound (think how a gravelly old man sounds different compared to a young girl’s soprano), and chronological placement respectively. Dr. Kraus noted in a previous paper that these components are also used to recognize speech. Pitch and placement are needed to understand what people say, particularly in more tonal languages, and timbre helps us distinguish different voices from each other.  Music has also been linked to the adaptability of the brain to learn new tasks and has already been used in speech and motor therapy for stroke victims. Observing how fast a brain responds to sounds may shed further light on how musical training affects auditory responses.

This study looked at nearly 100 participants. They were divided into four categories: older nonmusicians, younger nonmusicians, older musicians, and younger musicians. “Younger” people were 18 to 23 years old, and “Older” people were 43 to 65 years old. Musicians were defined as individuals who began their musical training before the age of nine and continued to play at least three times weekly throughout their lifetimes.  The research team played the speech syllable “da” (chosen for its mix of consonant and vowel sounds) periodically through headphones for participants during a silent captioned film of the patients’ choice. The research team then measured brain responses via electrodes, observing how soon the subcortex responded after the syllable was played in microseconds. 

The researchers found that older participants had slower responses to speech syllables than younger participants. However, the older nonmusicians had significantly later responses than young nonmusicians, while the disparity between older and younger musicians’ responses were narrower. As the speech syllable transitioned from the consonant ‘d’ noise to the vowel ‘a’ sound, older musicians actually had similar response times to younger nonmusicians. The research team concluded that aging negatively affects the processing of noise, especially consonant sounds, but also that musical training reduces those effects.

While these findings are preliminary, previous studies from Dr. Kraus’s laboratory show that musical training is also linked to reduced hearing and memory loss. The research team believes their findings should encourage future investigation into training for keeping neural resilience, the capacity for learning, intact over a lifetime. Dr. Kraus also noted that the study doesn’t necessarily show that musicians have a neural timing advantage to every neural response to sound, but "instead, this study showed that musical experience selectively affected the timing of sound elements that are important in distinguishing one consonant from another." For now, musicians take notice— if you spend more time in the practice room, you might stay sharp in your later years. 

Neurobiology of Aging, Available online 9 January 2012. “Musical experience offsets age-related delays in neural timing” Alexandra Parbery-Clark, Samira Anderson, Emily Hittner, Nina Kraus http://www.sciencedirect.com/science/article/pii/S0197458011005471

 

Stuck on You: Tiny Squid makes Two Kinds of Glue

Like the previous article, I had difficulty trying to find an application that college students could appreciate. As previously mentioned, this was part of BioSc 494: Popular Science Journalism and appeared in the Fall 2011 issue of Tigra Scientifica which can be downloaded here.

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While other mollusks like snails and mussels often secrete sticky ooze, cephalopods like octopus and squid generally aren’t known for chemical adhesion. Hoever, members of one squid family Idiosepiidae, are identified by their sticky secretion organ. Idiosepius squid can be smaller than your pinky fingernail and glue themselves to seaweed in order to hide from predators. They can then quickly unstuck themselves for a speedy getaway. In a study published in the Journal of Marine Biological Association of the United Kingdom, Mag. Norbert Cyran and his team from the University of Vienna investigated Idiosepius’ adhesive organ at a microscopic level for the first time and found that the diminutive squid makes two different types of glue.

Many kinds of chemical adhesion are found in nature. Barnacles are infamous for the strength of their attachment to any surface, gripping on everything from boat hulls to living whales. Spiders use natural adhesives to construct intricate webs. These organisms usually use mixtures of proteins and carbohydrates to make their glue. Humans have tapped into this, by boiling animal bones, tendons, and skin to make the animal glue used in stringed instruments and deriving shellac from a species of beetle in India.

            Samples of the squid skin were prepared and examined under electron microscopes. The adhesive organ was also stained and sliced for 3-D analysis in a computer. The outer skin layer consists of two cell layers made up of six different cell types, which correspond to structures initially described in 1921. Three of the different cell types are specifically restricted to the adhesive organ and are likely linked to glue production. One type of cell was evenly spread throughout the organ, and the other two clustered together. Both the evenly distributed cells and the clustered cells use a similar secretion pathway, but based on where the two types of cells are in the skin Cyran and colleagues determined that these are two different types of secretions. Cyran proposed two different models: in the first, the two different types function as a duo-gland system where one secretion glues the squid to a surface and the other secretion unsticks, and in the second model both cell groupings produce the same type of glue. The researchers suggest more biochemical research is necessary to truly unlock the sticking mechanism.

Further research into Idiosepius’ glue methods could be promising. Bioadhesives could be used in the medical field where needed, as the body might be less likely to reject a biologically created adhesive than a synthetic one- a possible technology for stitches.   Biomimicry, or taking ideas from structures and processes in nature for human use, can lead to novel applications. Barnacles have been studied for their incredibly strong glue. Idiosepius’ temporary glue could have equally useful applications. Once the reaction is figured out, the glue-making method can be applied elsewhere. For now, though, Idiosepius’ exact glue recipe remains a mystery.

Ultrastructural characterization of the adhesive organ of Idiosepius biserialis and Idiosepius pygmaeus (Mollusca: Cephalopoda)
Norbert Cyran, Waltraud Klepal and Janek von Byern (2011) 
Journal of the Marine Biological Association of the United Kingdom, http://journals.cambridge.org/action/displayJournal?jid=MBI&volumeId=91&bVolume=y - loc91, Volume 91, Issue 07 , November 2011 pp 1499-1510 
http://journals.cambridge.org/abstract_S002531541100021X

Sharks in the Dark: Deep Sea Cold Vents as Shark Nurseries

This is a pretty good example of an article I wrote for BioSc 494: Popular Science Journalism where I struggled to figure out how to relate really neat science to a college audience. While I wish I could say 'This is super duper cool because SHARKS and COLD VENTS aaaah', that's not a very effective way to communicate. I ran into the issue during round table review of not being able to use the word 'elasmobranch' as often as I'd like. This appeared in the Fall 2011 issue of Tigra Scientifica which can be downloaded here.

The sun provides energy for nearly everything on Earth, although some alien exceptions exist.  The sulfur and hydrogen loving bacteria of Yellowstone or the methane worms of deep-sea vent communities are just two examples. There might be more familiar species that also don’t use solar energy.  In the September Marine Ecology Progress Series, Dr. Tina Treude from Leibniz Institute of Marine Sciences in Germany and colleagues discovered shark and skate (a flat fish similar to a ray) egg capsules at two deep sea cold seep sites and discovered fossil evidence of similar behavior in Washington. This indicates that these fish use cold seeps as nurseries.

Like hydrothermal vents, cold seeps are locations in the deep sea that provide energy to a community that cannot rely on photosynthesis. They look very much like the vents; however, temperatures at cold seeps are usually less than 10 degrees Celsius. Instead of geothermal heat, energy is released in the form of hydrocarbons like oil and methane that oozes, or “seeps” out of fissures in the sea floor. Initially extreme species of bacteria colonize the area, then mussels and eventually tubeworms can move in to form a community. More complex organisms may eventually follow.

Dr. Treude and her team used remotely controlled devices to examine two locations: a mud volcano in the Mediterranean Sea and a cold seep off the coast of Chile.  At the Mediterranean Sea site, hundreds of shark egg cases were strewn across a dense field of tubeworms. Based on the size and shape, the team guessed they belong to deep-water catsharks. In addition to the egg cases, anemones, shrimps, a squid, and other fish were found living in the tubeworm field. At the Chilean site, hundreds to possibly thousands of large skate egg cases were discovered on a large sheet of rock exposed to open ocean. The sheer number of embryos and a possibly pregnant skate seen at the site indicate this may be a nursery for generations of the bottom-dwelling fish.

In the second part of the study, the research team looked at the fossil record, taking samples from a 35 million year old seep deposit in Washington state. Fossils of mussels dominated the deposit while tubeworms and snails were also present. The researchers collected 30 fossilized egg cases and fragments. Based on the shape of the fossilized capsules they determined that the egg capsules belonged to some species of deep-water catshark.  Fossil tooth evidence proves that catsharks lived in that part of the ocean at that time.

Putting together the prehistoric evidence with modern observations, Dr. Treude concluded that cold seeps serve as nurseries for elasmobranches, which are cartilaginous fishes like sharks, skates, and rays. These locations provide protected and ventilated holdfasts for the egg cases to cling to. While more research needs to be done, Dr. Treude suspects that the presence of small fishes, crustaceans, and mollusks could provide food for newborn elasmobranches. While not fully understood the presence of a large predator in a nonsolar-based community is intriguing because higher level predators are normally found in a solar-based food chain. Humans have considered using methane hydrate deposits from the ocean floor as an alternative fuel source. If a baby shark can gain enough energy to live eating chemosynthetic organisms, perhaps humans can use and farm extreme bacteria for fuel.

Treude, et al. “Elasmobranch egg capsules associated with modern and ancient cold seeps: a nursery for marine deep-water predators” Marine Ecology Progress Series. September 15h, 2011.

Level Up: Gamers Advance Scientific Knowledge

This article was originally written for Biol 494: Popular Science Journalism during the Fall 2011 semester. It was published in both The Tiger on Dec. 8th, 2011 and in the Fall 2011 edition of Tigra Scientifica, which is available here.

Most of us have a favorite mindless video game  -- some farm digital crops on facebook; others shoot mad birds with a slingshot. What if we could turn those hours and hours of screen time into something of good use? Within a two-week span during September 2011, gamers have solved problems in the biological and astronomical fields. Players of a protein-folding game called Foldit developed by the University of Washington generated a number of possible molecular models for an enzyme that retroviruses like HIV use to replicate themselves. Players of a game called Planet Hunters, developed by Yale and collaborators, also discovered two new planet candidates outside our solar system.  Both of these games used crowd-sourcing: a large group of people performs tasks and solves problems traditionally done by a specific person.

A large part of scientific research is trying to piece together how things work, whether in terms of mechanisms of action or three-dimensional structures. Foldit allows players to manipulate the 3D structure of a protein for ‘points’ when they get an ideal structure. The program constantly updates with new puzzles based on protein structures, and players can work alone or share ideas in groups.

As described in the September Nature Structural and Molecular Biology, Foldit players discovered molecular models for a retroviral protease (what viruses like HIV use for replication), whose structure had eluded scientists for years. Researchers at the University of Washington asked a group of Foldit players to submit models to the Critical Assessment of Techniques for Protein Structure Prediction, an experiment that takes place every two years where the amino acid sequence of a protein is posted, and teams must find the closest match to a protein’s native structure -- its natural working state.  The Foldit team Void Crushers correctly found a near-native model of the protease but also improved it with some structural modifications. The models discovered allowed researchers to determine the crystal structure of the protein. Now that science know the structure, the new model makes finding potential cures to retroviral diseases like AIDS a possibility.

The Planet Hunters game is a collaboration between Yale and Zooniverse, a developer of amateur-based science projects. Plant Hunters allows players to sift through data collected by the Kepler space telescope, monitoring shifts in brightness of stars.  When dips in light occur, a planet is passing between the star and our field of vision. 

Planet Hunters involved 40,000 players poring over data from the Kepler space telescope.  Users viewed light curves, indicated whether it was “variable” or “quiet”, and marked interesting features. Planet Hunters also allowed users to discuss the data with other citizen scientists in a forum, where similar curves were grouped in discussion threads. After 4 million games, 69 planet candidates were identified. Two of the planet candidates were described in a paper in the September Monthly Notices of the Royal Astronomical Society. The Planet Hunters involved in their discovery were identified as coauthors of the paper.

Despite the computational power available today, both papers used crowd sourcing as a tool, citing the ability of humans to detect patterns more intuitively than a computer program. In the future, games like this could make research more accessible to people who may not have a background in a particular topic. If you want to do science from your laptop, you can download the Foldit at fold.it/portal/ or play Planet Hunters at www.planethunters.org. So keep in mind – you don’t have to be a Ph.D to advance scientific knowledge, you may just have to play some video games.

Fischer, et al. “Planet Hunters: The First Two Planet Candidates Identified by the Public using the Kepler Public Archive Data”, RAS, MNAS. September 26^th, 2011

Khatib, et al. “Crystal structure of a monomeric retroviral protease solved by protein folding game players”, Nature Structural and Molecular Biology. September 19^th, 2011

The Birds & Bee-eaters: Murderous African Birds Attack Nestmates

I ought to have posted these when writing them last year, but no time like the present, hm? These articles were written for Dr. Temesvari's BioSc 494: Popular Science Journalism. This appeared in the Fall 2011 issue of Tigra Scientifica which can be downloaded here.

The Birds & Bee-eaters: Murderous African Birds Attack Nestmates

Blindly yet brutally stabbing underground, the invader kills his foster siblings. Although it sounds like the premise for a horror film, this is the reality for African honeyguide chicks and their host families. A study published in the September 2011 Biology Letters, Dr. Claire N. Spottiswoode and Jeroen Koorevaar observed within the underground nest honeyguide chicks killing host chicks (their would-be foster siblings) with specialized hooked bills for the first time.

This murderous behavior is part of brood parasitism- the parents lay eggs in the nest of other birds and do not deal with the responsibility of childrearing. Unlike babies left on doorsteps, however, these youngsters will hatch early and actively take out their nest mates for primacy with their foster parents. Many species of cuckoo are brood parasites; their preferred method of siblicide is pushing the other eggs or chicks out of the nest. It certainly puts a spin on those hourly popouts by a cuckoo clock.

Honeyguides are drab African birds that are roughly the size of a pigeon. Honeyguide interactions with humans are generally positive – they are well known for guiding humans to beehives, eating the grubs left behind when the people take the combs. Their parasitic nature is known; however the only prior description of killing behavior is from 1952, when a chick bit a host chick while being held.

Spottiswoode and Koorevaar placed infrared cameras at the end of common bee-eater bird tunnels. The bee-eater is the most common host for the honeyguides, and they typically nest in underground burrows. Honeyguides visited most of the bee-eater nests that were observed and laid eggs in occupied ones. The parents actually punctured host eggs with their beaks to improve their offspring’s chance of survival. Luckily for the bee-eaters, sometimes they would miss some eggs, or the bee-eaters would lay additional eggs later.

The honeyguide chicks hatch days before the bee-eaters and are very aggressive- the authors noted that chicks immediately tried to bite them with considerable strength when handled. In the videos, the honeyguide chicks attacked the host chicks and held on, blindly stabbing by opening and closing their jaws and shaking the host chick. Although it does not cause open bloodshed, the biting produces bruising and hemorraghing under the skin. Host chick deaths varied from nine minutes to seven hours after initial attacks. In most nests, the corpses stayed and decomposed- a grisly background while the imposter grows and develops.

Without a doubt, this systemically brutal system works for honeyguides. But does such a well-developed system come at a cost? Spottiswoode speculates that accelerated growth and exertion may have a huge energy cost for honeyguides, though more research needs to be done to determine this. Honeyguides are like the fairies of folklore: they leave changlings in nests, equipped with built-in knives and the initial strength to wield them and cause mischief.

Spottiswoode, C. & Koorevaar, J. A stab in the dark: chick killing by brood parasitic honeyguides. Biological Letters. http://dx.doi.org/10.1098/rsbl.2011.0739