Blast from the Past: UNC Charlotte's excavation in Jerusalem.

UNC Charlotte students who are interested in religion, history, and/or archaeology are being given a very unique opportunity unlike anything other universities in the United States have to offer.

I’m speaking of the excavation currently taking place in Jerusalem under academic oversight of the University – the only American university licensed in Jerusalem to carry out excavations. This project, which is located in Jerusalem in an area called “Mount Zion,” gives students the opportunity to unearth the rich history of the land first hand, while learning about the cultures that once inhabited them.

Map of the location of the excavation.

This ongoing project is spear headed by Dr. James Tabor, chair of the Department of Religious Studies at UNC Charlotte, and Dr. Shimon Gibson.

While there have been many intriguing finds at the site, the most notable was discovered in 2013. Archaeologists believe to have found the well-preserved lower levels of an early Roman period mansion. Particularly intriguing is the well-furnished bathroom, complete with a bathtub, adjacent from the mikveh: a large belowground pool used for cleansing. This addition is a sign of status and wealth of the resident that lived in this part of the site.  Usually, bathrooms of this type are only found in palatial buildings.

The bathroom found in the mansion, adjacent to the Mikveh

Early excavations revealed a wide array of finds including a stamped handle

that could be traced back to the second Iron Age, houses, pottery, and coins from the Early Roman age, a mosaic floor thought to be from the Byzantine era, more building traced back to the Early Islamic age, remains thought to be the remnants of a battle in the Crusader era,  and Porcelain from China and other foreign lands traced to the Late Ottoman era.

            What is so remarkable about this site is how well preserved the artifacts seem to be, due to, at least in part, to the construction work during Byzantine times. During that time, in order to make a foundation to support new buildings, an artificial leveling fill of stones, soil, and other debris were poured atop the remains of the Early Roman period houses.

Looking down into the lower level of the mansion. 

“The area got submerged,” said Gibson. “That’s why we found an unusually well-preserve set of stratigraphic levels.”

            This is not the first time this site has been excavated. Back in the 1970’s, Magen Broshi of the Israeli Museum, conducted excavations in this area. Later, in 2000 and 2005, and then largely in 2007, excavations were resumed by UNC Charlotte under a license from the Israeli Antiquities Authority and the Israeli Park Authority.

            If you are a student of UNC Charlotte that is interested in knowing more about this awesome opportunity you can find more information about the dig, as well as information on getting involved in their 2015 season, which we be on June 14^th through July 10^th, 2015, at the Dig Mount Zion website, https://digmountzion.uncc.edu.

How is Bioinformatics Helping the Ebola Outbreak?

In recent months, Ebola has moved from a winning disease on the popular Plague Lab and Epidemic phone apps to a very serious global health issue. According to the Center for Disease Control (CDC), as of November 11, 2014, the total cases of the Ebola virus totaled 14413; 8920 of those were confirmed laboratory cases, and 5177 constitute total deaths. Though there have been a few well-documented cases in the United States and Spain, the vast majority of these cases have occurred in West Africa, in the countries of Guinea, Sierra Leone, Liberia, and Mali.

            Many reasons can be cited for the spread of the Ebola. West Africa lacks proper infrastructure, facilities, and resources to handle the disease. In addition, Ebola doesn’t show symptoms until at least two weeks after contraction of the disease, and the first symptoms manifest in the same manner symptoms from a common cold or flu do; by this time, everyone that person has come in contact with has been exposed to the virus. Further, once the affected have passed away, most villages do not have proper disposal techniques, and in many areas, burning the body (the most sanitary and available means of disposal) is seen culturally as an improper means of burial.

            Though all of the problems mentioned above (and the problems Ebola poses are by no means limited to those) do not have a panacea, there are things being done to combat aspects of the unprecedented difficulty Ebola has posed to West Africa and to the world. In addition to all of the humanitarian and medical aid needed, aid is also being given in the form of bioinformatics. Bioinformatics is the field that combines technological methods and software programs in an effort to develop more tools for understanding biological data. Scientists of bioinformatics must be versed in computer science, mathematics, and engineering, amongst other fields.

            Dr. Ketan Patel, of the US Naval Medical Research Center and former postdoctoral fellow in bioinformatics at the University of North Carolina at Charlotte, has used his experience in bioinformatics to assist in the establishment of a high-technology mobile laboratory in Liberia, a project located near a treatment unit that is supported by the World Health Organization (WHO).

Ketan Patel in the laboratory separating genomic material. (Photo courtesy of WHO).

            This laboratory, situated in what was previously an abandoned house of sorts, is meant to speed up the time for diagnosis. As can be inferred from the earlier explanation of Ebola symptoms, early diagnosis is key for control. Prior to the establishment of Patel’s lab, even preliminary Ebola diagnosis took anywhere from two to five days. Because of the advanced bioinformatics technology in this fledgling laboratory, results can be rendered in just three to five hours; a significant decrease in time and the effective elimination of days of potential exposure of Ebola victims to those uninfected.

            To diagnose, the laboratory follows three steps. First, the Ebola virus within the sample is inactivated, allowing for safety of testing. Secondly, all genetic material is extracted from the blood sample- by doing this, doctors can identify unique ribonucleaic acid (RNA) associated with Ebola. Once this is identified, copies of the RNA are made through a process called polymerase chain reaction (PCR). Depending on the prevalence of the virus in the provided blood sample, this last step (the actual diagnosis step) can take anywhere from just a few cycles to very many cycles. The entire process is streamlined and carefully monitored for cleanliness and safety; workers use biological safety hoods and suits, in addition to chlorine “dunk tanks” to avoid direct contact and eliminate any potential or accidental contamination.

Ketan Patel prepares to work in the laboratory. (Photo courtesy of WHO). 

            Amalgamated, these steps take anywhere from three to five hours, with a maximum of sixteen samples in a rotation. The laboratory was established in October and, since then, over 500 blood samples have been processed and, of those, approximately fifty percent identified as positive for Ebola. Thanks to Dr. Patel and the help that his bioinformatics experience has aided to the laboratory in Liberia, the fight against Ebola has advanced that much more.

A Toy Story

A Toy Story

During my interview with Dr. Maher, Chair of Software and Information Studies at UNC Charlotte, we played with multiple interactive technology tools as she demonstrated to me how she was using them in her research. While we played with various toys, I noted to her that remembered when the most “interactive technology” that was used in the classroom was an etch-a-sketch.

I still remember the day in kindergarten when our chalkboard was replaced with a whiteboard, and everyone became incredibly excited because, at the time, the whiteboard was the second thing that defined our classroom as “modern”- succeeded only by the old computer we had for occasional rotation, on which we were allowed to play Oregon Trail and KidPix in fifteen-minute intervals in groups of four.

I remember even more vividly the day that the Ipod was released, and the Ipad, and the first online class I took- a revolutionary step at the time.

Looking back to those memories, it’s difficult to fathom how far we’ve really come in classroom interactive technology, and even more difficult to fathom to what lengths technology is aiding actively in the learning process.

Dr. Maher showed me just how far we’ve come when I sat down with her to discuss her research. She has a background in design and works with various students and institutions to develop new and more innovative ways to improve the relationship between cognition and technological interaction.

She explained to me that she worked in conceptual blending and the connection between cognition and formal representation of that cognition- in other words, the relationship between what we’re thinking and how we tangibly represent that thought. In the past, we were only limited to writing and to various forms of art. Now that digital interfaces are available, our potential to directly relate the original cognitive thought in a more “honest” tangible form has grown.

 Dr. Maher believes that if we approach this connection innovatively, we can improve learning and our representation of it into ways that are more relatable and far more instructive.

Still mystified by these vague terms, I asked her to show me examples of what she was talking about. How was her team more innovatively connecting our cognitive functions and their formal representations, and how was it more useful in instruction?

First, she showed me a device her team was working with for younger students. Called “siftables,” they are small cubes that are activated by Bluetooth and can be connected to each represent any number of patterns. Below you see them being used to create math problems, but they can also display any number of patterns, shapes, and images. Dr. Maher and her team are already implementing these into schools to see if they are useful in the classroom. Thus far, the evidence points to the benefits of the siftables.

For middle and high school kids, she’s envisioned using a device called “Arduino.” Pictured below, the Arduino is a device that can be used to create small robots and other interactive devices, and is an introductory tool to learning robotics and engineering.

Perhaps the coolest thing she showed me, though, was the Colorado Tabletop. After we played with the two toys above, she led me across the hall to a small laboratory where there were many students working. In the middle of the glass-walled room was a massive interactive touchscreen tabletop.

She began to explain that this tabletop was meant to be the precursor marrying nature with technology. She showed me how, on the table, there was an interactive map of a local nature trail. She showed me how I could follow the trail virtually, clicking on different spots to view images, facts, extended information pages, and videos.

Even cooler was that all of this information was crowdsourced- she calls it “citizen science.” The idea was that as visitors walked through this nature trail, they would take pictures and videos. When they came across one of the installed interactive tabletops, they could share their photos, videos, and other information with the table, joining their experience to dozens of previous other ones. If they had any questions, they could interact virtually with their surroundings to get answers.

While the table she showed me in the small room at UNC Charlotte was a prototype of a local trail, she was preparing to travel Colorado to establish an outdoor tabletop in one of its national parks. It would be the first of its kind, and the success of the Colorado Tabletop, she says, will indicate how society truly interacts and uses such technology, if made available freely.

Though her research seems to be varied, it centers around one thing- interaction with the user. She worked previously on something she calls “gesture interaction,” with installments that viewers can actually “walk up and use.” In a world that is driven by the growth of technology, she says, it’s important to develop technology that engages the user to the highest degree possible.

She has high hopes for the potential of bringing the formal representation of our cognition as close to our actual cognition as possible, creating tools and resources that can be used efficiently and effectively- and rather than becoming tools for distraction, they’ll become toys for instructive interaction.

Dr. Maher is at the beginning of the pursuit of the ultimate toy story.

Probing the History of the Planet Through the Genes of Shy Creatures

Creep-out! A harmless, but ancient (in form) daddy longlegs from Brazil.

They are in your basement, or in your yard, hiding in the fallen leaves at the foot of your trees. They are living relics, walking the earth virtually unchanged since they first appeared 400 million years ago-- about twice as long ago as the first dinosaurs. They are hiding in plain sight, but in their genes they hold a record of the deep history of the planet and its landmasses.

And they are also the reason National Geographic helped send UNC Charlotte bioinformatics postdoctoral researcher Ronald Clouse to the Philippines this summer, and asked him to blog about the experience.

These unusual animals are Opiliones, otherwise known as daddy-long-legs or harvestmen. Though most of us confuse them with spiders (there are some varieties of spider that are called “daddy-long-legs”) they are actually a significantly different group of arachnids more closely related to scorpions, from which they diverged a little over 400 million years ago, shortly after scorpion ancestors first came on land. Contrary to their popular name, not all daddy-long-legs have long legs – those Clouse will be studying (Cyphophthalmi, or “mite harvestmen”) look like tiny short-legged spiders and live in humid leaf litter, where they tear up and eat plant matter and even tinier insects with the miniscule claws they have in place of spider fangs.

One of Clouse's litter-dwelling "daddy longlegs," greatly enlarged.

They are obscure animals, and though widespread and probably present nearly everywhere on the planet, there is a lot we don’t know about them. Some of the things that we do know about them, however, make them important to science, Clouse points out. “We think they are exciting animals, we think they give us a lot of great information about deep, deep history,” he said.

 First of all, they have passed through a very long stretch of time virtually unchanged. “Daddy-long-legs evolved from scorpions – they are sister groups – and scorpions started to come out on land about 425 million years ago and at 400 million years ago there is a beautiful fossil from Scotland of a daddy-long-legs that looks almost exactly like the ones in your basement today,” he said.

What may just seem to you like a garden spider is, in fact, a living fossil
that lived on this land before your ancestors were mammals!

Clouse notes that Opiliones seem to have quickly found land niches everywhere and then remained happily in them. “We have a fossil of the southeast Asian ones from 100 million years ago in amber,” he said. “It looks like they first showed up from 425 to 400 million years ago and they quickly evolved into these really elaborate morphologies that we have today. And it was another 200 million years before the dinosaurs showed up, and the dinosaurs blink out after a little more than a hundred million years. These guys have been hanging tough the whole time.”

Second of all, it turns out that daddy-long-legs have perfected a lifestyle that makes them extreme homebodies.

“The reason we like this group of animals is they don’t go anywhere in their lives and when we find them in the forest floor in the leaf litter, even if we find a bunch of them, there will be a completely different species a few kilometers over. They are very highly local,” he said.

“What makes them so localized is that they really require humid leaf litter. They don’t like leaf litter that gets too wet or too dry. And so they like pristine forest, deep leaf litter where there is the right kind of layer for them.

“So why didn’t they just evolve the ability to not need that humid leaf litter?” Clouse asked. “Because they also have behavioral issues where they just don’t go anywhere. Even super long-legged daddy longlegs that have the ability to move around a lot, they also don’t go anywhere. During the day they are under a log and at night they walk out a couple of meters and they will sit there all night.”

Clouse knows that Opiliones are confirmed stay-at-home types thanks to bioinformatics. “When we sequence their DNA we find that all the ones in this forest, even though some groups may be spread out over wider areas, when you look at it population by population, there is almost no gene flow,” he noted. “Everyone here has one set of sequences, everyone there has a completely different set of sequences.”

And the small, leaf litter dwelling types turn out to be even more localized.

“For these little guys – we were down in Florida sequencing and we found that just a few meters away the sequences were different. When we find them in the forest floor in the leaf litter, even if we find a bunch of them, there will be a completely different species a few kilometers over. They are very highly local. And the entire group, which is found around the world, exhibits the same the same high-need microniche requirements and the same behavior.”

This old, established pattern of localization has some important implications that go far beyond invertebrate biology. You can find markers for the ancient history of the earth in a daddy-long-legs’ genes, Clouse explained.

“The end result of this is that their current distribution around the world is due to the movement of continental landmasses. So, when we reconstruct their history from their DNA, we get a nice match to the history of the landmasses on which they live,” he said.

“There one is South Carolina on Sassafras Mountain – its genes show its closest relative is in West Africa. These species split apart about 200 million years ago. And guess what? Geologists say the Atlantic Ocean opened up about 200 million years ago.”

Continental drift and the movement of landmasses. If you stay
in one place long enough, you get moved around.

According to the geology and the theory of continental drift, evidence indicates that all the planet’s landmasses have not always been where they now are, but have drifted around the planet, colliding and joining with each other and then separating -- again and again. Around the time Opiliones first established themselves on land, all landmasses were shoved together in a supercontinent geologists refer to as Pangea, and geologists know that what is now North America was continuous land with what is now Europe and Africa.

But on other parts of the globe, the evidence for exactly what happened is not quite as clear. Just like we might think daddy-long-legs are spiders, we might assume that the Philippine Islands all came from the same place… but again we would be wrong.

“It turns out that the geologists don’t always have a very good handle on what is going on,” Clouse notes. “The Philippines is one of those places where they really have a very poor view of what happened in the past. All those islands are coming from different directions. So the Philippine Opiliones project kind of got legs because these animals are a nice model for tracking origins of the land.”

Though the animals are small, this is big science -- which is perhaps why National Geographic, one of the premier public providers of scientific content on the internet, has asked Clouse to blog about his work in the field, though the animals he studies are not as charismatic as jungle birds and butterflies.

“I was apologetic to national Geographic about the possible lack of action in our field work and said most of it consists of us sitting on a log, looking at a pan of leaf litter, examining it for daddy long legs. These guys will curl up in a ball and look like a piece of dirt.”

“They just try to wait until they think you’re gone. That’s why they are so obscure, so poorly known for centuries and why people have overlooked them. Now that we really look for them, we find that they are everywhere.”

“They said ‘Oh, don’t worry. That gives us new ideas – in fact you could take a picture of your pan of leaf litter in high resolution and we could put it up and ask people if they can find the daddy-long-legs.’”

In a sense, Clouse said, it is a chance for daddy-long-legs to get their “close-up” in the spotlight of science.

“The animals I want for the science but it’s also a chance to put these animals up on a stage because there are a lot of myths about them – people think they are dangerous or poisonous, and we know that they are not but that they are really, really interesting. In fact some of them are right here in South Carolina tell deep, deep history about the southern US. I think that’s very exciting.”

So, if you run into a daddy-long-legs in the garden or in your basement, be respectful. Chances are, its ancestors lived in this place a lot longer than your kind has.

And oh, the stories they can tell.

You can follow Dr. Ronald Clouse blogs from the field at: http://www.nationalgeographic.com/explorers/projects/ or from a link at his author page: http://newswatch.nationalgeographic.com/author/ronaldclouse/

     

Social Sustainability

Social Sustainability

Sustainability has been on the forefront of innovation of scientific research for generations. An economy cannot thrive unless it can sustain itself, and many of us think that the things we use in our daily life must be made to sustain the health of our environment with greener technologies, but how do you determine the sustainability of a society, a culture, and a civilization? That is what Dr. Nicole Peterson is trying to figure out through a grant that allows her to further research this field.

On January 24^th, I sat in on a talk by Dr. Peterson in which she talked about an idea called “Social Sustainability.”

            Dr. Peterson explained to us her definition of sustainability, which was maintaining “the world in which we continue to live as humans without sacrificing the ability of allowing future inhabitants to exist.”  Her idea of sustainability was split into three “legs” of a stool, in which two legs were Economic and Environmental sustainability.  Dr. Peterson identifies the last leg to be the Social leg, or the leg that deals with the social aspect of sustainability.

            She then used the example of a fishing village in Mexico and how this fishing village was affected by a changing global economy and climate. Fishermen in this village were starting to see a decrease in fish stocks in the surrounding ocean. Fisherman blamed many things from the Colorado River no longer reaching the Gulf of California, tourism, different fishing techniques, and large industrial fishing. She points out the fact that the things affecting this fishing village were both economic and environmental issues.

            The three “legs” of sustainability, she argues, are interrelated. The vitality of an economy is reliant on healthy ecosystems, and as the recent recession illustrated, economic and social integrity are also linked.

            Despite its interconnectedness, social sustainability is the least understood and defined. If one were to try and explain it, it might be best explained as the relationships, interactions, and institutions that affect and are affected by social development. For example, the way a social protest can affect the place it is focused on; a government can be hurt by a social protest, its stability then loses integrity, and its economy takes a blow.

            Dr. Peterson also took her research home here to Charlotte, NC, with her project of understanding food systems within the city. A project she was involved in and studied, Mobile Markets, takes fresh produce from the gardens and other places and sells it at the transit hub in uptown. This provides a place for people to buy fresh produce in a location  that wouldn’t originally have it.

            This research, however, is just touching the beginning of understanding social sustainability… if it can be understood at all.

            In the global community we live in, the means to achieve sustainability is dependent on many different aspects. Geography, political systems, and culture can all directly affect what a certain country may need to sustain itself.

            In my opinion, social sustainability should instead be used as a measure of overall sustainability, and instead of seeing sustainability in three separate segments, it can be be concluded that they are all, in fact, the same. Economic sustainability IS environmental sustainability and ALSO social sustainability. They are all interdependent and therefore wouldn’t exist without the other.

            If we hope to perfect one, we must perfect the other. So is perfection ever really possible at all? What, then, is considered perfect sustainability, and can it be really viewed as a blanket statement for all involved?

            These are the kind of questions that Dr. Peterson and the Integrated Network for Social Sustainability (INSS) are trying to answer. You can even get updates from their page at http://clas-pages.uncc.edu/inss/.