SFSYO Scientist of the Month: Philipp Schiffer

Science For Six-Year-Olds (SFSYO for this school year) is a recurring segment on Science Decoded for Mrs. Podolak's first grade class at Lincoln-Hubbard elementary school. This year the posts are inspired by #iamscience (also a Tumblr) and #realwomenofscience two hashtags on twitter that drove home for me the importance of teaching people who scientists are and what they really do.

Hello first graders! I hope you are all okay and back at school after hurricane Sandy. Now that it is November we have a new scientist of the month. I am so excited to introduce you to Philipp Schiffer who is finishing up his PhD at school in Cologne, Germany. Like I did with Dr. Penny, I asked Philipp a bunch of questions to find out more about what he does. I hope you will enjoy learning more about him. Below you can read my interview with Philipp, and if you'd like to ask him any questions, be sure to leave them in the comments!
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At work in the lab. Courtesy of Philipp Schiffer.

Erin: What type of scientist are you?

Philipp: I'm an evolutionary biologist [this means he studies genetics, DNA, and how different living things came to be,] currently I've morphed into a computer geek but I'm hoping to move away from the computer screen a bit more in the future. 

Erin: What did you study in school, and where did you go?

Philipp: I studied Biology, majoring in Zoology with minors in Genetics and Palaeontology. I did most of my studies at the University of Cologne, Germany with some time in Australia studying and catching wombats.  I'm currently finishing my PhD thesis in Cologne, but I've also studied at the University of California Riverside where I was learning about nematodes. I also got to spend some time in Edinburgh in Scotland. 

Erin: Where do you work and what does a typical day at work entail?

Philipp: It's called the Cologne Biocenter, in the middle of Köln am Rhein. At the moment I am spending most of my working hours in front of my computer, doing science in-silico, which means I am analyzing data from the genome sequencing assays I conduct. In between I hop over to the lab to study the nematodes, look at their DNA or run some other experiments. 

Erin: Why did you decided to become a scientist?

Philipp: I have always liked to think about things. I guess when I was in the 9th or 10th grade I wanted to tackle the big problems/questions like finding a cure for diseases. Now of course, I do something totally different, which I actually like better!

Out of the lab! Courtesy of Philipp Schiffer.

Erin: What is your favorite thing about your job?

Philipp: There is a new and intriguing question to answer every day, more than one on most days. That is the main thing, I am really interested in answering questions about life - why it is the way it is and how did it become like that? Why are species different and how does it happen. There is a woo hoo! moment when things finally click into place and make sense, which is really cool. It is also really nice to work with people around the world - I like the exchange of thoughts and ideas in different cultures. I enjoy talking to colleagues very much, and working with students. It is also fun to be able to listen to music when working, and so much more. 

Erin: What is something about your job that might surprise us?

Philipp: There is no magic in science, actually most ideas or experiments don't work the way you think they will, and once something really works the main thing is to wonder why did it work this time? So there is a lot of frustration in being a scientist, but then there is also a lot of fun. Still, the first thing is the most important, science is hard work. 

Erin: What are your favorite things to do for fun?

Philipp: Science IS fun. I also like wind surfing and sailing, I like rugby too and wish I had more time to do that. I also read about history, politics, and the world in general as much as I can. I very much enjoy chatting with friends over coffee.

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What do you think first graders? I think Philipp has a pretty cool job, and he's gotten to go to school in so many different places, can you find them all on a map? If there is anything you'd like to know about his research, make sure to ask him questions in the comments. 

For any of my regular (adult) followers you can catch Philipp on Twitter @evolgenomology. If you'd like to be featured as a scientist of the month send me an email or DM me on twitter, I'd love more volunteers and thank you Philipp for lending us your time to share what you do!

Science For Six-Year-Olds: The Bear Skull

Science For Six-Year-Olds is a recurring segment on Science Decoded for Mrs. Podolak's first grade class at Lincoln-Hubbard elementary school. This year in first grade we've also learned about groundwater in Africa, noctilucent clouds done an experiment with butter, talked about hurricanes and sugar maple trees, and learned a song about the states of matter.
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This science for six-year-olds post is a little different than my previous posts, because this time I'm back-blogging about a presentation that I already gave to the first graders in person. Since I'm now back in New Jersey, I was able to visit their class to talk about my favorite subject, bears. While we know I'm partial to polar bears, in Mrs. Podolak's class we talked about black bears. 


Black bears are the type of bear that can be found in New Jersey. The reason I decided to talk about them with the first graders is because I brought Bob in for a bit of show and tell. This is Bob: 

Credit: Erin Podolak

Bob is a black bear skull that a friend passed along to my Dad a couple of years ago. The skull was found by a hunter in the woods in northern New Jersey within the normal range for black bears (Ursus americanus) in this area. The skull was pretty clean, but we boiled it just to be sure and now it makes for a great show and tell item to talk about the species and how it lived. The kids really loved getting to hold Bob and take a look at his jaws. They asked some great questions, like "where did his brain go when he died?" To answer that we had to talk about decay and how bacteria will break down tissue that isn't alive anymore. Deep stuff for first graders, I was impressed. 

I was also impressed with their existing knowledge of animals. The class has been working on research projects to learn more about specific animals of their choosing. We talked about whether or not black bears are predators and if they are dangerous to people. I started to explain to them that black bears are omnivores, which means that they are opportunistic eaters and will consume plants, berries, bugs, or meat. The kids already knew what omnivore meant, and they were also able to tell me about cartilage and that sharks are cartilaginous fish. It was a lot of fun to see what they already knew about black bears, and to listen to their observations. 

Credit: Erin Podolak

I just wanted to share a few more facts about black bears that we didn't get to talk about in the time we had in class: 

• There have been confirmed sightings of black bears in all 21 counties in New Jersey, but they are more concentrated in the northern area of the state. 
• Black bears are the largest land mammal that can be found in New Jersey
• Female black bears can weight around 175lbs, while males weight around 400lbs
• Black bears have very strong senses of smell and hearing
• Their habitat typically includes hardwood forest areas, but they can also be found in dense swamps or forested wetlands.
• The most common problems humans experience regarding black bears occur when the bears are attracted to garbage that has been left outdoors. 
• Black bears can run as a speed of 35 miles for hour. 
• Contrary to their name, not all black bears have black fur. Some black bears are brown or cinnamon colored, or they can have a white patch on their chest. 
• Black bears stand about three feet high when on all fours, and can reach five to seven feet tall when they are standing upright. 

For more information about black bears in New Jersey, you can check out the New Jersey Department of Fish and Wildlife website (they have some good resources specifically for kids!) It was a great learning experience for me to try to communicate science to first graders. I was continually surprised by the complexity of the material they were able to understand and often stumped, but impressed, by their questions. I hope everyone who reads this blog who isn't in the first grade also enjoyed the subject of these posts. Happy summer vacation, everyone!

Zoos and the Protection of Rare Animals

This semester as an elective I am taking another course in the zoology department (the first being Patricia McConnell's Human and Animal Relationships last semester). In Zack Peery's Extinction of Species we have been discussing the role that institutions like zoos play in helping to preserve and ensure the survival of rare species. Often we think of zoos in terms of their enjoyment factor for humans or conversely the lack of enjoyment (we think) that animals have being caged. I've visited the zoo here in Madison and had a nice time being there with my family, but I was definitely thinking about the care and condition of the animals. Now, I thought all of the animals in the zoo I visited looked healthy and happy, but it did get me thinking overall about how important zoos are for the care and conservation of animals, particularly those that are rare or in need of special healthcare.

Zoos play an important role in conservation efforts, because the good ones provide animals with a safe place to live that is protected from outside threats (predators, pollution, loss of habitat, etc.), in addition to access to veterinarians. I was reminded of this fact when I saw the story of Manukura, a rare white kiwi being covered by the BBC. Not that we really needed further proof that a good cute animal story is going to make it into the news, but I wanted to mention the kiwi story because I think it is a good example of the public rallying behind a very charismatic animal, and a zoos effort to save and protect it.

Manukura. Source: Zooborns

A kiwi is a flightless bird that lives only in New Zealand, and is similar in size to a chicken. There are five species of kiwi, which are all endangered. Kiwis are typically brown or tan in color, but as a result of a naturally occurring genetic mutation Manukura was born white (note that this isn't the same as being an albino). Manukura was living in Pukaha Mount Bruce National Wildlife Center when rangers noticed that the six-month-old bird wasn't eating. Veterinarians at New Zealand's Wellington Zoo were called in to examine the bird and found that two large stones were obstructing its intestines.

Manukura was able to pass one of the stones naturally, but the other had to be taken out by a urology specialist from Wellington Hospital who broke the stone up with a laser and then removed the pieces with an endoscope. According to the Wildlife Center, the procedure was comparable to the removal of kidney or gall stones in a human. The bird is doing well following her procedure, much to the joy of her Facebook followers who were able to follow her progress throughout the ordeal.

I think that this story is a great case study for a lot of the topics that we've been discussing in my zoology class. It shows a viable option (the creation of wildlife refuges) for the conservation of a species, how a the public can rally behind a species that is particularly like able and important (the kiwi is a national symbol of New Zealand), how zoos can provide access to resources necessary to save an animal, and how communication with the public (particularly through social media) is an important part of conservation and animal protection efforts.

The Arabian Oryx's Comeback Story

We see so many stories proclaiming the final nail in the coffin of so many species around the world (and indeed, species extinction is a serious issue) but today there is actually some good news about the Arabian oryx, which was previously considered extinct in the wild. Good news needs to be talked about more, so inspired by this post from New Scientist I wanted to share the Arabian oryx's story.

Arabian Oryx, via Wikimedia Commons

Around 1972 the last wild Arabian oryx (Oryx leucoryx) was killed, most likely in Oman. While the species was extinct in the wild there were still several in captivity, particularly at the Phoenix Zoo, which received four wild Arabian oryx in 1963 as a part of a conservation effort called Operation Oryx.

After the species went extinct in the wild, individuals from the zoo’s breeding program were brought together with individuals from royal collections in Abu Dhabi, Qatar, and Saudi Arabia to make a last “world herd.”  A breeding program began and in the early 1980’s the first individuals were reintroduced into the wild in Saudi Arabia, Israel, the United Arab Emirates and Jordan. 

The Arabian oryx has since flourished, reaching a wild population of more than 1000 individuals, and is continuing to increase. This had led to the Arabian oryx officially being moved from endangered to vulnerable on the IUCN Red List. A 2008 assessment showed that the Arabian oryx had recovered enough to no longer qualify as even an endangered species.

The IUCN Species Program produces, maintains and manages the IUCN Red List, and implements worldwide species conversation projects. The Species Program is headquartered in Switzerland and is designed to determine the relative risk of a species facing extinction. The Red List is used to keep track of and bring attention to the plants and animals that directly risk global extinction. 

Under IUCN Red List Guidelines a species can only move to a lower category if none of the criteria for the higher category have been met for five years or more. To be considered endangered there must be 250 or fewer mature individuals of a species, so the Arabian oryx, which is doing well at over 1000, will be listed as Vulnerable starting this year.

The Arabian oryx is native to the Arabian Peninsula, and doesn’t have many natural predators; humans drove the animals to extinction from hunting. In addition to the 1000 in the wild there are another 6,000-7,000 individuals alive in captivity around the world, many within the Arabian region.

Interestingly, the population that was re-introduced to Oman (where the last wild Arabian oryx were killed before it went extinct in the wild) has been struggling. The Oman population was hurt through illegal live capture for private sale, and has been rendered ineffective because only males remain.  Most new populations are in secure areas that are relatively safe from poaching, but animals that wander outside protected sites have no guarantee of safety. Future release locations for animals bred through captivity will be determined by the potential effects of drought and overgrazing, which have reduced available areas where populations could thrive. 

Now that I'm spending my days perusing the internet (so much more than ever before!) I've seen a lot of strange, strange, and I mean STRANGE things. In addition there is also so much negative news from hackers to politicians to criminal cases and everything in between that I feel like little glimmers of good news, particularly about successful conservation efforts should to be recognized. It doesn't make the bad news easier to swallow, but it still makes things seem brighter. 

Wisconsin's Place in the History of Animal Research

I decided to apply to graduate school at the University of Wisconsin-Madison at the recommendation of my undergraduate advisor. I honestly wasn't thrilled with the idea of coming to the midwest. I had never really considered what the cheese state was like before I applied - as a strictly east coast girl it was so far removed from everything in my life I couldn't even imagine living here. But, when the college admission chips fell where they did, it was obvious to me that UW Madison was the clear first choice for grad school.

That being said, when I arrived in Wisconsin nearly nine months ago, I knew very little about the history of the University I was attending. I knew that UW-Madison was home to an amazing amount of scientific research, but I had no idea how rich the tradition of scientific inquiry really was. I quickly became aware of the Wisconsin National Primate Research Center (WNPRC) and notorious, and immensely important, psychology researcher Harry Harlow.

Those who follow this blog regularly know that I have written a lot of posts this semester inspired by my zoology class on human and animal behavior. It is this class that really got me motivated to learn more about animal research, and in particular UW-Madison's role in animal research. That brought me to two books, both written by Deborah Blum a professor in the journalism school here at UW.

In 1992 Blum won the Pulitzer Prize for a series of articles on the ethical dilemmas posed by primate research. She turned this into the 1994 book The Monkey Wars. I was enthralled by the history of primate research in the United States, and am ashamed to admit how little I knew prior to reading the book. The story of Edward Taub, the Silver Spring Monkeys (named after the site of the lab in Maryland,) and the rise of PETA in 1981 had me riveted. The condensed version of that story is that PETA founder Alex Pacheco volunteered undercover in the lab of Taub, who was conducting neurological experiments on monkeys (severing the nerves to control a limb and then coaxing nerve regeneration.) The monkeys were held in filthy conditions - but there was no legal standard for research animal care at the time. Pacheco took photographs (some admittedly staged) and went to the police to have Taub arrested (which he was - for animal cruelty.)

The majority of events described in the book take place long before I was even born, and I suppose thats why I felt so removed from them. I didn't realize I was taking the idea that animals have rights for granted until I learned about the history of animal research in this country. I knew that people are cruel to animals, but I was blissfully oblivious to the cruelty that was standard in research labs in the 1950's, 1960's, and 1970's. After finishing Monkey Wars, my blissful respect for science felt somewhat dingy - and I needed more information.

The book I picked up next, to explore the history of animal research and in particular its role in Wisconsin, was Blum's 2002 biography of Harry Harlow, Love at Goon Park. I don't think I had ever heard the name Harry Harlow before moving to Wisconsin - yet his work is something that I reap the benefits of in my daily life. Harlow is both famous and infamous for his "mother love" and "pit of despair" (a catchy term for depression) studies. His research used rhesus macaque babies to show that children need love and social interaction - particularly touch - to function and develop normally, and that being isolated can be the cause of a complete psychological breakdown.

The reason Harlow is so controversial is that the way he studied depression and isolation from one's mother was to psychologically "break" baby monkeys. These were horrible studies. The monkeys were taken away from their mothers and given a variety of fake substitutes to see which the babies would cling to most (warm, cloth, animated mother was the winning surrogate but cold metal mother caused psychological damage to her babies.) For the depression studies the babies were put in isolation cages for 3-6 months at a time, with no interaction at all. The monkeys suffered tremendously. The concept of love as a necessity needed to be proven, to move parental nurturing into the mainstream. But the question remains if it needed to be proven in that way.

Considering that I was surprised by just how awful the United States history of animal research is, you can imagine how shocking I found it that studies were needed to prove that mothers should hug their children. But then again, as Blum so poignantly points out, the scientific standard at the time was to isolate children for health reasons (limit the spread of bacteria & disease.) What seems so obvious to me - that animals should be well taken care of, that children should be hugged - were really revolutions within the scientific community. Looking back we can say how ridiculous it is that such assertions needed to be scientifically proven, but then again think about where we might be if these ideas had never been generally accepted.

This semester has really driven home for me just how much I owe to animals. The idea that my mom would have been condemned as a bad mother for hugging me when I cried were it not for Harry Harlow and his baby rhesus macaques makes me very appreciative of the role of animals in research. I remember so vividly crying on my Mom's shoulder at maybe 4 or 5 years old. I remember the silky salmon colored blouse she was wearing. I remember staining it mercilessly with my tears, but I don't know why I was crying. I do know that all I wanted was to be held, and have my hair stroked and be comforted. I can't imagine my parents keeping me at arm's length.

We owe a lot to the animals who started the social movement that changed the way people parented, and the researcher who brought it all to light for making society take notice; and I had no idea about either before coming to Wisconsin. While I do my fair share of whining about being in the cheese state, my experiences here have opened my mind to a lot of new concepts - particularly with regard to the role animals play in society and how we as humans should regard them.

Hal Herzog, Animal Ethics & the Alien Problem

Last semester I read many more books (thus I did a lot more book reviews) than this semester which has mostly been devoted to academic research papers. But I do have two books that need reading for my zoology class on human and animal behavior with Patricia McConnell.

I finally finished the first of the two assigned books, Hal Herzog's Some We Love, Some We Hate, Some We Eat - Why It's So Hard to Think Straight About Animals. I've been reading Herzog's book all semester, so my evaluation of it draws on a slightly disjointed memory but I think I can summarize his main point with two statements:

1. Most people choose not to (or don't know enough to) think about their personal moral philosophy. Not thinking about how we feel about animals is what allows us to love puppies so much while we happily chow down on a Big Mac.
2. Those people who have spent a tremendous amount of time trying to discern their personal moral philosophy about animals either A. remain horribly conflicted or B. Choose a philosophy with regards to the treatment of animals that societal pressures make very difficult to implement (for example, all creatures are equal - if you save an iguana from a burning building instead of a human baby, society is not going to look kindly upon you regardless of your belief that the iguana and the baby are equals)

Herzog's answer to his main question "why is it so hard to think straight about animals?" largely comes down to because you're damned if you do and you're damned if you don't.

The book tries hard to cover a variety of topics that impact the way we feel about animals, some obvious (factory farming, animals in research, hunting) and some less so (cockfights, dog shows, gender roles.) I don't intend to go into his arguments for and against certain behaviors, but to give an example of the kind of analysis he provides I will share the anecdote from his chapter "The moral status of mice," on the use of animals for biological research.

Herzog frames animal research this way: Think of Steven Spielberg's 1982 classic film ET. Remember how close Elliott and ET became, and how heart wrenching it was to see ET go back to his home planet? Well, what if there was a disease destroying the alien's on ET's home planet, and the reason he really came to earth was to scout out organisms of lesser intelligence to test possible remedies on. Elliott's intelligence was far less than ET's. So how would you feel if at the end of the movie, ET kidnapped Elliott and took him back to his home planet to live the rest of his life as the subject of research. It would save millions of aliens. But ET still essentially destroys Elliott's life. Not really a satisfactory ending, I'd say.

So if we don't want ET to kidnap Elliot just because he is of lesser intelligence, then what do we do when humans are like ET and mice are like Elliot? Should we experiment on mice just because they are of lesser intelligence? Previous logic would lead us to say no, we should not experiment on the mice. But yet, I'm still in favor of animal research. Philosophically, I shouldn't be. But there is something about experimenting on a member of my own species that I find morally reprehensible. It is the reason we don't conduct experiments on people in coma's or with mental retardation. But if you are always putting humans first, how can you still treat animals with respect and moral standing?

I'm not here to answer the questions thinking critically about animals pose. Herzog has 280 pages of highly intelligent, moving, and entertaining explanation, and he still doesn't answer most of them. But he will get you thinking about your own behavior, why some animals matter to us more than others, and why humans think the way we do.

It is important for everyone: meat eaters, vegetarians, pet lovers, people who avoid animals, etc. to think about why they feel the way they do about animals. I was surprised by the conflicts in my own way of thinking, and sadly I now fall into column A - thinking critically, but still horribly confused. At least I'm thinking right?

Science For Six-Year-Olds: Animals & Tool Use

This is a special Science Decoded post for Mrs. Podolak's first graders at Lincoln-Hubbard Elementary School (yes that would be my Mom's class). My viewers in Lincoln-Hubbard's first grade liked my post Animal Cognition & The Genius Parrot about Dr. Irene Pepperberg and her experiments with Alex the african grey parrot, so I decided to do a post just for them to give them some more information about animal cognition (thinking) by sharing some videos about tool use in animals.

Animal cognition is a fascinating subject because we don't even know everything about how our human brains work, yet we have been able to observe other species demonstrating the ability to think. The following videos show some interesting examples of animals showing us that they do think about their surroundings by using tools to achieve their goals.
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Chimpanzees - termites are a source of food for chimpanzees, but they can be extremely difficult to catch because the mounds they build to live in are thick and hard for a chimp to break into. So, chimps have developed a way to infiltrate (sneak into) the mounds. They even modify (change) simple tools (a regular stick) by making them into brushes which capture even more termites.


New Caledonian Crows - birds like to eat nuts, but getting through the hard shell to the tasty part can be very difficult. These crows have devised a special way of cracking the nut, and even found a way to safely collect the edible part of the nut once it has been smashed. (Because this is a BBC video it needs to be watched on YouTube but clicking below will take you to the right link).


Octopus - Researchers have found an example of tool use by the octopus. The organism takes coconut shells and gathers them to use as a shelter which is a startling and significant use of an object external to the animal's self to achieve a goal among invertebrates (animals that don't have a spine, the bones in their back.)


There are many other examples of animals using tools, which shows that the ability to manipulate an object and use it to accomplish a task is by no means a uniquely human trait. If there are any questions, leave them for me in the comment section and I'll be sure to answer them!

Animal Cognition & The Genius Parrot

In my previous post Osteoarthritis, Cognition and Animal Healthcare I raised some questions about animal cognition - basically how can we understand what animals know and how they think? In my zoology class we are studying animal cognition, and we watched a really interesting video of Alex the African Grey Parrot, who is famous for the cognitive abilities he demonstrated when asked complex questions. 

Alex died in 2007 (check out his obituary in the New York Times,) but prior to his death he was the subject of very interesting work by Dr. Irene Pepperberg at Brandeis University (she is also an associate researcher at Harvard University) and the subject of her book Alex and Me. Even though it isn't new research, I wanted to share the video of Alex going through some of the cognition tests, because I hadn't seen it before, and I was pretty impressed by just how much he knew. 

Since Alex's death researchers in Pepperberg's laboratory are working with other parrots. Although, cognitive abilities as extensive as Alex's haven't been reported. Alex shows us what parrots are capable of, but I can't help but wonder if he showed the highest boundary of what parrots can learn and most parrots are not as smart, or if it really is just a matter of training parrots to communicate with us. 

Osteoarthritis, Cognition and Animal Healthcare

As I've talked about in previous posts, I'm taking a zoology class this semester on the biology and psychology of human and animal relationships with Patricia McConnell. I'm really enjoying the class so far because it has me thinking more critically about the way humans think about and treat other animals.

Case in point, I read the article Polar Bear Mercedes' Health Failing mostly because it is about a polar bear (as I've proclaimed before, they are my absolute favorite animals and have been since I was a child). I was having a gushy "oh poor polar bear" sort of moment. BUT reading the article made me think a lot about veterinary science and the way that humans take care of the health problems of other animals.

The article is about a specific polar bear in the Highland Wildlife Park in the United Kingdom that has been diagnosed with osteoarthritis. Currently the bear is being treated with painkillers for the condition, which is a degenerative disorder of the joints. Joints are places in the body where bones meet. They are held together with cartilage, tendons and muscles that enable the joint to bend. When an individual has osteoarthritis the cartilage starts to break down, causing the bones to rub directly together. This can cause pain, swelling and stiffness that drastically limits movement as the disease progresses.

At the Bronx Zoo.
Source: Wikipedia Commons

There is no known cure for osteoarthritis (which it should be noted affects many different species, and is very common in humans) but the symptoms can be controlled with painkillers. The condition typically effects older individuals. In the case of the polar bear, the patient is 30 years old which makes her a very old lady as far as polar bears go. Because there is no cure for the condition it is possible that the polar bear will be put down when her condition progresses enough to reduce her quality of life.

I can't help but wonder how we define quality of life for a polar bear. Even though she is suffering from a condition that also effects humans, we can't necessarily define the polar bear's suffering or quality of life the way we would our own. How do veterinarians or zoologists decide when enough is enough for a polar bear? She can't tell us when she's tired of living with the disease. Quite frankly assisted suicide isn't legal in humans, so what is it that makes euthanasia in animals alright? I support trying to limit the pain and suffering of animals that have been brought under human care, but what needs to be considered before deciding that it is time for them to die?

In humans a joint that no longer functions due to damage from osteoarthritis could be replaced with an artificial one made of plastic, metal or cement. That type of invasive surgery wouldn't be done on other species. Not only are these procedures extremely expensive, they require strenuous physical therapy and rehabilitation to come back from. This is a case where the condition might be the same across species, but the way it is treated is different. Really all they could do to alleviate the bear's symptoms is treat it with painkillers (which is what they are doing.)

A human joint with osteoarthritis.
Source: NIH-NIAMS photo gallery

It is interesting to consider how the polar bear would deal with the disease in the wild. They certainly wouldn't have pain killers at their disposal. In this case the polar bear wouldn't even have made it to old age (and have developed this disease) if it weren't for human interference. It was rescued after being shot in the wild and brought to a zoo, and later moved to the wildlife park.

These aren't easy questions. Animal behaviorists are still searching for answers about how much other species are self-aware. The fact is we don't know how much the polar bear thinks, or what it thinks - about its life or its condition. Even though I don't have answers, I appreciate my zoology class for getting me to think like this about how humans manage other animal's health.

If you are interested in animal cognition there is an entire journal dedicated to scientific research being done in the field called (shockingly) Animal Cognition where you can learn more about studies of what and how animals think.

Sheep

To shake things up, today I don't have a journalism trend or scientific discovery to talk about. Instead, I want to discuss sheep, more specifically sheep herding.

I mentioned a while back that I'm taking a zoology class this semester with Patricia McConnell about human and animal behavior. Today our class was held in the stock pavilion (yes, I attend a University that has its own stock pavilion) and Prof. McConnell brought in her own sheep from her farm for a demonstration of how her herding dog Willie gets the sheep to do what he wants them to through body movements, and also how she controls Willie.

Not my professors sheep (my pics didn't come out so well)
There sheep are from Wikimedia Commons.

To prepare for class we had done some readings about how animals respond to sounds. In the demonstration we were shown that short, staccato sounds are best for motivating an animal to move and low long sounds are best for getting it to slow down or stop. I find it really interesting that this is a universal trend among animals. Its also interesting that the sounds to get the dog to go clockwise or counterclockwise (moving the sheep right or left) vary by the animal's handler, but also tend to be short yet distinguishable sounds.

It was fun to demonstrate the principles we are learning in class in real-life settings and not just through reading academic papers. Plus, I got to see sheep and for a Jersey Girl that still has a lot of novelty.

Sequencing Genomes to Save Species

For this post I’m trying something a little different. I mentioned a few weeks ago that I’m using Science Decoded for class, and as a part of that we were assigned to write a post in the form of a list.

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All living organisms are made of DNA, a series of nucleotide bases (Adenine, Guanine, Cytosine, and Thymine) contained in chromosomes. Genome sequencing is an analysis of DNA, conducted by “reading” the different patterns of nucleotides A-G-C-T for differences between species, and abnormalities within a species. Researchers around the world are working to sequence the genomes of a variety of organisms, including those on the endangered species list.

1. Orangutan (Pongo abelii) – In January 2011 the National Institutes of Health (NIH) announced the publication of the orangutan genome sequence. Funded by the NIH, researchers from Washington University School of Medicine in St. Louis, MO and Baylor College of Medicine in Houston, TX sequenced the genome of a female Sumatran orangutan, five additional Sumatran orangutans, and five Bornean orangutans (Pongo pygmaeus.) The research shows that orangutans share 97% of their DNA with humans, but compared to humans and chimpanzees, orangutans have evolved much slower leading to fewer mutations (variations in the code between individuals of a species). (Read more) 

2. Tasmanian Devil (Sarcophilus harrisii) – Fifteen years ago a facial cancer was identified in tasmanian devil populations. The cancer has ravaged the species, resulting in an 80% decline that has forced the species to the brink of extinction. This cancer is transmissible, which means that biting the face of an infected animal passes it between individuals. In September 2010 researcher from the Wellcome Trust Sanger Institute and the genome sequencing company Illumina announced that they sequenced the tasmanian devil genome in an attempt to learn more about the cancer and how to stop it from wiping out the species. (Read more)

3. Giant Panda (Ailuropoda melanoleuca) – Arguably one of the cutest endangered species, the giant panda is a prominent symbol of China, where it lives in a restricted mountain area. According to the Beijing Genomics Institute (BGI) the number of giant pandas left in the wild is estimated between 1600-3000. In December 2009, BGI published the complete sequence of the giant panda genome. With the information obtained by the genetic analysis researchers hope to learn more about the genetic and biological factors that shape this species behavior to assist in disease control and conservation efforts. (Read more)

4. Tibetan Antelope (Pantholops hodgsoni) – Listed by the United Nations as an endangered species since 1979, the Tibetan antelope could hold the key to understanding the pathogenesis of chronic plateau sickness. The species calls China’s Qinghai-Tibet Plateau home, making them ideal for studying the evolution of species that thrive in environments characterized by extreme cold and low oxygen levels. The genome sequence of the Tibetan antelope was announced in December 2009 by researchers from BGI and Qinghai University. (Read more)

5. Coral Reefs (Acropora millepora) – Coral reefs are among the world’s most diverse ecosystems, yet according to the Genome Center at Washington University it has been predicted that in the next 50 years between 40%-60% of the world’s coral reefs will die. In 2005 the NIH funded the sequencing of the coral A. millepora (which is not an endangered species, though coral reefs as a whole are endangered ecosystems) to serve as a “lab rat” for studies of the environmental factors (light, sediment load, or acidity) that can cause coral death. (Read more)

Not quite endangered & not fully sequenced:

6. Polar Bear (Ursus maritimus) – Recently removed from the list of endangered species recognized by the United States, researchers at BGI are still working to sequence the polar bear genome. The polar bear sequence is a part of a three-pronged project to sequence the Tibetan antelope (completed in 2009) and emperor penguin genomes.

7. Emperor Penguin (Aptenodytes fosteri) – One of the most recognizable penguin species, the Emperor Penguin is found in Antarctica. The emperor penguin is currently under consideration for inclusion under the Endangered Species Act, due to the effects of climate change. The genome sequencing project is being conducted by researchers from BGI in conjunction with sequencing the polar bear, and Tibetan antelope genomes. (Read more)

8. Snow Leopard (Uncia uncia) - In October 2009 researchers from Oregon State University, the Western University of Health Sciences, and the Miller Park Zoo (IL) announced plans to sequence the genome of the snow leopard (which is on the Endangered Species list). According to Oregon State, the snow leopard is prone to diseases that do not plague other big cats including pneumonia, enteritis, hip dysplasia, and papillomaviruses. Sequencing the genome could help researchers identify what makes the snow leopard susceptible to these disorders. (Read more)

Genome sequencing technology continues to develop, making it easier and cheaper to sequence the genomes of various organisms. While an endangered species has yet to be saved due to the information obtained by sequencing its genome, what researchers learn will help them gain a better understanding of endangered species, which is a step in the right direction towards improving conservation efforts. 

Bear Stun Gun

Those of you who read this blog regularly know that I love bears, particularly polar bears, but in a pinch any Ursus arctos (I've seen the taxonomy with and without 'horriblis' on the end) also known as the Brown or Grizzly bear, will do. I am thus drawn to all stories regarding bears, it is a personal bias I suppose.

Source: Wikimedia Commons

Taking Patricia McConnell's Biology and Psychology of Human and Animal Behavior course this semester has me thinking a lot about the human role in the lives of other animals (and today in particular, bears.) I took a course at Lehigh to complete my environmental science minor that had more to do with animal rights than McConnell's class but there were some similarities to what I'm studying now. These classes have appealed to me because no matter what your opinion on animal rights or human and animal relationships, I think its important to question and think about these issues..

I say that because once you get your brain into the habit of questioning the things you see, hear, and read you might view things in a very different light. In my daily perusing of the BBC website today I was drawn to the article Company in America Launches Taser 'Bear Stun Gun'. This is the kind of article you could very easily glance over, I mean what could be wrong with giving members of the National Parks Service Tasers to protect themselves? Obviously, park rangers getting mauled by bears is a bad thing.

BUT, my first thought when reading this article was that bears live in the woods, and I wouldn't like it if someone came into my house to take a tour, and then shocked me with a stun gun when I got upset about their presence. So why then is it OK to do it to bears? Tasers used by police have reportedly killed people, so does that make it more or less OK to use it on an animal? While the taser might not be humane due to the acute (sudden onset) pain that it causes, is it a better option than just shooting a bear with a regular gun and killing it? Or would you be doing the bear a favor by killing it (something along the lines of putting it out of its human-induced misery)?

This all then circles back to the question of whether or not people should be in the woods in the first place. Would it be more or less OK to use Tasers on bears if they were used by people who live in towns near forests, who need to occasionally protect their lives or property? In that instance the bear is then in the human habitat, not the other way around so would the violence be justified? Does the bear have an inane right not to be Tased, considering it can't choose to follow or not follow human rules and thus can't know that it has broken them? Should humans assume a guardian role over lesser animals and protect them from the kind of violence we use against each other?

Human taser. Source: Wikimedia Commons. 

I don't intend to answer any of the questions I posed above, the point I'm trying to make isn't for or against the use of Tasers. My point is that even an issue that seems straight forward can have many layers when you tease it apart. Questioning things is one of the easiest ways we have to educate ourselves, especially on science-related issues. I encourage everyone to try to think critically when they see science topics in the news, you might even be surprised by what conclusions you draw.

I would like to give the BBC article's writer Dan Cairns a positive review for explaining how the bear taser works in a clear and concise way. He writes, "Like other Tasers, it delivers an electric shock by shooting two electrode darts attached to conductive wires. The subjects motor nerves are immediately affected and the brain is unable to send signals to the muscles until the charge is turned off."

I wanted to draw attention to this description because this type of background knowledge about how the weapon works is really essential to helping readers determine how they feel about the use of the bear taser. You can't be for or against something you don't understand (well, if politics is any indication you can - but I don't recommend it). Even for a short little news article like this, you need to have background, and I like this article because I think it gives you the information you need to really think critically.

Animals On The Black Market

I've been thinking a lot about how humans use animals due to the readings I was assigned for my zoology class for next week. I like to think that my position on the use of animals is somewhat middle of the road. I believe in animal research, in work animals (like a sheep dog), and I do eat meat. BUT, I am a firm believer in protecting animal welfare and conducting all animal related activities in a humane way.

Chimpanzee (Pan troglodytes).
Source: Wikimedia Commons

I bring up animal welfare, because I saw an article in the BBC today about a huge raid on suspected illegal animal traders conducted by Gabon's ministries of water, forestry, and defense. The government agencies weren't able to save any live animals, but they found enough evidence (heads, hands, skins, etc) to charge the five suspects with poaching.

According to the World Wildlife Federation, the raid resulted in the largest haul of dismembered animals in Central Africa in the last decade. Included in the seizure were parts (I know, awful) of a gorilla, at least 15 chimpanzees (probably several more if the parts came from different animals), 12 leopards, a lion, five elephants, and several snakes.

I feel like animal poaching is the type of issue that can be easy for people to ignore because we associate it with being a far away problem, it can be easy for us to forget about. I realize that there are some cultures that hunt and eat these animals - but selling them for exorbitant prices on the black market, when killing them is illegal in the first place is a problem.

About a year ago I wrote an article for BioTechniques about a new method to track animal poaching using genetic analysis of poached animals. Genetics Cracks Down On Animal Trafficking focuses on animals poached in Nigeria and Cameroon, but it is still an interesting way to crack down on illegal animal trafficking.

First Day Of School

Yesterday was the first day of classes for the spring semester. As much as I struggled to come back to Wisconsin this semester I know that it will be a busy and productive few months. My first class was my science elective, the Biology and Psychology of Human and Animal Relationships.

A border collie like Willie. Source: Wikimedia Commons

I was a little concerned signing up for a zoology course, considering the majority of my science background is in environmental science (with a little biology on the side.) But, I think this class will be incredibly interesting, and judging by the readings the material won't be anything that I can't handle.

My professor Patricia McConnell brought her dog Willie to class for the first day. He served as an example of the emotions that some humans feel toward animals, and started a discussion about why we feel more connected to animals like dogs than we do to say a chicken. Willie is a border collie and a trained sheep herding dog, so he was well behaved enough to be allowed to wander the huge lecture hall walking up and down the rows to be petted.

It is just the beginning of the semester, but already I've got the ball rolling on several projects. I'm still doing background for my first Primate Center assignment, but I've got my first interview for that scheduled for next week. I've got a freelance project that I'm working on that is more health/medical writing so that is also something that is taking up my time. Being so busy is helping with my homesickness.