All posts by erin

Sequencing Genomes to Save Species

BioTechnology, Conservation, Environment, Genetics, New Research, Sequencing, Zoology

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. 

Sweet, Sweet Rejection

Conservation, Employment, Past Articles
Hi Erin,
Thanks for the e-mail. This is definitely up Audubon’s alley. Unfortunately, we recently ran a story that touched on a species relocation, so it’s unlikely we’d run another story soon after.

Thank you again for considering Audubon, and best of luck placing your work elsewhere.

Best,
Audubon magazine
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My article on managed relocation of endangered species got rejected from Audubon Magazine, and I couldn’t be more excited. I have pitched the story all over creation, and haven’t gotten a single response, until this one. So even though it was a rejection – the fact that they were nice about it, and that they felt it was a topic they’d be interested in (so I picked well when deciding where to pitch) was encouraging and has re-invigorated my hope that perhaps I can get it published somewhere.

Audubon’s response highlights a very important aspect of pitching an article to a publication – you have to make sure they haven’t already covered it. In this case, my article is a critique of managed relocation as a conservation policy not about moving a specific species so I felt it was still worth inquiring about. But alas, they still felt it was too similar to their previous story. I still very much appreciated the kind response.
Its a sad day when rejection is thrilling, but to me it feels like progress. Rejection (when kind) can be so much better than just being ignored because it can help you improve and actually get you somewhere. 

Finding A Place For Al Jazeera

Public Perceptions, State of Journalism

Chaos has erupted in Egypt this week as protests calling for the removal of the president Hosni Mubarak turned violent. I do not mean to say that the conflict is as simple as pro or anti government groups, I know it is a complex issue. But as a disclaimer, I’m not a political writer, or an international relations writer.

The reason I bring up the conflict in Egypt is because I read a very interesting opinion piece on Al Jazeera English: US viewers seek Al Jazeera Coverage which says that the conflict in Egypt has led to a considerable increase in the number of people from the United States choosing to get their news from Al Jazeera. I think Al Jazeera is a very interesting curveball for the broadcast news industry that we should be watching.  
The article and comments section make the case that other news outlets (MSNBC, CNN, ABC, CBS) have done a poor job of covering Egypt, while Al Jazeera has excelled. The claim that American coverage is lacking is convincing. More people seem to know that Anderson Cooper, Christiane Amanpour, and Katie Couric were attacked by the protesters than they know about the causes of the conflict (myself included). 
For those who are unfamiliar, Al Jazeera is the dominant news outlet (television and internet) in the middle east, and is popular all over the world. Except here. Cable providers in the United States have largely chosen not to pick up Al Jazeera. Some say this is because the audience isn’t interested in Al Jazeera and the cable companies would lose money. Some say that Al Jazeera has been blacklisted for being sympathetic to terrorists. 
But for those who want it, Al Jazeera can be streamed live online which gives many Americans access even if it is not a choice on the television. Al Jazeera has dominated coverage of the situation in Egypt for several reasons, namely because they were already there and they know how to operate in the country. 
I visited the headquarters of Al Jazeera English in Washington D.C. with a college group in 2009. They actually let us in the control room during a live broadcast, and gave us what I consider to be a lot of access to their newsroom. The opinion piece I mentioned above is definitely something to think critically about, and consider the points for and against broadcasting Al Jazeera in the United States. 
The comments section on the article brings up some really great points about how Al Jazeera is seizing the opportunity to play up the “discrimination” against them by American viewers and also how Al Jazeera is a legitimate news source that Americans deserve access to. Internet is good but Americans get their news from the TV, and until Al Jazeera is given a channel the network just isn’t going to take hold in the United States.
Check out Al Jazeera’s coverage and let me know what you think. I’ll be watching to see if the situation in Egypt gives Al Jazeera the momentum it needs for a cable provider in the US to pick up the network. 

What We Don’t Know

Government Regulations

The site of the Chernobyl Nuclear Power Plant, where one of the world’s worst environmental disasters took place in 1986 doesn’t have a protective casing around it. Seriously? I wasn’t even born when Chernobyl exploded, how is it possible that all this time it hasn’t had a permanent casing around the radioactive wreckage?

Chernobyl in 2004. Source: Wikimedia Commons.

Radiation contaminated huge swatches of land across Europe in the late 80’s due to Chernobyl, and no one ever found it important enough to spend the money to build a permanent casing around the damaged nuclear fuel rods. How is that possible?

Twenty five years after the Chernobyl explosion the money needed to put a protective casing around the damaged nuclear fuel rods hasn’t been raised. The existing protective casing was intended to be only temporary, and won’t be a permanent solution to the radiation problem. A permanent structure has been under construction, but money to build it is going to run out before it is completed.

Countries all over the world have pledged money to build the containment structure, with European countries leading with the most donations. I understand that we are currently in an economic crisis, but how have 25 years passed without enclosing the radioactive ruins becoming a priority? This should have been done long before the world experienced its recent economic downturn.

This story has me thinking about all the things we don’t know. I never would have thought that there wasn’t a permanent structure around Chernobyl. It wouldn’t have even occurred to me to find out if there was one because its the sort of thing I would just assume had been taken care of. I can’t help but wonder what other issues are just never publicized…scary things to think about.

From Novelist to Lepidopterist

New Research, Public Perceptions, Science History, Science Policy

My first encounter with Vladimir Nabokov was in my high school AP English class. My teacher Mr. Kaplow (author of Me and Orson Welles, which fun fact: is a movie starring High School Musical’s Zac Efron) kept a movie poster of Lolita (based on Nabokov’s most well known novel) hanging on the classroom wall.

I next encountered Nabokov while working through my undergraduate English major. Due to his Russian roots, Nabokov fit nicely into the course materials for my international literature class. I read his memoir Speak, Memory which talks a lot about Nabokov’s interest in lepidoptery, the study of butterflies.

Karner Blue Butterfly. Source: Wikimedia Commons.

I bring up Nabokov and his butterfly hobby because I just read an article on Nabokov’s scientific theories in the New York Times.  Nabokov’s theories were dismissed by lepidopterists during his lifetime,  but genetic analysis has shown that he was exactly right about the origin of a group of butterflies known as the Polyommatus blues. Nabokov theorized that the butterflies had originated in Asia and come to the United States in waves, but in the 1960’s and 1970’s no one took him seriously.

Researchers at Harvard University (where Nabokov was curator of lepidoptera at the Museum of Comparative Zoology) decided to do a genetic analysis on the butterflies to test Nabokov’s 30-year-old theory. The results showed that Nabokov was right all along, Polyommatus blues are genetically linked to butterflies in Asia. Genetic analysis has also been used to validate Nabokov’s hypothesis that Karner Blue Butterflies are a distinct species.

By this point you might be wondering why it matters that this long dead Russian novelist has been vindicated as a legitimate scientist by new technological advances, so I’ll get to my point. Nabokov is an example of how members of the scientific community can be quick to dismiss the work of anyone who isn’t an expert.

If we hold anyone who does scientific research to the same standard of peer review (analysis by other scientists, and the ability to replicate a study or experiment and get the same results as the original researcher) then even people who don’t have their doctorate in a specific science can still contribute new knowledge.

Please note that I’m not advocating that any quack with a theory should be taken seriously by the scientific community. But if promising research or theories are developed by people who might not call science their profession, their value should still be evaluated.