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.
Sweet, Sweet Rejection
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
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
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
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?
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| 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
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.
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| 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.
Revising Taxonomy
Very few people in the United States give a damn about the Egyptian Jackal. While I have nothing to offer as proof of this, I stand by my hunch that this specific canid isn’t high on the list of most popular animals, because really, who has even heard of it before? (I hadn’t until today…)
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| Golden Jackal. Source: Wikimedia Commons. |
Why then should people care that genomic analysis has revealed that the Egyptian Jackal is actually a wolf, not a jackal at all? Well, because even if you don’t find the power of genomic analysis fascinating (like I do) this revision of current taxonomy (the classification of species based on how they are related to each other) is a great example of how science is a fluid thing that continually changes as new things are discovered. I think that understanding how even accepted scientific information can change is a hurdle that many people have to clear before they can really start to follow science in the news.
For years, the Egyptian Jackal (Canis aureus lupaster) was believed to be a subspecies of the Golden Jackal (both species that call parts of Africa home.) Researchers from the University of Oslo (Norway) noticed physiological differences (ie: differences in the way it looked) between Egyptian Jackals and other Golden Jackals, which led them to pursue a genetic analysis.
Sequencing the Egyptian Jackal’s genome has shown that it is a closer evolutionary relative to wolves found in India and the Himalayas (even to the United States’ Grey Wolf) than to Golden Jackals. Revising the taxonomy could have important impacts on conservation efforts. If Canis aureus lupaster (now renamed the African Wolf — and the only wolf now known to live in Africa) is a distinct species, an evaluation needs to be done to see how many members of this species there are, to determine if it is endangered.
I like this story because its a great example of how scientists are constantly revising accepted information the more they learn. However, I think when you tell people that science is constantly changing it is important to distinguish between making a revision and being flat out wrong. Scientists weren’t just wrong in their taxonomy. The Egyptian Jackal/African Wolf is a canid, so that part of the taxonomy was and still is correct. The genetic analysis enabled research to put the species into an even more specific category.
So when we say that science changes, we mean that it gets more specific and thus more accurate. But that doesn’t mean that the scientists who came before had everything all wrong. Often when scientists revise information their predecessors/colleagues were close, but didn’t have the necessary tools to learn enough to get things exactly right. There is always more that scientists can learn, and as they do, they fine tune, which is the case with the Jackal/Wolf taxonomy.
For more on the Jackal/Wolf revision, the research paper was published in PLoS One.
Can Journalists Be Celebrities?
I’ve been thinking a lot lately about the distinction between television news personalities, and print/internet journalists. I feel pretty strongly that being a TV news anchor, doesn’t necessarily make you a journalist. But then what does make someone a journalist?
With the “sudden” departure of liberal commentator Keith Olbermann from MSNBC’s program Countdown last week, I think the issue of journalists as television personalities, and ultimately as celebrities has been brought into the spotlight. Olbermann has been in trouble with the network for donating to liberal political campaigns, which would be a big no-no for a journalist because it would be a clear violation of the need to be unbiased. But Olbermann has never been unbiased. He has always made his affiliations clear, so does the fundamental journalistic quality of trying to be fair go out the window? If we don’t hold him to journalistic standards, does he then become nothing more than just a television star?
Where do we draw the line between Matt Lauer and Anderson Cooper? Are they both journalists? Are neither of them journalists? How does being on television make someone different from a print journalist? How many print journalists do you know by name? If I had to guess, I’d say not that many. I ask these questions because I think there are important distinctions between journalists that people need to be aware of. But at the same time, I’m not sure that I can quantify what it is that makes or discounts someone from being a journalist.
When I think about television journalism, I automatically think that Anderson Cooper is more legitimate than your typical nightly news anchor. But is this just a reflection of the way he is displayed on TV? Is he really a journalist in the sense that he develops stories, cultivates sources, does the digging and background research necessary to make a story? Or does he send an intern off to do the real journalism and then just read the cue cards? I certainly don’t know how Cooper operates, but I think its important to consider why he seems so much more like a journalist than the people who read the news every night on television.
Print journalists are rarely as recognizable as television personalities. Does that make print journalism more legitimate? For whatever reason, I feel a bias against people on television. If someone wants to be a television star, I don’t consider that the same as wanting to be a journalist. But why can’t a journalist also be a television star? What is it about TV that somehow cheapens what may very well be outstanding journalism?
Perhaps it is nothing more than the difference between an editorial and an article. But then why do the people who read the news on television (which would count as articles) not seem like journalists, when someone like Cooper who can easily cross into the realm of editorial seems legitimate? Especially when the Olbermann’s of the world, who are clearly editorialists, have so obviously crossed the line between journalist and television talking head.
I’m not sure. But as I figure out what kind of journalist I want to be, and how I want to direct my career, it is definitely something that I’m thinking about.
Some background on the Olbermann/MSNBC split:
The Washington Post: Keith Olbermann Leaves MSNBC, Speculation Follows
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.
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| 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.
Blogging Experiments
This semester for my long form journalism class (J880) with Deb Blum, everyone is going to be blogging in their speciality. I considered creating a specific blog just for the class, but I really like Science Decoded and I felt like if I was trying to keep up with a second blog, this one would fall to the wayside.
So, that being said there will definitely be some changes to my posts for the next few months. I want to keep the casual and personal feel that this blog has, but I’m only going to do personal posts if they are related to my work or school. I’m also going to be putting up lengthier posts with more background research in them, as opposed to my current standard of short posts filled with my own commentary.
Hopefully I can keep up a cohesive feel while I’m experimenting with different styles and types of posts. I’ll probably differentiate posts for class vs. regular daily posts in some way. I think using the blog for class should be fun to get more traffic to this site, and help me try to develop Science Decoded into a way to market myself.
To Test, Or Not To Test: A Regulatory Question
My internship with BioTechniques dumped me headfirst into the world of genome sequencing. One of the hottest (and by that I mean most talked about, funded, and hyped up) biotechnology fields, genome sequencing has a lot of power. The media loves genome sequencing because it attracts a lot of public interest, so its no wonder the technology is a headline maker.
For those who are unfamiliar with the term, genome sequencing is a process by which a machine takes a sample of your DNA (from saliva or blood) and “reads” it by identifying the nucleotide bases (Adenine, Guanine, Cytosine, or Thymine) that make up your personal DNA sequence. By comparing this sequence to the human draft sequence (a previously “read” and studied human DNA strand) researchers can tell if anything in your DNA sequence is out of place, indicating a chance for genetic disease.
I tried looking into personal genome sequencing companies for an article for my J800 class last semester. While I did come up with an article eventually, I decided not to pitch it on the grounds that none of the personal genome sequencing companies would make a representative available to talk to me, therefore my article was slightly off kilter. Apparently, no one wants to bother with helping a student, and if you don’t have a definite place to publish you just aren’t important enough for the corporate world to give a damn.
But, I still find personal genomics incredibly interesting, which is why the New York Times article Heavy Doses of DNA Data, With Few Side Effects caught my eye. The article takes a look at research from the Scripps Translational Science Institute that shows that people who pay money to have their genome analyzed often did nothing with the data, and even when the results indicated a higher risk for disease people didn’t feel any extra anxiety.
The results are interesting because they go against what you would think the common reaction to obtaining your genetic data would be. There has been controversy about public access to genetic information on the grounds that people won’t understand it and will thus act rashly or misunderstand their results. The new research shows that most people either didn’t do anything with the information they obtained, or consulted a medical professional before acting.
The new research doesn’t close the door on the issues surrounding personal genomics by any means. The idea that the technology and service should be regulated, and by who, and how strictly are all still prominent concerns. However, the study could serve to help policy makers decide how to regulate the industry.