Monday, February 28, 2011

Defining & Finding the Higgs Boson Particle

I know that I love on the BBC quite a bit, I make no bones about it being my preferred source for daily science news coverage. However, the article "LHC has two years to find Higgs" is an unfortunate departure from the BBC's typically stellar science coverage.

The article caught my attention because I'm already familiar with the Large Hadron Collider (LHC) a particle collider operating underground along the France/Switzerland border. A particle collider takes protons (a small part of an atom), runs them around at speeds close to the speed of light, and crashes the particles into each other. Hence the name, particle (the protons) collider (the smashing them together part.)

The other part of the BBC article's title that caught my eye was "Higgs" which refers to the Higgs Boson Particle. The Higgs is a theoretical particle - meaning that it is a particle that physicists THINK exists, but they don't actually know for sure, it might not exist at all. In trying to understand the universe and what gives all matter mass, physicists have come up with several theories.

One of these theories is the Standard Model - which is based on the existence of the Higgs. If it exists the Higgs would explain how particles get mass. The LHC is looking for the Higgs by analyzing the teraelectronvolts (TeV - a measurement of energy) that would be emitted by the process through which particles get mass. The LHC should be able to detect the TeV of the Higgs - if it exists.

Part of one LHC tunnel. Source: Wikimedia Commons
I realize that the BBC's article is clearly an update piece about ongoing research, but it just glosses over some very important explanations about the LHC and the Higgs. If I didn't know that LHC was a particle collider or that the Higgs is a theoretical particle I would have no idea what this article is about from the title. Even as you go through the body of the article, there is no background information. To say that particle physics is complicated is an understatement. All the more reason why this article needs background information to make it understandable. As it is, this article is not appropriate for lay audiences.

The timely component of this article, or the reason why an update on the LHC is needed, is that researchers have announced that if the Higgs isn't detected by the end of 2012 they will conclude that the particle does not exist. If the Higgs doesn't exist then the Standard Model is not the way by which the universe is organized, meaning researchers would have to re-define their understanding of sub-atomic physics.

This is a news worthy update, however I feel like the reporter didn't do the story justice. Even the quotes do nothing to explain what LHC is, what the Higgs is, or what the significance of its existence or non-existence would be. I have a particular problem with the paragraph:
"According to Professor Tom LeCompte of the Argonne National Laboratory, US, who works at the LHC: "The most likely place for the Higgs to be is in a very good place for us to discover it in the next two years."

I have no idea what this quote means. "The most likely place for the Higgs to be is in a very good place..." What? My best guess is that the scientist is trying to say that research at LHC has progressed to the point that if the Higgs isn't detected in two more years, it doesn't exist. But obviously, that is NOT what he actually said.

This is a prime example of a quote that shouldn't have been used. Rather than just using the confusing quote the reporter could have asked the source to clarify or say what they meant in a different way. The reporter could also have paraphrased what the researcher was trying to say. Just because an intelligent and successful scientist makes a statement, doesn't mean that statement is gold. As a writer you have to decide what quotes add to the story, and what quotes are just confusing. You shouldn't put in quotes just to have quotes.

I realize that this is just a short article and it isn't trying to do an in depth analysis of the LHC, the Higgs, or particle physics, but that doesn't mean that background information and good quotes should go out the window. This topic is particularly complex and nuanced, and I've struggled to provide a decent explanation here - but just because something is hard doesn't mean you don't have to even TRY to explain it clearly.

I think the BBC article could have been a lot better if more effort was put into trying to at least define the LHC and the Higgs for the reader. After all, the reader isn't going to care that some particle might not exist if you don't explain what that particle is and why it matters.

If you want to learn more about the LHC, I can't help but recommend the following video. I still get a kick out of watching physicists try to rap and dance. You will find the explanation of the Higgs in the video far more complex than mine. Physics is out of my realm of comfortable understanding - but I gave it a shot and tried to keep it as basic as possible.

Sunday, February 27, 2011

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. 

Friday, February 25, 2011

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.

Tuesday, February 22, 2011

Thunder Thighs

Perusing the BBC today, the headline "Dinosaur had thunder thighs" leapt off the page and made me laugh, so I couldn't help but share it here. Coming from a background where I was in a sorority as an undergraduate, I can assure you that when someone dropped the term "thunder thighs" they were not talking about dinosaur muscles. But this is a case of scientists having a sense of humor, using the term to name a new dinosaur species.

The species is a sauropod, a type of dinosaur characterized by their long necks and tails. According to the researchers, the fossilized hip bone is larger than the hips in other similar species. This along with the unique shape of the hip socket which shows a large space for muscles to connect, led the researchers to conclude that B. mcintoshi would have had powerful legs capable of delivering strong kicks.
A representation of some long necked sauropods.
Source: Wikimedia Commons
The dinosaur species is technically called Brontomerus mcintoshi from the Greek bronto for thunder and meros for thigh. Leading to the common name, thunder thighs. The researchers from University College London who discovered the significance of the fossilized remains (which are fragmentary, but enough to draw conclusions) named the species the way they did because it would have had extremely powerful and muscular legs.

The fossils date back to the Early Cretaceous Period, and are estimated at 110 million years old. The finds were uncovered in the Hotel Mesa Quarry in Grand County, Utah. The site is known to have been scoured by fossil hunters, leaving researchers to speculate whether other interesting finds (like thunder thighs) may have been carried off to private collections.

I like the BBC's coverage of this scientific find so much, because they had fun with the name of the species, but not so much as to dilute the importance of the find. The article is detailed and (I think) does a good job of explaining what is significant about the species and the location where it was uncovered. If nothing else, the title alone is clearly a success because it got me to read the entire article.

It is important to note that the bones were discovered in the 1990's and stored at the Oklahoma Museum of Natural History, but the significance of the hip bone wasn't discovered until Dr. Mike Taylor from University College London evaluated them in 2007. Results of this study were published recently in the journal Acta Palaeontologica Polonica.

Saturday, February 19, 2011

Budget Breakdown: Federal Funding for the NIH

As my regular readers know, I use Science Decoded for my long form journalism class. As part of that, sometimes my posts have to meet requirements outlined by my professor. This week, the assignment was to write about budget. My recent post on Wisconsin's budget protests brought up the issue of understanding what your government pays for, so I've decided to do a breakdown of the 2012 NIH budget.
As citizens it is important to know what is included in the federal budget. Among academics, intellectuals, people who are informed about their government, and people who pretend to be informed about their government this is a generally accepted statement. But why is budget important, really?

Well, my first answer is that you shouldn't whine or praise something that you don't understand. So (even though people do) you can't say you disagree with or approve of the way things are budgeted, when you don't even know what is in the budget, or why it is included and thus deemed worthy of public funding. I think it SHOULD be generally accepted that you don't open your mouth about things you don't understand (even though people always do...) so for the sheer ability to speak intelligently about your beliefs, I think people should know what is federally funded.

The other reason that I think people should take the time to look at budget appropriations (what money goes to who for what) is because people take federal funding for granted. The beautiful thing about being Americans is that what we want matters, and what we say can effect our government. We trust our government to do with our money what we want them to, but we should still make sure that the government follows through. You can't just assume that what you believe deserves funding, is actually being funded. Do you want your money to be spent finding a cure for cancer? (I'll assume you said "yes") Do you know how much money the government actually spends trying to find a cure for cancer?** (I'll assume you said "no") Isn't that a problem?

To be a part of the American democracy you need to know what your government does. At the very least, you should know who the government is giving your money to, so you can then decide if you support or are opposed to the government's actions. Have an opinion. Have an informed opinion. The information is out there and readily available for those who seek it.

So now that I hope I've convinced you that you should care about budget, I come to the National Institutes of Health (NIH). I know I'll sound like a snot for saying this, but it AMAZES me that many people, whom I consider to be quite intelligent, don't know what the NIH is, or what it does. The NIH is the federal government's biomedical research organization. In addition to conducting its own research, the NIH is a huge funding machine that awards grants to thousands of researchers around the country (and even internationally) to pay for the costs associated with doing research. These costs include, but are not limited to, lab equipment (your test tubes and bunsen burners,) technology (from microscopes to genome sequencers,) consumable supplies (your reagents and pipettes,) and researcher or technician salaries.

Biomedical research is a multi-million dollar industry. But only a fraction of the research conducted in the United States is actually funded by industry. By far, the most important funding organization for researchers who are not industry based (ie: most college professors) is the NIH. Without federal support for these researchers, most would not be able to conduct their experiments. The budget that has been requested by President Obama for fiscal year (FY) 2012 to fund the NIH and all of its programs is $32.0 Billion. Yes, Billion.

The request by President Obama must be passed by the House of Representatives and the Senate before it is approved. But, these proposed numbers still demonstrate exactly why the NIH and its budget are so important. The proposed $32.0 billion represents an increase of $745 million from FY 2010 - an increase of 2.4%. However, current estimates place inflation from 2010 at 3%. So, even though the budget is going up, the NIH will be able to fund LESS projects than it did in 2010 because the increase will not be enough to counter the effect of inflation. In spite of this, the budget request still shows that research is a priority for this administration (ie: it could be much worse).

What does that $32 billion actually get you? Well, the NIH office of budget has a great table that outlines how the money is expected to be allocated among its institutes, in addition to a great document (with diagrams) that compares the budget for each institute over the last few years (which is where I pulled the following numbers from).

What falls under the NIH, and thus gets parts of its $32 billion? (listed from most funds to least):
National Institutes of...

  • Cancer (NCI) - $5,196,136,000 (**this is what the government spends finding a cure for cancer)
  • Allergy and Infectious Diseases (NIAID) - $4,915,970,000
  • Heart, Lung, and Blood - $3,147,992,000
  • General Medical Sciences (NIGMS) - $2,102,300,000
  • Diabetes and Digestive and Kidney Diseases - $1,837,957,000
  • Neurological Disorders and Stroke (NINDS) - $1,664,253,000
  • Mental Health - $1,517,006,000
  • Child Health and Human Development  - $1,352,189,000
  • Office of the Director - $1,298,412,000 (Former NHGRI head, Francis Collins is NIH Director)
  • Center for Research Resources - $1,297,900,000
  • Aging - $1,129,987,000
  • Drug Abuse (NIDA) - $1,080,018,000
  • Eye Institute - $719,059,000
  • Arthritis and Musculoskeletal and Skin Diseases - $547,891,000
  • Human Genome Research (NHGRI) - $524,807,000
  • Alcohol Abuse and Alcoholism - $469,197,000
  • Deafness and Other Communication Disorders - $426,043,000
  • Dental and Craniofacial Research - $420,369,000
  • National Library of Medicine - $387,153,000
  • Biomedical Imaging and Bioengineering - $322,106,000
  • Minority Health and Health Disparities - $214,608,000
  • Nursing Research - $148,114,000
  • Complimentary and Alternative Medicine - $131,102,000
  • Buildings and Facilities - $125,581,000
  • Environmental Health Sciences - $81,085,000
  • John E. Fogarty International Center - $71,328,000

The NIH funds a lot of smaller agencies, each with their own specific health focus. Still, even the smallest money allotment represents way more money that I could ever imagine having at my disposal (how my bank account would rejoice at seeing $71 million dollars). I hope that seeing the numbers actually broken down by agency will help people see why budget is important. There are a lot of agencies, handling a lot of money, but they are working on problems that effect the everyday lives of millions of Americans - from malaria to depression and everything in between.

Budget, particularly federal budget is a complex issue, and I haven't by any means covered everything here. I encourage everyone to take their new understanding of how the NIH is broken down to follow the money trail even more and see what specific research projects are funded by each agency under the NIH's leadership. The NIH's RePORT system is one place where you can learn more about how much is spent on specific diseases. The NIH's Office of Extramural Research can also help you learn more about how researchers go about applying for and receiving money from the NIH.

There is a lot of good information out there about budget. If you aren't one for reading budget documents online, here is a video of the FY 2012 Health and Human Services (HHS) Department budget presentation. You'll see Francis Collins (head of the NIH) third from the right, because the NIH falls under the jurisdiction of the HHS (that $32 billion for the NIH comes out of the even bigger HHS budget of $79.9 billion). Head of the HHS Kathleen Sebelius gives a pretty easy to follow breakdown of the important points in the FY 2012 budget.

Budget matters. It's your money, don't you want to know where it goes?
Update 2/21/11 - It is important to remember that the $32 billion number is just a request. It could very well change if Republicans pull their support from the NIH. Current predictions say the Republicans aim to cut $1 billion from the proposed budget. Check out the New York Times coverage for more information

Thursday, February 17, 2011

What's Up Wisconsin? (Protests, That's What)

My adopted state of Wisconsin (don't worry New Jersey, I'll always love you most) is making major headlines this week due to protests against Governor Scott Walker's budget proposal which would essentially tie the hands of the teacher's union (WEAC) while simultaneously requiring state employees to pay a significantly increased amount into their benefits.

While I don't write about politics or education, and I am in fact quite biased on these issues being the daughter of two New Jersey state employees, I still think that it is important to highlight the media coverage being given to these events.

Madison, which is my temporary home while I'm attending UW, is the state capitol of Wisconsin. The protests that have been going on in opposition to the budget (an estimated 20,000 people outside the capitol building, according to CBS News 3) are just steps outside my front door. Classes at the University have been disrupted due to the protests (in addition to schools throughout Wisconsin having to close due to the absence of teachers).

As a grad student I have been privy to at least half a dozen (but I think more) emails about how teachers should act in response to the protests. Grad students are often tapped at TA's or in some cases teach lower level classes, and while I don't teach at UW, many of my colleagues have had to choose whether to show up for class, or throw their support behind the protesters.

When I talk about politics, I try hard not to spout my own views, so I'll just wrap up by giving you some links to check out for more information about the causes of the protests, the details of the proposed budget, how the city of Madison is being effected and how the nation is taking notice.

Reuters: Democratic Lawmakers Leave Wisconsin To Protest Union Curbs 
New York Times: Democrats Missing, Wisconsin Vote on Cuts is Delayed
Politico: The Politics of Education Upended
CNN: State Democrats Absent for Vote as Wisconsin Budget Protests Swell
CBS News: Wisconsin Protests Continue As Dems Leave State to Stall Budget Repair Vote
ABC News: Wisconsin Teachers Protest Ed Budget, Union Cuts
Bloomberg: Public Employee Protests Spread from Wisconsin to Ohio
Huffington Post: Wisconsin Protests: State Police Pursue Democratic Lawmakers Boycotting Vote

This is just an amateur video I snagged off of YouTube, but I think it gives you a good sense of what being in the crowd out here is like.

Wednesday, February 16, 2011

Humans Contaminate DNA Databases

Interesting research has been published in the online journal PLoS One, describing a problem with contamination in non-human DNA databases. DNA databases are libraries of genetic information about specific species. When a species has its genome sequenced, its genetic data goes into a database so that other research can be conducted based on that known genetic information.

When a DNA database becomes contaminated it means that there is other information that has corrupted the data stored in the database. In the new PLoS One paper the researchers (from the University of Connecticut) evaluated human contamination of databases that were supposed to contain other species - like the zebrafish. So contamination occurs when human DNA gets incorporated into the database for another species. When researchers go to work with the data about the zebrafish for example, they are actually working with human data without knowing it.

The University of Connecticut researchers looked for human contamination in NCBI genome databases, the University of California Santa Cruz (UCSC) databases, and the Joint Genome Institute databases. They found human DNA where it shouldn't have been in a total of 492 of 2,749 evaluated databases.

This contamination issue is extremely problematic because research conducted based on contaminated information can not be trusted to be accurate. It can also be very difficult to track down which databases are contaminated unless the resources (time, money, etc) are spent to evaluate databases for clarity - as was done in this new research.

Database contamination is a relatively new issue brought to light be the massive influx of new genetic information made possible by improved genome sequencing technology. A similar issue that has existed for decades is cell line contamination which occurs when cells that are suspended in culture (alive outside of the body) are contaminated with cells that aren't supposed to be there.

No regulatory body has stepped up and put a stop to cell line contamination in the last thirty years. I just hope that database contamination doesn't follow suit.

To learn more, read the paper about Database contamination, or read an article I wrote for BioTechniques about cell line contamination. As taxpayers we spend a lot of money to fund scientific research, so it is important to know what problems (like contamination) exist in the research community.

Tuesday, February 15, 2011


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.

Friday, February 11, 2011

Fossil Foot Shows Bipedalism

I recently did a post on the taxonomy of the African Wolf, (formally the Golden Jackal) where I talked about how as scientists gather more information and make new discoveries, they revise their theories. There is an interesting article in the BBC today about a new fossil find that has helped scientists fine-tune their theories about how the human-like species Australopithecus afarensis moved. This fossil is a great example of scientists learning from new discoveries.

A. afarensis is the species made famous by the "Lucy" skeleton discovered by Donald Johanson in 1974 in the Hadar region of Ethiopia. Previously, researchers had fossilized remains of the spine, hips, and knees of A. afarensis and developed a theory about how the species moved based on those fossilized remains. Researchers believed that A. afarensis was bipedial (walked upright on two feet, like humans).

Until recently the theory that A. afarensis was bipedal lacked certainty because while researchers were confident that the spine, hips, and knees supported the bipedal theory, A. afarensis foot bones had never been found. Without the foot bones, the researchers could not confirm just how the species walked, or how much it relied on walking.

Now a research team from Arizona State University (including Donald Johanson) has found a fossilized fourth metatarsal bone from A. afarensis, in the same Hadar region of Ethiopia where the Lucy skeleton was found. The metatarsal is a foot bone that provides evidence of how the foot was arched. Understanding how the foot was arched goes a long way to explaining how the creatures would have walked, confirming the researchers long-standing bipedal theory.

In addition to supporting the bipedal theory, the foot bone and the fact that it is arched shows that A. afarensis would have been able to move quickly and easily on two feet. The arches in feet serve to help the foot move the body forward, and act as a "shock absorber" each time the feet pound the ground. The fact that A. afarensis had arched feet makes it even more similar to the anatomy of modern humans showing an important link in the evolution of upright walking.

I think this is such a great example of how science changes and revises itself because it showcases how very specific details and pieces of information can shape entire theories. In this case, finding the fossilized metatarsal bone confirmed a theory and also shed more light on how the species would have walked, providing additional information. It is a good example of science changing - and getting better.

Tuesday, February 8, 2011

Discover Raises The Dead

I want to draw attention to a great info-graphic spread in Discover Magazine's photo gallery. Dead People Science Won't Let R.I.P. is a really interesting and fun way to do an article about all the different old deaths that modern technology has been able to shed light on.

From King Tut to Copernicus the graphic gives really good, concise descriptions of how certain historical figures died, why their deaths were controversial (or at least their cause of death disputed), and how modern technology helped clear up the details. Its definitely worth checking out, not only to learn a few things about science and history, but also to check out how Discover is doing their gallery articles.

Sunday, February 6, 2011

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.

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. 

Friday, February 4, 2011

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.

Audubon magazine

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. 

Thursday, February 3, 2011

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. 

Wednesday, February 2, 2011

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?

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.