Monday, January 31, 2011

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.

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.

Friday, January 28, 2011

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...)

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.

Wednesday, January 26, 2011

Saving Journalism, One LOLCat At A Time

I got sent this article today from a professor: Time for change in science journalism by John Rennie for the Guardian. Rennie is the former editor and chief of Scientific American, and currently blogs for PLoS (Public Library of Science) - which has a great blog network for those who are interested.

He makes an interesting argument that the way science journalism operates like breaking news journalism is inadequate. Having to write on deadline and keep up with what is new to oust the competition doesn't work when reporting on science topics because it doesn't leave enough time to report on new findings in the overall context of the field.

I appreciate his humor in the critique of what science journalism needs to improve, "My vehemence sprang not just from enthusiasm for the improvements possible through linking to primary sources, fostering dialogues with readers, incorporating multimedia and tapping the awesome power of LOLcats." Hilarious. But I also agree with his point.

Writers need time to thoroughly research a new science finding in order to craft stories that are unique and not just cookie cutter turn outs from press releases. Science journalists can do better, and having turned out some press release dependent fluff myself, I know that we can do better. If the comments on Rennie's article are any indication, there is an appetite for good science news, now we just need to step up to the plate.

We'll just have to be sure to fill up on inspiration from those lolcats first...

Tuesday, January 25, 2011

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:

Sunday, January 23, 2011

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.

Friday, January 21, 2011

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.

Thursday, January 20, 2011

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.

Wednesday, January 19, 2011

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.

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.

Tuesday, January 18, 2011

Shark Vision: It's a Black and White World

A great white shark. Source: Wikimedia Commons.
Interesting research out of Australia analyzed the cell types in the eyes of 17 species of sharks, and found the the predators are largely color blind. The find is significant because it could help developers create new fishing industry equipment and water activity gear to reduce shark attacks based on visibility.

The researchers, from the University of Western Australia and the University of Queensland, looked for different types of cone cells in shark eyes. Humans have three different types of cones that enable us to receive and process blue, green, or red light waves. Sharks have only one cone, meaning they do not have the ability to distinguish between colors.

Monday, January 17, 2011

Just to Clarify: The Blackbird Incident

Source: Wikimedia Commons.
There was a great article in the New York Times about the confusion that took place between the media, scientists, the government, and the public regarding the New Year's Eve bird deaths in Arkansas. Conspiracies Don't Kill Birds, People Kill Birds by Leslie Kaufman does a great job of explaining how the bird story got blown out of proportion.

Basically, birds die all the time. It's not all that unusual for flocks of birds to die, according to the article's statistics (from the National Audubon Society) approximately five billion birds die in the US every year. Rural cats kill 39 million birds a year. So basically, the whole incident wasn't a conspiracy or a case of poison run amok. Birds die, thats kind of all there is to it.

Flying objects can interrupt birds' flight and send them careening into buildings and billboards. So while I was pretty skeptical of the fireworks explanation on the basis that if fireworks cause bird deaths we would have heard about it before this, it is possible that was what happened in Arkansas. That would mean that all the subsequent bird death articles in the media could very well be a case of the media being bored and picking up on a story that really wasn't a story because it happens all the time.

Back to the Mad City

I'm back in Wisconsin after my holiday break, getting ready to start a new semester of classes tomorrow. It snowed in Madison today, which made me pretty nervous about my flight but I got in right on schedule. I got a taxi from the airport to get downtown, and by that time the roads were already starting to get pretty bad (I know I saw a plow at one point but I swear it was just pushing the snow around.)

This ride home was fairly interesting considering I've never had a cab driver pull over so that he could stop to go get a sandwich for the ride. Seriously. I was nervous enough being driven around in the snow, the fact that the driver was eating a sandwich with one hand while steering with the other didn't exactly inspire confidence, especially after I heard the cab company's dispatcher report an accident involving a different cab coming from the airport to downtown. But I got home in one piece and I guess thats really what counts.

This should be a good semester, between the classes I'm taking, working at the Primate Center, and some freelance projects I have going on, I'll be pretty busy. But I have to say I'm already counting down to spring break and another visit home, 52 days...

Friday, January 14, 2011

What's In A Name?

I found an interesting little article (New Dehli superbug named unfairly says Lancet editor) in the BBC about naming bacteria, and whether or not it is fair to name a bacteria after a place.

Map of India. Source: Wikimedia Commons.
The bacteria in question is called New Delhi metallo-beta lactamase 1 (NDM-1) and was discovered by researchers from Cardiff University in the UK. According to the BBC's article the researchers named the bug after the city because the patient whom they first noticed it in, had been in a hospital in Delhi.

The Lancet, the journal that published the article about the bacterium has made a statement saying that the name of the bug is unfair because it stigmatizes India. The bug has since been found in Europe, the US, Canada, Australia, Africa, and East Asia.

While I get why India might be pissed off (no one wants bad things named after them) I think you really have to analyze the impact that the name will have. Honestly, the bug is going to be known as NDM-1. Very few people would use the term 'New Delhi metallo-beta lactamase 1' in conversation. Of the people that will use and know the real name of the bug, it will not be the tourists interested in coming to India. Therefore I find the argument that the name will harm India's tourism industry kind of overblown.

I also find it interesting that the Lancet essentially threw the Cardiff University researchers under the proverbial bus. Again, I understand that the journal has to protect itself and its reputation, but if the researchers stand by the name I don't think its the journal's job to denounce it. If nothing in the research is wrong factually, I don't think the journal should issue a public statement saying that the researchers showed poor judgement. It makes me wonder who was putting pressure on the journal to make a statement.

Thursday, January 13, 2011

The Plant That Took Over America

Sphagnum subnitens. Source: Wikimedia Commons.
It grows, it spreads, it takes over North America... its peat moss. Now I know that peat moss isn't exactly the most exciting of topics, but the article Single peat moss plant 'conquered America' stood out to me for a few reasons.

I have written a lot about genome sequencing and genetics, and this research sequenced the genome of the peat moss Sphagnum subnitens, and found that all the samples they collected were genetically identical. This means that there is a common ancestor for the peat moss that spread prolifically throughout North America. 

The research was conducted by teams from Ramapo College in New Jersey (another reason why this article caught my attention,) Binghamton University in New York, and Duke University in North Carolina.  The different types of peat moss vary in color and are found in distinct locations, which makes the 100% genetic match all the more amazing. 

The moss species reproduces sexually, but a single plant can make both the necessary sperm and eggs so its offspring are genetically identical, without being asexually reproduced clones.

Animal Tagging Ethics

King Penguins. Source: Wikimedia Commons.
New research published in the journal Nature says that the most popular way for tagging penguins for scientific analysis - putting a band around a flipper - may be detrimental to the penguins' reproduction and survival. This brings up the ethical issue of whether or not the practice of tagging with a band should be continued.

Researchers from the University of Strasbourg and the French Centre National de la Recherche Scientifique (CNRS) wanted to clear up debate about whether or not the tags, which have been in use for over a decade, have an effect on the penguins detrimental or otherwise.

The study, in king penguins, showed that penguins tagged with the bands had 40% fewer chicks than un-banded penguins. Banded penguins also lived shorter lives. The finding is likely to be controversial because it draws into question the validity of past research done using the bands.

The research also has ties to climate change because many penguin species are already threatened due to changes in their environment. In addition to the typical ethics of whether or not its right to do something that could be harmful in any way, tagging with the bands could also be seen as unethical for stressing an already challenged populations.

Wednesday, January 12, 2011

Universal Flu Vaccine

H1N1 Virus. Source: Wikimedia Commons.
A new study in the Journal of Experimental Medicine reports that people who fight off the swine flu (H1N1) develop antibodies that can help them fight off other flu infections as well. This finding could be used to create a universal flu vaccine that would eliminate the need for a yearly flu shot against that year's most likely problematic strains.

Five antibodies isolated from patients that had successfully fended off swine flu appeared different than those antibodies created to fight more typical flu strains. Those antibodies have proven able to fight off even virulent flu strains like the "spanish flu" from 1918 and bird flu (H5N1).

The important thing to remember with a breakthrough like this is that even thought the results are promising, it takes a long time to get from the basic research stage to human trails and widespread availability as a treatment. So even if this works, don't expect a universal vaccine anytime soon. It is likely to be five years or more before doctors can even think about saying goodbye to yearly flu shots.

Monday, January 10, 2011

Poison That Packs A Punch

My holiday break is starting to wind down (as evidenced by the Christmas tree that has made its way out to the front lawn to await collection) but thing are just as busy as ever. I spent a large chunk of today applying to internships for the summer, and pitching one of my articles from last semester. We'll see if I get responses, but for now I feel productive having at least sent out so many emails.

After such a productive morning I treated myself to an afternoon of reading and was able to finish my advisor Deb Blum's latest book Poisoner's Handbook. I said back in the fall that I wanted to read her book, and I was lucky enough to win a signed copy at the end of the semester event for UW's online literary magazine Corkboard (which features the work of some very talented student writers, so you should check it out.)

Poisoner's Handbook tells the story of New York City's first chief medical examiner, Charles Norris and famous toxicologist Alexander Gettler. The book is a work of literary journalism that chronicles the rise of toxicology and forensic medicine in the 1920's and 1930's covering prohibition and the great depression. I thought the book was well written, and I'm not just saying that because Blum has say over my grades. She does a great job of making chemistry approachable, and I hate chemistry so that is actually a big compliment.

The book is organized with each chapter representing a different poision, with some paragraphs on Norris, Gettler, and the science of toxicology and some paragraphs describing a murder case showing the effects of each chapter's poison. If anything I would say that because some of the people described in some of the murder cases reappear in other chapters, it can be hard to remember who is who. But even so, that did't dampen my enjoyment of the book. The structure was easy to follow, and even in moments where I had to think back to remember a character I was never really lost.

Knowing Deb Blum personally there were points where I could actually hear her in my head reading aloud the words on each page. In our literary journalism class she would read us experts from each of the authors we studied so I've gotten used to the cadence of her speech. I found it pretty interesting that I could see the same rhythm in her writing, and it made me wonder if I write the way I talk.

Poisoner's Handbook is the fifth book I've read since coming home, and hopefully I'll be able to finish one more before heading back next week. I am running out of space on my bookshelves at home, but I still love seeing my little library. It makes me feel oddly accomplished.

Sunday, January 9, 2011

Snake Banishment Bias

The New York Times article, Snake Owners See Furry Bias in Invasive Species Proposal caught my eye today because I love snakes. I know that it is a little unusual for a girl to love snakes, typically snakes induce a lot of frightened yelping. But, I have always found them awkwardly beautiful.

Normal and Albino Snake. Source: Wikimedia Commons
According to the article the US Fish and Wildlife Service is cracking down on snake ownership due to the increased prevalence of invasive snakes in various ecosystems. Boas, Anacondas, and Pythons are among the types of snakes included in the crack down, but they are popular as pets. Pet snakes become problematic when they escape or get released into the wild and prey on local species.

Opponents to legislation to restrict the sale of snakes say that there should be a distinction between snakes that can't thrive in the wild (suffering from albinism, or in unsuitable climates) versus snakes that are likely to become invasive.

Snake enthusiasts are opposed to legislation that would restrict the sale of snakes on the grounds that there could be a significant loss of revenue for breeders. Because the animals are pets, restrictions would also bring up the issue of whether the government should be able to dictate what type of pets people keep.

Split in Sudan

A few weeks ago I read Dave Eggers' What is the What about the civil war in Sudan. When I posted about it, I said that one of the main things that struck me about the book was the complexity of the conflict in that part of Africa - politically, socially, and economically.

I wanted to do a short follow up post, because right now all eyes (or at least those with an interest in foreign affairs) have turned to southern Sudan, where polling is going on to see if the people that live in the south want to form an independent country, breaking Sudan into separate North and South countries.

According to the BBC, there is no doubt that the people of the south will choose independence, but the poll will only have merit if 60% of the regions 3.8 million residents turn out to participate in the poll. Right now the focus is on getting people to the polls in an orderly fashion, and so far there have been no incidents.

One issue to watch as southern Sudan makes its stride toward independence is territory boarders. Sudan does have areas that are rich in oil, that the North doesn't want to lose to the South. If the South claims areas that the North wants, there could be a fresh outburst of violence in Sudan.

The BBC has a great interactive map that you can check out for more information, or for a visual representation of how the northern and southern regions differ by ethnicity, infant mortality, water and sanitation, education, food insecurity, and the location of oil fields.

Saturday, January 8, 2011

NIDA pledges $10 million to develop addiction treatments

Here is another article that I wrote for J800 last semester (in September 2010) that wasn't timely once I had edited it, and I couldn't get it picked up anywhere. But for those of you interested in research funding, this is an interesting look at basic vs. preclinical and clinical research. 

NIDA has announced the four winners of the first funding award specifically designed to support research to create a viable human treatment for cocaine or nicotine addiction.

There is the patch, the pills, the gum, and even going cold turkey, but for some nicotine addicts, nothing seems to stop the urge to reach for a cigarette. Instead of feeling dejected, people suffering from addictions can now pin their hopes for quitting on the National Institute on Drug Abuse (NIDA.)

NIDA, a member of the National Institutes of Health (NIH), recently announced the four winners of a funding initiative for research that develops addiction treatments for human application. The initiative seeks to produce new addiction treatments by providing more government-based funding for the development of pharmaceutical treatments.

“Usually pharmaceutical companies support potential drugs,” said Jia Bei Wang, a pharmacology researcher at the University of Maryland, Baltimore, and winner of the new award. “But I don’t think these companies are interested in addiction because it’s not profitable, so drugs for addiction are very much in need of government support.”

The new NIDA award will provide a combined total of $10 million to develop ways to counteract cocaine and nicotine dependency. The initiative hopes to create viable human treatments at the end of five years.

“I think that this is something very new,” said Wang. “As a researcher I have gone through a lot of grant applications, and this is the first of its kind that I have tried, that is not a mechanism for basic research but that is a drug development grant.”

According to Wang, the majority of federal funding for research is for basic research, projects that evaluate scientific questions without a definite sense of the outcome. The NIDA Avant-Garde Award for Innovative Medication Development is different because it is focused on pre-clinical and clinical research, projects that are outcome driven and based on extensive basic research.

“I think NIDA realizes there is a gap between basic research and clinical outcomes, and the research that bridges that gap is very important,” said Wang. “A lot of progress is made in the basic sciences, but on the clinical side we still don’t have any useful drugs [for cocaine addiction].”

Why is a clinical-only grant needed?
Every year the government spends billions on scientific research. According to the NIH Office of Budget, in fiscal year 2010 NIDA dedicated just $118,546 million to their pharmaceutical development department out of a total budget of $1.06 billion. According to Wang, by pledging an additional $10 million specifically for pharmaceutical development NIDA is finally stepping up to the plate to help find new addiction treatments.

“There isn’t a lot of interest from industry, but NIDA is the public health institute and they have a responsibility to develop treatments for these diseases for the people, and I think this grant came out of recognizing that need,” said Wang. 

Ivan Montoya, deputy director of NIDA’s division of pharmacotherapies and medical consequences of drug abuse will oversee the Innovative Medication Development award. According to Montoya, this funding is part of a NIH push to support innovative research, while addressing the risk involved in providing government support for drug development projects. 

“If [a research proposal] is very innovative it carries more risk, but it has to guarantee that results will be obtained after the five-year period,” said Montoya. “It is critical that the background science is successful, otherwise NIDA won’t give funds to someone that the committee doesn’t think has a good idea. It has to be supported by a good future for results.”

Creating the Innovative Medication Development award addresses the lack of interest from the pharmaceutical companies, but also satisfies NIDA’s need for confidence in the projects they fund. According to Montoya, to this end, the four winners of the award will be monitored for the duration of the grant, and required to provide progress updates about how they spend the money. NIDA hopes keeping tabs on the researchers will push the winning ideas toward the complete development of new therapies.

Potential abounds, but what about results?
According to William (Stephen) Brimijoin, a researcher in molecular pharmacology and experimental therapeutics at the Mayo Clinic, and a winner of the award, a government focus on human application is vital to making progress on addiction treatment.

According to Brimijoin, NIDA should be commended for selecting promising clinical research projects and cultivating them for human applications. “If some of these projects do result in a useful therapeutic agent we should all celebrate,” said Brimijoin. “Right now we just don’t know which projects will go all the way to real human applications.”

Friday, January 7, 2011

Vaccine Autism Research Fraud

For over a decade, controversy has raged about whether or not vaccinating children causes them to develop autism. British doctor Andrew Wakefield published a study in 1998 that claimed there was a solid link between the MMR Vaccine (measles, mumps, and rubella) and autism in children. The study induced panic among parents world wide who refused to have their children vaccinated.

Measles Virus. Source: Wikimedia Commons.
Since Wakefield's original study 12 years ago, 14 independent studies have found absolutely no link between the vaccine and autism. Yet, to this day parents still refuse to have their children vaccinated. This has led to a surge in the numbers of measles, mumps, and rubella cases.

Last year the British Medical Journal (BMJ), the Lancet, issued a full retraction of Wakefield's study and he was stripped of his medical license in England. Now, the BMJ has published the results of an investigation into Wakefield, calling him a fraud. The investigation led the BMJ to conclude that Wakefield was not only unethical in his research, he also fabricated data.

Essentially, the guy made stuff up, he scared parents and confused them about what was the best course of action to care for their children, and ultimately numerous children became seriously ill with preventable diseases. This is infuriating. It makes me mad that even with all the precautions and restrictions we impose (peer review, for one) bullshit research still manages to get published in a reputable journal causing people to panic.

This case is pretty notable for the way that the belief of a link between vaccines and autism has persisted, even though the medical community considers the theory completely debunked. I hope that the media will step up and disseminate the (relatively) new idea that there is no link to help combat the misinformation that has already become so widespread.

Wednesday, January 5, 2011

Bubble Tip Anemone

The picture of the day on Wikipedia Commons was science related so I thought I'd re-post it. It is the Entacmaea quadricolor, also known as the Bubble Tip Anemone.

BioTech's New Hot Shot

There was an interesting article in the New York Times today (yes, I was magically granted access to their website again, not sure why but I'm glad) by Andrew Pollack. Taking DNA Sequencing to the Masses takes an in-depth look at the work of Jonathan M. Rothberg.

Dr. Rothberg is the founder of the genome sequencing company Ion Torrent. The article looks at Ion Torrent's role in providing cheap (under $50,000) sequencing technology with the launch of their Personal Genome Machine. The technology isn't intended for the general public, but will make obtaining a sequencing system more feasible for smaller universities and clinics that can't afford larger machines.

The article draws a parallel between Rothberg and Apple founder Steve Jobs on several occasions. Pollack paints Rothberg as a bit of a rebellious nerd, who certainly has high hopes for his company and the technology they are developing.

Pollack ends the article with Rothberg saying that he believes that genome sequencing will become as useful for medical applications as imaging (like X-rays, CAT Scans, etc.) I like this article because statements like that aren't blown out of proportion. I think that for an article that is focused on what can be achieved in the future the ideas all stay grounded in what is really feasible, which can sometimes be difficult in a science technology article.

USGS says the nose knows prominent lake toxins

I wrote this article for my J800 class last semester at the beginning of October. Unfortunately I wasn't able to get it published in any of the local papers when it was still timely. But, the nice thing about having a blog is that I can use it to publish pieces that don't get picked up elsewhere, so here you go...

A U.S. Geological Survey study has found that cyanotoxins in Midwest lakes emit odors, adding smell to the public’s arsenal against exposure to hazardous aquatic toxins.

Before you enter your local lake, stop and smell the water. A new study shows that lakes in the throes of a toxic algae bloom give off a characteristic scent that can warn people to stay away. According to the United States Geological Survey (USGS) the findings should help the public identify hazardous lakes based on their smell, reducing the instance of cyanotoxin-related illness.

“Cyanotoxins pose the largest hazard to human health during recreational activities, so public health is one of the motivations behind studies of these toxins,” said Jennifer Graham a researcher at the USGS’ Kansas Water Science Center, and lead researcher on the study.

Simply avoiding lakes with algae isn’t a realistic way for residents to stay safe because algae occurs naturally and is not usually harmful. According to Graham, residents need new ways to tell whether specific algae blooms contain toxic compounds. The researchers tested for chemical signatures that indicate the presence of odor, and found that cyanobacteria blooms give the water what Graham describes as a musty smell.

The study showed the odor consistently occurs when toxins are present, but toxins can occur without the odor. According to Graham this makes smell a useful indication that toxins are present, but not something the public can rely on with absolute certainty.

“Smell is something that anybody should be able to use, the human nose is very sensitive to the compounds produced by the cyanobacteria. It is musty and might smell like dirt and so that could be used to evaluate a situation,” said Graham. “From a recreational perspective it is useful because odor gives a cue that there might be something of concern going on in an area.”

Would your nose know?
While Graham maintains that the odors given off by toxic algae blooms are distinctive enough to identify a toxic bloom, some Madison residents have doubts.

University of Wisconsin-Madison (UW-Madison) sophomore Martin Feehan doesn’t think smell is a reliable way to identify cyanotoxin episodes in Wisconsin’s lakes. Feehan is president of Hoofer Scuba, a recreational group at UW that uses the lakes surrounding campus regularly.

“I think smell could be a good way, but it could also be misleading because the different smells in the lake could come from several sources,” said Feehan. According to Feehan, the decomposition of plant material or fish could easily cause earthy, musty smells at the lakes that could be confused with the toxin scent.

Feehan says participating in Hoofer Scuba has made him aware of cyanotoxins, but the group does not actively look for toxic blooms. Instead, they rely on notices from the Madison Department of Public Health. “We have warnings that go up at the boathouse if there are blooms,” said Feehan.

Todd Miller, a postdoctoral researcher at UW-Madison is wary of encouraging the public to sniff out cyanotoxins.  Miller, who holds a doctorate in marine estuarine environmental sciences from the University of Maryland, College Park, has worked as a postdoctoral researcher in the laboratory of Trina McMahon since 2007.

“The study is intriguing and I think opens the door to potential new methods for early toxic bloom detection,” said Miller, in an email message. “But there are many sources of the odor compounds the researchers measured, and as the study shows toxins can be present in the water at dangerous levels even when the odor compounds are not present.”

According to Miller, smelling the lakes to identify the presence of toxins is unreliable. “It is probably not reasonable to expect the public to identify toxic or non-toxic waters based on smell,” said Miller. “I tell people to enjoy the lakes, but don’t swallow the water, pay attention to public warning signs by the health department and don’t enter the water if the lakes are closed to recreation.”

Graham says smell is not the only one way that the public should identify potentially toxic blooms, and advocates using multiple means to avoid exposure to cyanotoxins including visual cues (green or red tint to the water or scum floating on the water’s surface) and checking for warning notices before entering a lake.

A persistent problem
Cyanobacteria and the toxins they produce are a problem that has affected Midwest lakes for several years. According to the Global Lake Ecological Observatory Network and the UW-Center for Limnology nine beaches in Madison were closed due to cyanotoxins in July 2009, the largest cyanotoxin episode in Wisconsin that year.

According to Graham, cyanobacteria are microorganisms that occur naturally in aquatic ecosystems as part of algae blooms. Some of these blooms contain cyanobacteria, which can create toxic chemical compounds that can be dangerous.

The three main types of toxins are dermatoxins, which cause skin or respiratory reactions after direct contact; hepatotoxins, which are absorbed by the liver and cause gastroenteritis; and neurotoxins, which are absorbed by the central nervous system.

Though cyanobacteria exist naturally in lakes, according to Graham, the toxins they produce become problematic when they occur in increasingly large concentrations. This happens when algae the bacteria thrive on grow rapidly.

“Cyanobacteria blooms are a natural phenomenon, but they can be aggravated by human activities,” said Graham. These activities include land development that causes soil to erode and runoff from farms or landscaping that washes fertilizer and soil into lakes.

According to Graham in addition to testing for odors, this study was the first to quantify the presence of multiple toxins in a single algae bloom. The study evaluated lakes in Missouri, Kansas, Iowa, and Minnesota, chosen because they have long-standing cyanobacteria problems.

Until Next Year
With the outdoor recreational season ending and Midwest residents heading back to land, Graham, Miller and Feehan agree that cyanotoxins remain a pressing issue.

Cyanotoxins are continuously researched. Miller is studying how environmental factors like temperature and pH influence the production of toxins in freshwater lakes, and Graham is working to identify what organisms produce cyanotoxins and why.

“Cyanobacterial blooms are an issue that has been exacerbated by human activities, so it won’t be an easy issue to solve because it is something that has evolved over time,” says Graham. “But, with public education and increased information about what hazards are in natural water bodies the incidents of human illness and animal illness from recreational exposure can really be reduced.”

For water enthusiasts like Hoofer Scuba’s Feehan, research like Miller and Graham’s is a step in the right direction because staying out of the water every time there is a toxic bloom isn’t sustainable. “I understand that the algae is toxic and can cause health problems,” said Feehan. “But it makes people lose out on fishing and other water activities so I think something definitely needs to be done to fix the situation.”

The research paper, “Cyanotoxin mixtures and taste-and-odor compounds in cyanobacterial blooms from the Midwestern United States” was published in the September 2010 issue of Environmental Science and Technology

Tuesday, January 4, 2011

Blackbird Homicide

I hope everyone had a great start to the new year! Over my weekend blogging hiatus the big science story in the US was the mysterious death of thousands of birds on New Year's Eve in Arkansas.

Source: Wikimedia Commons.
More than 3,000 blackbirds fell in the town of Beebe, AK and samples have been taken for analysis to determine what could have killed the birds in one mass attack. Initial reports said that the birds have died due to trauma (they fell out of the sky, so clearly that was a shocking conclusion.) Now the Arkansas Game and Fish Commission is reporting that fireworks launched to commemorate the new year caused the birds' demise.

However, today it was reported that approximately 500 red-winged blackbirds (the same species found dead in Arkansas) and starlings fell from the sky in Labarre, Louisiana, hundreds of miles south of the original bird deaths. Early reports from Louisiana also state that the birds suffered some trauma, although an official cause has yet to be determined.

One theory on the mysterious deaths is that the mere sound of new year's fireworks could have startled the birds, causing them to fly into buildings or billboards. Although, you have to wonder why we've never heard of fireworks (launched every year for new year's, the fourth of july, weddings, fairs, and numerous other events) causing birds to die in large, concentrated groups.

I think that we're definitely going to have to stay tuned to this story to see what happens after the birds from Louisiana are analyzed more closely, and also watch to see if more birds die in other areas -- which most certainly wouldn't be attributable to fireworks.