1000 Genomes Project

For as long as I can remember my parents have been telling me that I'm special (in a good way, not in the derogatory way the kids are using the term these days). Most of us start life out thinking that we're unique and the more we learn about life, and the more it kicks out asses we become so disillusioned that we cease believing we're really all that special.

But, new data generated by the 1000 Genomes Project recently confirmed that our parents have been right all along. The 1000 Genomes Project is an effort to sequence the genes of 2,500 people from around the world in an attempt to fill the gaps in the draft sequence of the human genome left by genetic variation. 

The draft sequence was established in 2000 by teams led by J. Craig Venter and Francis Collins. While that was a breakthrough moment in the field of genetics because it enabled the study of diseases caused by changes in our DNA, it only took us so far. 

Genetic variation refers to the differences in the human genome between individuals (ie: if my code is AGTCAGTC, yours might be AGCCAGTC). That kind of a difference can have a huge impact on how disease manifests itself, therefore studies looking for treatments for genetic-based disorders (Alzheimer's, Parkinson's Disease, Cancer, etc.) are hindered by these variations. 

The new data obtained by the 1000 Genomes Project, is a 95% map of human genetic variation. The results of the study show that each individual person has an average of 75 variations (single nucleotide polymorphisms, or SNPs, which are changes in the code like I described above). These variations are essentially what makes each of us different from everyone around us. My parents were right, I am special, but something tells me they weren't referring to my genes. 

This is exciting for a few reasons:

1. Millions of dollars have been invested in this project, it is good to see something actually come of it. 

2. A better understanding of variation can enable more progressive research on genetic disease, from causes to treatments. 

3. Genome sequencing technology is advancing quickly, and making interesting research like this a reality. Expect more projects like 1000 Genomes, it's definitely about to get ambitious in here. 

4. A project like this sets important standards for open access information and data sharing among researchers for genetic studies at this scale. 

Read more: 

Nature: 1000 Genomes Project reveals human variation

The BBC: 1000 Genomes Project Maps 95% of all Gene Variations

Telegraph (UK): Scientists from 1000 Genomes Project have identified 95 per cent of genetic variations

Lobster Lovin'

Go ahead, ask me about lobster sex. I know far more about lobster love than I ever really wanted or would need to know thanks to Trevor Corson's book The Secret Life of Lobsters. I read Corson's book for J669 and I have to say, it was a struggle to get through even though I did find a lot of elements in the book compelling.

Corson interweaves lobster research in with the lobster fishing industry of Maine to drive the book forward. The personal stories of the lobster men and their families add a lot of interest to the book. But, toward the end I really found myself struggling to finish the last few chapters because the research was so boring.

Homarus Americanus (The species found in Maine)
Source: Wikimedia Commons.

The first few chapters about scientific research focus on how a lobster molts (sheds it shell so it can grow) which I found really interesting, and about how lobsters mate. Is it stereotypical that I was entertained by the chapters about lobster sex, but once the book started focusing on lobster habitat and the lobster's life cycle I found myself hopelessly bored?

I really pushed myself to get through all of the pages of description detailing the fluctuations in the lobster population and how lobsters migrate and where lobsters live during certain parts of their life. The hardest part about those chapters was that Corson never arrived at any conclusions. The researchers he wrote about work really hard to pinpoint why the lobster population fluctuates, and after all those pages they don't reach a conclusion. Ending with the idea that populations naturally vary was so anti-climactic. I was disappointed.

Actually, the book officially ends with a discourse on whether or not it is humane to boil lobsters live, which I find sort of perfect. But the rather piddly end to the scientific research was still a let down.

Trouble in MarieClaire's Blogosphere

Now, I'm not a fashion or lifestyle writer but I think the controversy over MarieClaire blogger Maura Kelly's post "Should 'Fatties' Get A Room (Even On TV)" is worth mentioning. Kelly is a professional blogger, her career is posting her opinions on the internet. But, by coming out with the opinion that fat people shouldn't be shown in intimate scenes on TV because it grosses her out, she has caused a firestorm. The controversy has raised a lot of questions about professionalism in the blogging community.

I suggest you read her article, and then review the comments posted below it by readers. As a blogger it is all well and good to share your opinions, but where do you draw the line? Kelly is a representative of MarieClaire - not just of herself. By branding MarieClaire with her opinion she has apparently cost them a tremendous amount of business (if you believe the comment writers, at least). What standards do magazines and other companies use to hire bloggers? Are there any standards?

In the apology that she added to the original article, Kelly brings up that she suffers from anorexia and has had a life-long obsession with being thin. Hmm. That might have something to do with why she finds it unacceptable for overweight people to get romantic. Crazy thought, that MAYBE her personal background should constitute a conflict of interest and she should never have be allowed to blog about weight issues in the first place. As a writer, it was her responsibility to identify that conflict of interest.

Even if you feel you can be objective, you just can't write about issues with which you have a personal connection without disclosing that information properly. I can't write about issues involving law enforcement because so many members of my family are involved in that career field -- it is the reason I will always get tossed off jury duty. It gives me bias. As a writer you have to know yourself, and be honest with your readers about your personal conflicts of interest when they are applicable to the subject you are writing about.

But is a blogger really a professional writer? I am very interested in Ms. Kelly's background. Does she have a journalism degree? Does she do any research, or does she just spit out her own opinions? Why should anyone care what she says? Who is Maura Kelly? What makes her qualified to eschew her thoughts on an issue like popular conception of body image in the entertainment industry?

I wish someone would pay me to say whatever thoughts cross my mind. Maybe they'll be an open position for blogger at MarieClaire sometime soon? I wonder if they need a science writer...

The Immortal Life of Rebecca Skloot

Today I met Rebecca Skloot, the author of The Immortal Life of Henrietta Lacks, mentioned in my previous blog post. Skloot's book is the UW Madison Go Big Read program's selection for this year, so she gave a public lecture last night, and visited the journalism school this morning to take questions.

As far as author presentations go, I loved this one, because Skloot pretty much just plopped down in a chair and said what do you want to know? It was a small group (25-30 people) but the discussion kept up for over an hour just based on audience questions. My question for her was whether she was prepared for the Lacks family's lack of science education and how she viewed her role as a journalist but also as their teacher. Her response was that the two roles were essentially one because her reporting style is based around an informal conversation, but that she wasn't really prepared for how confused they were about what HeLa is.

Other questions that were asked ran the gamut from the business of publishing a book, to how Skloot handled Deborah's death and incorporated it into the book, how she decided on the structure of the book, and how she handled (and organized) 10 years worth of notes. She was an engaging speaker, and was even willing to talk about some of the criticisms of her that have come up since the book came out.

The biggest criticism of Skloot out there is that she isn't doing enough to help the Lacks family. But, she has set up a foundation for them -- and I think its important to remember that for 10 years Skloot was accumulating debt chasing down this story, if the book hadn't been a success she'd definitely be in the hole so I agree with her unapologetic attitude toward the money she's made from the book's success.

She also mentioned that she sometimes gets push back from people who don't agree with the fact that she kept all of the interviews in their original dialect (people saying it puts down the lesser educated black people who don't speak with proper grammar) but Skloot points out that she kept the dialect and "broken" English of European and Asian researchers as well as the Lacks family.

According to Skloot the biggest problem she's encountered so far has been from the white members of the Lacks family. In the whole two pages that the white Lackses are discussed, they definitely appear as racists. But, it is Skloot's word against the word of the children of her sources (her sources are now dead) who have argued that Skloot couldn't possibly have done the interviews because their parents wouldn't have said the things Skloot says they did.

Considering how utterly unimportant the white Lacks family is to the story, it's sort of absurd to think that Skloot didn't really do the reporting. It would be such a dumb part of the story to make up, so I'm inclined to believe that the interviews are true.

This book is undoubtedly going to be Skloot's literary legacy, so overall it was fun to get another first hand perspective on what it takes to research, write, and market a successful science book.

Cell Culture's Dirty Little Secret

My last assignment for BioTechniques web news was a cell culture themed newsletter article on the status of cell line contamination. It was while researching that article (Ending cell line contamination by cutting off researchers) that I got my first real education about HeLa cells. I recently added to that education by reading Rebecca Skloot's The Immortal Life of Henrietta Lacks for J669.

I already had a firm grasp on the science of cell culture and contamination of cell lines, but the book gave me a lot of background about Henrietta Lacks, the woman the HeLa cell line was harvested from (and thus named after). Cell line contamination is the dirty little secret of the biological research community, and the story of the Lacks family certainly doesn't make the research community look any better.

HeLa Cells. Source: Wikimedia Commons.

One thing that I like about Skloot's book is that she doesn't look at either the family or the researchers involved in the HeLa controversy with rose colored glasses. I think the book is fair because it drives home the point that the researchers involved in cell culture in the 1950's all followed protocol at the time. There isn't a single person to blame for the fact that Henrietta Lacks' cells were cultured without her consent or that no one ever bothered to educate her family about cells, what it means to grow them in culture, and the research that cell culture enables.

It wasn't standard practice back then to tell research subjects much of anything. Not that I think what happened to the Lacks family is ok, I believe in informed consent - even if that means giving someone the basic science education they need to understand what will happen to their tissues once they give them up to science. But, hopefully publicizing more stories like the Lacks family's will help people speak up and learn more about biological research.

I found Skloot's book compelling, but my biggest problem with it was the ending. To me, it just ends abruptly. The death of Lack's daughter Deborah (who is a major character in the book through her interactions with Skloot) gives the book an ending of sorts, but something is still missing. I wish that there was something that could tie the book together like a change in policy or new regulations put in place, but sadly no such changes have occurred.

Cell line contamination is a rampant problem in the biological research community, and currently in the United States there are no regulations that force researchers to verify the origin of their cells lines or identify the contaminants they may have been exposed to. Cell line contamination pisses me off. We spend billions of tax dollars on research -- that may end up completely worthless because researchers have no incentive to check and make sure that the cells they are working with are what they think they are. What good is research for treatments for blindness when you aren't working with corneal cells, you are actually working with cervical cancer cells?

If you want to learn more about cell line contamination, a search in PubMed (a database of academic research papers) for Roland Nardone will yield several academic papers on the issue, but I suggest reading "Recommendation of short tandem repeat profiling for authenticating human cell lines, stem cells, and tissues," because it actually offers a solution to the problem of how to authenticate cells.

Water on the Moon

Source: Wikimedia Commons.

Since I was a little kid, I've loved space. The whole idea that there are other worlds surrounding us has always fascinated me. But, alas I am not so good with chemistry, physics, and math so studying space was never really within my academic dreams. I still got to daydream though, and who doesn't love imaging what it would be like to live in space?

Well, NASA scientists are one step closer to colonizing the Moon, according to research reported earlier this month. Researchers performed experiments that used rockets to collide with lunar craters to loosen rocks and dust that could be evaluated for their chemical compounds, and found a significant amount of water in the craters.

Access to water would be necessary to sustain a colony anywhere, so the discovery that there might be water resources on the moon that could be used by people is a step in the right direction toward people branching out and living on the moon.

The BBC article by Johnathan Amos: Moon's water is useful resource, says NASA

Commercialized Space Flight

NASA Space Shuttle Atlantis. Source: Wikimedia Commons

People have been taking about commercializing space flight for years, but according to the BBC article "Runway opens at worlds first spaceport" Sir Richard Branson (the Virgin group) is going to make it a reality within the next few weeks.

Of course you don't get to spend any real time in space, they are marketing a three hour journey where you get launched into space and then come back. If you have the money though it would be pretty cool to be able to say that you've been to space. At least 300 people at $200,000 each think so, and have already signed up for the flight.

The Long Run

As this is a personal blog, I have no qualms about shamelessly promoting people (and writers) that I like, as long as I give full disclosure as to how I know them and why I want to promote them. One of those people that I am going to promote now is Charlie Butler - he was a professor of mine from Lehigh and was tremendously supportive of my quest to get into grad school. He is an editor at the magazine Runner's World, and has just released his first book, which I remember him working on when I was his student.

The Long Run: A New York City Firefighter's Triumphant Comeback from Crash Victim to Elite Athlete is about Matt Long, a firefighter who was in prime shape in 2005 when he was riding his bike to work because of the NYC transit strike, and was hit by a bus making an illegal turn. He was impaled by his bike, and dragged by the bus. His doctors thought he'd never walk without a cane again, but he surprised everyone by dedicating himself to recovery and coming back to run the NYC marathon in 2008. It is a classic comeback story of triumph against the odds.

When I was in his class at Lehigh two years ago, Charlie would occasionally talk about the story, and what it was like to interview someone who had been through so much. He was drawn to the story for Runner's World because of how amazing it was that Long was able to run the NYC marathon after the injuries he sustained. As he was reporting, Charlie developed a relationship with Long and his friends and family and was able to get a great picture of what it was like to work through that kind of recovery.

I have not had a chance to read the book yet, it is going on my list of things to read once the semester is over, but I have read magazine pieces by Charlie and I can attest to the fact that he is a great writer, so I encourage everyone to check out his book, and of course let me know what you think if you do!

Blending In

The BBC is reporting new research on why certain species of wild cat have the color patterns in the fur of their coat that they do. Its long been claimed that the patterns (spots, stripes, etc.) help the animals blend into their surroundings, but the new study goes into more specific detail about how these new patterns actually help the cats blend in.

The research was published in Royal Society Journal, and conducted by a team from the University of Bristol. The BBC article by Katia Moskvitch is, "On how the leopard got its spots."

Bait and Vaccinate

Island Scrub Jay. Source: Flickr

Researchers are working to save the island scrub jay, a bird native to Santa Cruz Island (part of California). By luring the birds with peanuts, and then trapping them under a wire basket the researchers are able to vaccinate the birds against the West Nile Virus. The virus has been deemed a serious threat to the birds, because they all live on a single island so an outbreak would spread quickly.

The LA Times article: Taking a rare jay under their wing, tries to get an interesting hook in by describing the simple way (like a Wile E. Coyote prank) the researchers are undertaking such a complex conservation effort. I think it draws you in enough, although the article is a little long, and I did find myself skimming toward the end. I was able to skim it though- which means that the writer did a good job of explaining the science in a clear way.

Sleepy Skyping

This morning I got up at what I consider an un-godly hour (6am) to call a researcher in Wales for my last article for J800, before going to class. Business hours in the UK run from the very early hours of the morning here until around noon, which left before class as the best time to do the interview.

I wanted to just use Skype to call his landline, but when he found out I was using Skype, he suggested that we video chat. It is a good thing that I decided to get ready for class and got dressed before I contacted the researcher, otherwise he would have seen my pajamas. I do 90% of my interviews by phone, and probably the other 10% by email. I haven't interviewed someone face to face in over a year. So compounded by the fact that it was really early, I was caught off guard with the fact that he could see me, and that I was talking about some really complex genetics - I am fairly certain I sounded like a babbling moron.

I think I got a few good quotes though, so at least it was worth it, though the more I write them, the more I dislike feature-length issues pieces. They are unruly to say the least, but I hope I am becoming better at wrangling information.

Rare Variants

My article from the October issue of BioTechniques is out! I reported this one back in August right as I was moving to Madison. It is exciting to finally be able to see it in print. It is also available online, which means you should be reading it right now.

Diamonds in the Rough: Rare Variants Scratch the Surface

Many thanks to the scientists who spent so much time talking to me about rare variants, and to the editorial staff at BioTechniques for editing, and editing, and editing some more. 

Posing with the October issue!

Before you dive into the article, I'm sure you are asking yourself what is a rare variant, and why do I care? Well - rare variants are specific mutations in the genome that only happen in a few individuals, in some cases even just a single person. These variants are important because any time that something is amiss in your genome, it has an effect on you. At times these effects include causing disease. So, studying rare variants can tell doctors important things about disease and possibly help come up with new treatments. But, studying these rare variants is extremely difficult. To learn why, read the article!

Fractals

Benoit Mandelbrot, the mathematician who discovered fractals, died recently. While its true that I don't really like math - I do love fractals. It probably has to do with the fact that they are such an amazing natural phenomenon. Francis was explaining fractals to me in terms of geology recently, but the main idea is that some things in nature (rocks, vegetables, etc) have an essential structure that always remains the same. So, it will be the same shape no matter how many times it is divided. Probably one of the most well known fractals is cauliflower - try breaking it apart into little pieces and you will see what I mean, it always looks the same, even when its really small.


From the BBC:
Fractal mathematician Benoit Mandelbrot dies aged 85
Pictures of Fractals

Giraffe Love

Giraffe at the Henry Vilas Zoo Madison, WI August 2010.
Credit: Erin Podolak

Now I know special interest stories are important, getting the personal angle that appeals to the audience's emotional side is a great way to sell as story, but now the BBC is writing about giraffe love? I think everyone will sleep easier tonight knowing the Gerald the Giraffe has a new girlfriend. To think people are worried about the future of journalism. Bachelor giraffe in bristol finally gets a girlfriend.

Isaac Newton and Alchemy

I was greatly amused by the article "Moonlighting As A Conjurer of Chemicals" by Natalie Angier for the New York Times. It is about Sir Isaac Newton and how in addition to giving us the laws of gravity and inventing calculus among other solid scientific findings, he was also very interested in alchemy.

Yup, alchemy - turning lead into gold? I liked the article because Angier did a good job of describing why someone of Newton's genius would believe that alchemy is real. I also love science history, so overall that probably explains why I found this fascinating. I also love the title.

I also find this greatly amusing, and I was reminded of it by reading about Isaac Newton:

Man: 2 Viruses: Millions

Smallpox Virus. Source: Wikimedia Commons.

Scientists are reporting that the rinderpest virus has been wiped out. This marks the second virus to be eradicated by humans, the first was smallpox. Although, its not really eradicated because scientists, governments, and god knows who else have samples of small pox, and I'm sure will keep samples of rinderpest too. The BBC Article: Rinderpest virus has been wiped out, scientists say.

According to the BBC article, rinderpest killed cattle in Africa, Asia, the Middle East and Europe. Most notably in the mid 19th Century it caused the death of 80%-90% of African cattle and buffalo. Fun fact that I learned from this story: there are buffalo in Africa. Who knew?

Chilean Miners

In case you happen to never turn on the television or read any news of any kind, here are a few links to the story of the 33 miners in Chile who have been trapped underground since August 5th. Rescue workers have been pulling the men up above ground one by one since late last night.

The LA Times: In Chile 21 Miners Rescued and Counting
The New York Times: Chile Rejoices as Capsule Brings Miners to Freedom 
Washington Post: Chile Mine Rescue Underway, Two Thirds Hoisted to Safety
Chicago Tribune: Chile rejoices as two-thirds of trapped miners freed; men look healthy after 2-month ordeal

You get the idea...

From a strictly media perspective this story is important because:
A. There are THOUSANDS of reporters from around the world who have descended on Chile to await the rescue of these men to get the first pictures, sound bites, video, etc.
B. This could have been a tragedy, but instead is an uplifting story of survival and hope -- how often does anyone get to write a story like that these days? Answer: Not very often.
C. This story has such significance because so many men were trapped, because they are all alive, and because they are all alive after being underground for over two months... its just plain shocking.
D. There are dozens of story angles that can be pursed from this one event. For a reporter with the means, and incentive this event is a journalistic piñata... so many pieces of candy are now raining down on journalists everywhere in the form of story ideas.

The follow-up to this event is going to be spectacular. I am excited to see who gets the movie rights.

What Makes A Writer Special?

I've been thinking a lot lately about why I chose to specialize in science. Whenever people ask, I typically tell them it is because I was really awful at science itself. This is only a half truth. I was absolutely awful at Chemistry and Physics, but I have always loved and succeeded in Biology and Environmental Science. I know my difficulty in chem and physics was directly tied to the trouble I have with math.

I know math has been described as beautiful for the ways in which numbers work through a charted path to arrive at a solution. But I have never been able to follow that path. I always get hopelessly muddled in trying to understand the principles to the point that I can't follow the equation or the rule or whatever I'm supposed to be applying. I'm not stupid, so I wonder sometimes why I was so terrible at math. If I had a single teacher that cared enough to go off script and try to explain things in a different way, would I actually have been able to excel at a subject that didn't come naturally? Things I"ll never know I guess. 

But anyway, consequently when I arrived at Lehigh I wanted to be a biology major, but I was so behind in math (barely scraping through Algebra III was a far cry from passing Calc I & II) that I would have had to pass pre-calc for no credit before I could even start on my major track. I wonder if in choosing to write about biology instead of struggle through the math that I needed to be able to do biology if I took the easy way out. Although, I'm not sure there is anything easy about being a science writer. 

I bring up my specialty and why I chose it because today in J800 Adam Lashinsky, a feature writer for Forbes, spoke about his work as a finance writer. He said he was working hard to avoid getting labeled as a tech writer, although he has done a lot of reporting on business in the Silicon Valley. His reasoning was that he wanted to be free to write about whatever interested him. 

There are positives and negatives to specializing, but for me it was the whole reason I got into journalism in the first place. I wanted to be connected to the science, so for me without that bond with my speciality I can't say that I would be in journalism at all. I wonder if that will make me a better or worse science writer? 

Seeing Is Believing

Today in J620 we watched the documentary Seeing Is Believing: Handicams, Human Rights, and the News by Directors Kateria Cizek and Peter Wintonick. The film is a little old, and because it is about technology it is thus a little outdated, but some of the general principles are still pretty interesting.

Video has tremendous power in terms of reporting human rights issues, both for good and for ill. In the film journalist Joey Lozano follows the Nakamata, a group in the Philippines that are given a video camera by the human rights group Witness, to help document their struggle to reclaim their ancestral lands from sugar cane producers. Lozano serves as a go between for the native people and the media, teaching them how to use their camera and helping them take their footage to the mainstream media in the Philippines to get attention for their cause.

This would be the good side of the power of video, it helped the Nakamata document violence that was being perpetrated against them, and helped to ward off violence once it was well known that they had a camera available. On the flip side, the film also showed that violent extremist groups also have access to video and use it to recruit new members and spread their own messages. The film specifically showed videos made by the Taliban and Neo-Nazi groups.

It was an interesting film, but at the same time I don't think its exactly a revolutionary idea that video is a powerful communication medium. Since the film was made, I think that film has just increased in power for the good and the bad groups around the world. In doing my own research on the film, I also learned that Lozano died in 2005 of cancer. Its sad in its own right, but in the context that a disease took down a man that survived an assassination attempt, I find his story particularly moving.

Zeitoun

This past weekend I spent all day Saturday reading Zeitoun, by Dave Eggers. I thought it was a great example of literary journalism, and also personally thought provoking. The book tells the story of one family in the days before, during, and after hurricane Katrina hit New Orleans in 2005. In addition to your typical survival story, it is also about being a Muslim in a post-September 11th America.

My only first hand contact with Hurricane Katrina was through the students from Tulane who were displaced and so spent the Fall 2005 semester at Lehigh. College all over the country took in the Tulane students until the campus could reopen. Other than that, I don't know anyone who lives in that part of the country. Of course I followed the media coverage, but there is nothing like hearing someone tell their own story of what they went through. Eggers' reporting of the Zeitoun family's story was like hearing them tell it to me themselves. I felt like I was right there with them and it was more moving than a lot of the reporting that I was exposed to in the days after the hurricane struck.

As a Muslim family they had to also deal with the fear or being attacked for their faith, and ultimately Abdul (the father/husband) was suspected of terrorism in a lawless New Orleans, when there was no real evidence against him and arrested by the makeshift police forces in place. As someone deeply and permanently affected by September 11th, it was hard at first after that attack to distinguish between subsets of faith, to try to figure out who had struck out against my family. But ultimately by educating myself I've come to the conclusion that Islam is a peaceful religion, which believe me has been a hard sell to some of my friends and family.

I feel conflicted sometimes because I don't believe people should be persecuted for their religion, the United States is grounded in religious freedom, but at the same time we need a way to protect ourselves from people who believe their religion entitles them to hurt anyone who isn't of their faith. I'm not sure what the answer is, but arresting Muslims based on no evidence certainly isn't it. The Zeitoun's story made me angry because with all the resources this country has it its disposal, lawlessness should never be a concern, even in a decimated city. How does a country like the United States lose total control like that?

I don't particularly have any answers to the issue of how to maintain religious freedom in the face of Terrorism, I am after all a mere journalism grad student, but you should read Zeitoun because it is important to at least think about these issues. You need to be exposed to other people and their stories and perspectives to understand the implications of public policy.

The Grad Student Brain

 

"Piled Higher and Deeper" by Jorge Cham, www.phdcomics.com

I hope that I don't have as much ego as this comic would suggest. I also don't have to write a thesis so lucky me, but I do agree with the free food. There should also be a spot dedicated to coffee... just saying.

Genetically Modified Corn Makes Cents

Corn Field. Source: Wikimedia Commons.

Researchers from the University of Minnesota have released a study showing that genetically modified (GM) corn crops have a notable economic benefit for farmers. GM corn is designed to kill the european corn borer, a bug that eats the corn plants. By killing the insect, the GM plants actually help non-modified corn crops. The combined affect on both types of corn adds up to a decrease in losses for farmer's whether they plant the more expensive GM seeds or not.

The study is the first documented evidence that genetically modified crops can help farmer's make money, even though initially they are more expensive to plant. It is a good indication that a mixture of GM and regular crops are likely to be pursed in the US. 

The BBC article: GM crops bring cash harvest to non-GM varieties

The New York Times also recently ran an interesting article (After Growth, Fortunes Turn for Monsanto) about a down turn in profits for Monsanto, the most well known of the GM companies. Monsanto has been losing money on their newest type of GM corn, in addition to other products because farmer's just aren't buying them as the company had predicted.

The Rundown on Runoff

Credit: Erin Podolak, Sept.  2010

There is an article in the BBC this week about algae that have toxic affects on coral reefs. This article stood out to me because I just finished working on an article about toxic cyanobacteria (which come from algae) in lakes in Wisconsin for J800.

Most of us know what algae looks like, it is the green slime you see floating in natural bodies of water or growing on rocks, docks, or other items that stay in the water continuously. Algae occur naturally and aren't typically a problem. However, for the last decade researchers have been evaluating toxic algae, that is algae that blooms in a large concentration due to an increase of fertilizer in the water.

Where does the fertilizer in the water come from? Well the easy answer is agriculture. The fertilizers used by farmers get washed away and flow through the system of rivers and tributaries to larger bodies of water. The algae feed off the fertilizer and then "explode" in a huge bloom that can have toxic affects.

In the case of the coral, the algae are using up nutrients like oxygen and sunlight so that the coral are denied access to these resources and die off. What can be done? Well, find a way to allow farmer's to fertilize their crops that won't end up in our waterways causing algae blooms. But that is far easier said than done.

The BBC article: Toxic Algae Rapidly Kills Coral

When A Virus AND A Fungus Attack

Source: Wikimedia Commons

I haven't blogged about any actual science in awhile, so I give you the curious case of the dying honeybee. Since 2006, scientists have been trying to figure out what could be causing "colony collapse" where whole hives of honeybees die off. In the last four years, approximately 20-40% of the hives in the United States have died (that is a remarkably large amount).

Researchers have been struggling to figure out exactly what is killing the honeybees, an essential part of many ecosystems due to their role as pollinators. It took four years, but a joint team from the United States Army and the University of Montana are reporting that the culprit in the honeybee killing spree is an co-attack by a virus and a fungus. The researchers believe that the virus and the fungus may be interacting to disturb the absorption of nutrients, although the exact ways in which the bee's internal systems are thrown off is not yet known.

This is interesting for two reasons:
1. A virus and a fungus interacting to kill a species is rare
2. The United States Army teaming up with Academia isn't rare itself, but most partnerships occur to speed things up or keep costs down. This partnership was to really figure out what was causing the bees to die which is unusual.

New York Times coverage of the bees: Scientists and Soldiers Solve a Bee Mystery.

Storytelling At the Washington Post

In two of my classes this week Manuel Roig-Franzia came in to talk about his experiences writing for the Washington Post's Style section. After listening to him speak, I came away with almost a sense of awe at how ingrained it seems to be in him to tell stories.

For almost an hour today he just talked about the stories he's covered and what talking to the people he interviewed was like. He started off telling us about traveling to Haiti in the wake of the Earthquake earlier this year, and went on to discuss interviewing Bill Bond a man who fully admits to having killed his father (but who never served any time in jail for it), and getting the scoop on the White House puppy. Yesterday I heard him talk about his work covering lobbyists in Washington D.C. based on articles about Heather Podesta and the restaurant Tosca.

Typically listening to someone talk for an hour straight could get really boring, but I found Roig-Franzia's anecdotes about his work reporting to be highly entertaining. Not anything that I think I can really use in my own career mind you, but the guy can really tell an interesting story.

For those who don't know, Roig-Franzia caused quite a stir last year for his role in a fist fight that broke out in the Washington Post newsroom. I don't advocate punching people in the face, and I won't weigh in on whether Roig-Franzia deserved it, but I will say that it is a rare person who is enough of a bad ass to call their boss a cock-sucker and keep their job.

What Would Kurt Cobain Do?

Today in J620 we finally moved from discussing the history of humanitarianism and how the media works for and against humanitarian groups to the part of the class that incorporates celebrity. I did enjoy learning about humanitarianism in the sense of just building my knowledge base because I have no background in it, but I am looking forward to discussing how celebrities interact with the media.

In starting our discussion of celebrity, my professor brought up the fact that her favorite band is Nirvana.  I don't often have professors who profess their love for grunge or who have a Kurt Cobain poster in their office so I found that amusing. My professor said that when she's having a bad day she'll look up at her poster and think "what would Kurt Cobain do?" and she usually comes to the conclusion that her situation really isn't that bad.

But anyway, Nirvana was a segue into discussing what makes someone a celebrity and how celebrities can cause social movements. Michael Jackson, Lady Gaga, and Bono were the other celebrities that the conversation seemed to center around.

I find it kind of funny that for the most part everyone seemed to have a pretty extensive knowledge of celebrities, its like we all have this fascination that we try to keep hidden because we're supposed to be intellectuals. I guess that is why I appreciated my professor's Nirvana comment so much, it is always fun to see people divulge little parts of themselves. I find that especially true with music, and what certain people are drawn to. I love when people can surprise me.

In other news I got an A on my first paper for this class, which was a big relief for me since I was really scraping the bottom of the barrel in terms of my knowledge of humanitarianism.

Since I've now been inspired to re-visit Nevermind, I'll leave you with Nirvana's Lithium, which I argue is one of their best.

You've Got Mail

Even though I long abandoned AOL for Gmail, I still find it fun to see my email inbox full, even if a creepy computer voice no longer announces the presence of my new email. As I'm working on my new article topic for my J800 feature (which triggered my seething frustration and puppy-picture needing earlier this week) I'm running into the problems presented by email interviews.

I prefer to do my interviews over the phone, but I like to have an appointment set up, I find it easier for everyone than cold calling because no one gets caught unaware. Which reminds me of the time I interviewed National Medal of Science winner Elaine Fuchs on post-its when I was dressed as Wonder Woman last Halloween because I wasn't expecting her call, (the article didn't really turn out that bad)  but that is an unnecessary tangent.

Anyway, there are pro's and con's to the email interview, but for my latest topic I really just needed someone to talk to me to give me background, and that can't be done on email --it takes too much space and time. So after getting three requests for email interviews (which is largely due to the fact that I email before hand to set up an appointment, my own downfall) I was very happy to finally have one source come through over the phone.

I'm feeling much better about the whole thing just having the one interview under my belt because I have a better grasp on the topic and my source recommended other people for me to talk to (fingers crossed they'll be available by phone too.) I know there are some publications that make a point of not allowing email interviews, but I don't think they are all together bad. Email has its place in the proverbial "writer's toolbox" you just can't rely on it all the time.

You really can't build an entire article based off of emails, you need to get at least one source on the phone. But, email can be useful for getting direct comments from very busy people. Case in point, I would never have gotten comments from Francis Collins for an article I did for BioTechniques on the Rock Stars of Science campaign if I hadn't caught him by email. I would never have gotten him on the phone in time for the article because I would have had to go through his secretary and it would have gotten messy from there.

So email can be useful, but I still think that when you need a lot of information its best to actually talk to someone. You can't switch gears, or go off on tangents on email which is I think my biggest problem with it. You also can't gauge a source's reaction to your question. I find it strange actually that so many people prefer emailing responses to questions because I think it takes way more of their time to do so than to just answer a few questions verbally.

I also think I like the phone more than in-person interviews because I think it makes people less nervous to just talk into the phone and not see my typing away frantically. I think when people see you taking notes they clam up and in my experience I've gotten plenty of people to really open up on the phone. Every journalist has their own way of doing things, and I'm sure there are those that would completely disagree with me, and maybe as I get more experience my opinion will change, but for now I think the phone works best -- provided I can get someone to answer it.

Nobel Prize Science Winners

Every Fall the Nobel Prize is awarded in six categories: Chemistry, Physics, Physiology and Medicine, Literature, Peace, and Economic Sciences. It takes a long time to win a Nobel Prize (unless of course you are Barack Obama) and most awardees in the sciences end up being honored for initial discoveries that they made years ago that have had a tremendous impact on society since their discovery.

This year the winners are:
Physiology and Medicine - Robert G. Edwards for developing in vitro fertilization, which most people know is a way around infertility to help people have children who otherwise wouldn't be able to.

Physics - Andre Geim and Konstantin Novoselov for discovering the "two-dimensional material graphene" which is basically a new carbon-based material that is very thin but very strong and is useful in experiments  in quantum physics.

Chemistry - Richard F. Heck, Ei-ichi Negishi, and Akira Suzuki for "palladium-catalyzed cross couplings in organic synthesis" which is a method that helps organic chemists stabilize carbon atoms so that they can be manipulated and used in research.

The prizes in Literature, Peace, and Economic Science haven't been announced yet, but they will be on October 7, 8, and 11 respectively so be sure to check the news for those winners it is always interesting to see who gets recognized, and sometimes the results can be shocking (like Obama's win in the Peace category last year.)

Here is some more coverage of the science winners:
MSNBC: Test-tube baby pioneer wins Nobel Prize in Medicine
Scientific American: Robert Edwards Wins the Nobel Prize for Physiology or Medicine for Pioneering In Vitro Fertilization (by the way, way too long for a title)
Physics Today: Andre Geim and Konstantin Novoselov win 2010 physics Nobel for graphene
Associated Press: Nobel Prize honors super-strong, super-thin carbon
USA Today: 2 Japanese, American share Nobel Prize in Chemistry
Associated Press (via MSNBC): Trio wins Nobel for key chemical tool

Calculus, Zombies, World of Warcraft & Mean Girls

So after flipping out this morning about my article falling apart, I rallied myself and attended a lecture by UW's Science Writer in Residence Jennifer Ouellette. She specializes in physics as a freelancer and has written three books. Her lecture was called "Dangerous Curves: How I Learned to Stop Worrying and Love the Calculus" which was about the research that she did for her most recent book about math and how it can be applied in everyday life: "The Calculus Diaries: How Math Can Help You Lose Weight, Win in Vegas, and Survive a Zombie Apocalypse."

I had hoped that her lecture would be about what it was like to write about a subject that she has no background in (the calculus) but it was actually more about why she thinks math is cool and people should appreciate it. It was still an interesting lecture, and I give her credit for drawing an audience that merged the interests of undergrad journalism majors and graduate math students. For the record, graduate math students seem to function on an entirely different plain, and I for one do not speak graduate level math.

Ouellette did a great job of bringing in different clips and examples of how math is applicable in everyday life. She showed part of the television show Numbers (which isn't on air anymore, but is an interesting example of how to use math for dramatic crime fighting) and the mathlete competition from the movie Mean Girls, where a less controversial Lindsay Lohan realizes that it is okay to like math.

The zombie part of the title of her book has to do with a researcher who created an equation to figure out how best to survive a zombie apocalypse. Of course it is a multivariable calculus equation, which ultimately concludes that getting a gun and blowing away as many zombies as fast as you can is your best bet (although I think I could have concluded that without the calculus.)

The most interesting part of her talk for me (and the sorority girl in me does cringe to admit this) was when she starting talking about the game World of Warcraft. Apparently there was some sort of blood disease (similar to a highly contagious pandemic) that started spreading to the avatars in the game that was created by a player and started spreading rapidly through the program and the game actually had to be reset by its administrators to avoid all the characters dying of this plague-like disease. She brought it up as an example of how there can be technical models for real life situations, which actually didn't have much to do with math, but is interesting from a science-health angle.

Overall, I'm not sure how useful her talk was in terms of helping me as a science writer, but it was entertaining, it got me out of the apartment, and I got away from my frustration over my article for a little while. I think I have my article situation figured out, sometimes just scrapping an idea and starting over from scratch is the best solution. I'm now feeling optimistic, so if only my eye would stop twitching things would be back to normal.

Ouellette's blog Cocktail Party Physics is also a good example of science writing on the web, so be sure to check it out if physics is your thing.

At Least It Had the Clash

For the last week I have been trying to read Psychotic Reactions and Carburetor Dung by Lester Bangs. It is a collection of articles about music that originally ran in the 1970's. It is one of the worst things I have ever read, and I choose to read scientific reports for a living. As I was working my way through it I kept asking myself, am I just not getting it? What am I missing? Is this like when I read Tess of the D'urbervilles and hated it because I didn't realize that the main character had gotten raped (which is the basis for the entire story) and then got completely owned in class the day we discussed it??

I'm still not sure if the articles are actually as awful as I perceive them to be, or if I'm completely missing the point, but I guess I'll find out in class this week. For short pieces I found them incredibly hard to follow, and as music reviews I would say that most of the time I couldn't even tell whether or not he liked the album or artist he was talking about. It reads like a ridiculous stream of conscious, that goes off on completely unrelated tangents that in my opinion add very little to the writing. He also uses the longest sentences. A single sentence should not take up a whole paragraph, thats just bad technique. Actually, its the absence of technique, which is really all that Bangs style of writing is.

I wish someone would pay me to say whatever I damn well please, but until this blog gets bought and turned into a TV show (which is obviously my life's back up plan, lol) I'll have to settle for writing for my audience and employers. If only Bangs had such constraints. His pieces read like sprawling blog posts with no point, but lots of stories and personal opinion. He literally just says whatever he wants.

The only piece in the whole collection that I liked at all was his article on The Clash. I may be jaded because personally I love The Clash, but this article actually made sense. There was a point, which Bangs proved by painting the scene in a literary way. He describes his personal interactions with the band to prove how they are different from all of their peers in the way that they care about their fans. It is an argument that he is able to prove, and he does. It is the only piece in the whole collection with that quality.

In other news, I hate press releases that are misleading and confuse me because I read them when I am half asleep so that I leave messages for potential sources early in the morning that have nothing to do with what I want to write about and don't realize it until I get ahold of the PI hours later. So tomorrow I get to clean up my mess of messages, so that I can track down sources for an article due next week. Fun times. But there is always Rock the Casbah, and for today I guess that is enough.

Can't We All Just Play Nice?

One of the big topics right now in the media business is the dismissal of CNN's Rick Sanchez after he went on a satellite radio show and called Daily Show host Jon Stewart a bigot, and criticized the role of Jews in the media, saying as a group Jews do not experience derision like other minority groups.

I may be a complete and total journalism newbie, and this deals with TV news which is not my specialty, but I have to say that to me, Sanchez's remarks are no better than elementary school taunting, and I for one am glad that Jon Stewart is just refusing the play (the Daily Show has declined to release a statement about Sanchez's remarks.)

Stewart's New Book

Sanchez went on air and mistook the Galapagos Islands for Hawaii when covering the Chilean Earthquake that occurred in February 2010. He made a factual error which he should take ownership of, its not ok for journalists to not know what they are talking about, and its really not ok to give misinformation. It also wasn't the first instance of Sanchez making a factual error. So Jon Stewart called him out and made fun of him for it. Deal with it, that is what the Daily Show does.

The concept behind the show is pointing out the inadequacies in media, politics, science, etc. A lot of "rich white guys" have been called out by Jon Stewart too, he didn't highlight Sanchez's error because he's hispanic, he highlighted it because it was an unacceptable mistake. To say that Stewart did it because he's a bigot just shows that Sanchez is also ill-informed as to what the Daily Show does.

The other half of Sanchez's argument - that Jews in the media have all the power - really? Because no one has ever heard that one before. Get over it. Its like arguing on the playground because someone has a better toy than you do. So someone has a better toy than you Rick Sanchez, be creative and maybe you could have more fun instead of lamenting that fancy toy. But no, you decide to whine about it. Because people will respect you more for taking the low road (sarcasm intended.)

Here's a fun idea, how about instead of accusing someone of being a racist every time they point out that you made a mistake, you rise above and be better? Stop making mistakes. Don't give anyone fodder to try to take you down with. The media and the public would be better off. No one wants to hear about how the kids on the playground were mean to you.

Lisa de Moraes' article in the Washington Post about the Sanchez-Stewart incident: CNN's Rick Sanchez Fired After Explosive Interview on Satellite Radio. 

A Fossil Named Pedro

Francis and I were talking the other day about people who name objects. I can think of a few people who have named their cars (Oliver, Scarlet, the Mistress...) and Francis said she has friends who have named various other inanimate objects ie: a hammer named Fred. Then there is the issue of nicknaming people, which as a person with a short first name I've never really experienced (we will not discuss the name I got from a sorority pledge two years ago, and I do not count it as a nickname.) There is also the issue of choosing to call people a different name because it is a complete juxtaposition to what they are actually like, which makes it funny (for example calling the baby Carlos in the movie the Hangover).

I bring up nicknames because I was reading the article "Ancient Giant Penguin Unearthed in Peru" by Katie Moskvitch in the BBC, and the one fact from the article that stands out most in my memory is that the researchers uncovered an ancient penguin fossil, and chose to name it Pedro. Really, researchers? Why Pedro? Please tell me it is not because you were trying to name it something of hispanic-sounding origin simply because it was unearthed in Peru. How expected.

Why name it at all? When a new species is discovered it is given a scientific name, (in this case Inkayacu paracasensis) which is more than good enough to identify the fossil. I don't think calling the fossil Pedro makes any more sense then calling a hammer Fred. But there is a long trend of researchers giving nicknames to their fossil finds, most prominent is probably the "Lucy" fossil found in Olduvai Gorge (the controversy over which I will not go into here) that is named after the Beatles song Lucy in the Sky with Diamonds.

I can sort of understand naming a fossil, within the context that some of these researchers work their whole careers to make a find of the magnitude of a huge ancient penguin, and therefore feel a sense of attachment to it, and want to name it the way you would name a pet. I do get that, but honestly this is not a goldfish or a puppy, if you work so hard to find something of important scientific significance that should be respected and learned from, why would you ruin that reverence by calling it Pedro?

So there is my personal rant on naming scientific discoveries. If you want to name your houseplant, your car, or even all the inanimate objects in your home, its your life. But I think that giving important fossils goofy names diminishes their importance in the eyes of the public, and these finds (and the researchers who have worked so hard to uncover them) deserve more than that.