What Killed the Woolly Mammoths?

Last week, Francis and I visited UW Madison's free geology museum where they have several skeletal remains in addition to fossils and mineral specimens. With the woolly mammoth in my recent memory, this article from the BBC caught my eye.

The article reports on new research published in Proceedings of the National Academy of Sciences that disproves previously held notions about the meaning of nanodiamonds (incredibly small diamonds) found in sediments that date to the period of history 12,900 years ago that saw the rapid extinction of large creatures and human settlers across north america at the beginning of the cooling period known as the Younger Dryas. 

The presence of nanodiamonds in the sediment had led researchers to believe that an impact of something from space had disrupted the natural environment and led to the extinction. However, the new research seems to disprove the impact from space theory, as the strongest evidence - the nanodiamonds - have been shown to be just aggregations of carbon, not proof of a collision with a space-rock. 

The research isn't the final word on the issue however, because some proponents of the collision from space theory have claimed that the research from PNAS was looking at the incorrect sediments and didn't accurately study the nanodiamond evidence. 

Truly, the issue is an example of how the very nature of science, that it is always changing and adapting, can cause confusion. Researchers simply won't always agree based on the evidence that they have witnessed, which can make it very difficult for the public to draw conclusions as new findings are constantly introduced. 

On Personal Passions and Journalistic Detachment

An interesting post from Andrew Revkin's blog DotEarth for the New York Times, talking about how journalists can reconcile the issues they are personally passionate about with the need to be detached and well-rounded in their reporting.

The post is taken from a 2005 speech given by Revkin (when he was still a full-time Times reporter, instead of a blogger) but I think it drives home some interesting points about being a journalist.

Writers are people first, and journalists second but a requirement of the profession is not to insert your own voice into the reporting, unless you are a columnist. Writers have to conform to the style of whatever publication they work for. This can dilute their own voice even more as they adapt to specific structure and standards.

I also found Revkin's thoughts on how science writers approach content interesting. There is no doubt that it can be difficult to show a new scientific finding in the greater context of all the findings that have occurred before it. I think science writers need to find a balance between skill and instinct that informs how to explain an issue, something that only comes with experience.

Good Thing I Didn't Choose Colorado

When I was narrowing down programs and trying to choose which Grad School I wanted to attend I was split between the University of Wisconsin Madison and the University of Colorado at Boulder. Michigan State's Knight Center for Environmental Journalism was a big draw, but I didn't get the acceptance letter until just days before I had to make a decision, making a visit to the school impossible, so that pretty much counted them out. I chose UW because I loved Madison, and I felt like I would fit into the community much better than I would in Colorado.

As it turns out, its a good thing I chose UW instead of Colorado because CU Boulder is closing their Journalism school. It would have been incredibly unfortunate to be stuck there with the program completely restructuring. Most likely, I would have ended up with a graduate degree in something that didn't reflect my actual interests and job goals (probably information studies or multi media something or another.) I guess I dodged the proverbial bullet on that one.

Thanks to my Mom for this interesting article on the closing and how journalism, despite the massive loss of revenue in recent years, is expanding at an enormous rate due to the rise of new technologies. Universities need to find a way to fit the ever changing role of journalism into their programs.

One quote from the article that I just want to highlight is from David Hazinski an associate professor at the University of Georgia's Journalism and Mass Communication program. Essentially he's explaining why journalists still have a role to play in a society that has been bombarded by instant opinion and commentary through blogs, twitter, etc. People trained in the technology are not the same as people who are trained in telling the story.

"Journalism isn't hardware. It is content and context. Someone is still going to have to go to that fire and shoot some video, interview the mayor, and analyze that stock report. Someone is still going to have to package it, if for no other reason than to save audiences time. Writing, interviewing, editing, and working under pressure will still be needed skills. Ethics and standards will become even more important as the sea of opinion grows deeper. The content and context will be distributed over many platforms but someone has to be at the top of the information food chain. Those people will be skilled journalists, not technicians."

Immunizations For Fish

Most of us are pretty familiar with the concept of immunizations to help safeguard us against disease by giving our bodies a heads up, jump starting our immune system so it will know how to respond when it encounters disease. But now, researchers have successfully immunized fish against the Ich, the white spot disease.

The LA Times reported on the new research, which was presented recently at the American Chemical Society annual meeting. Ich kills 50-100% of fish that it infects, by affecting their breathing and making them lethargic. The disease is characterized by white patches that appear on a fish's body. It is common in farm fish that are grown in close quarters.

The researchers (from the US Department of Agriculture, Agricultural Research Service) developed two forms of the vaccine. First, the vaccine was created in the form of a shot, like a typical vaccine administered to a person, but the approach proved difficult to administer to hundreds of small fish. The researchers then developed a bath containing the vaccine that showed a 60% success rate at protecting the fish from Ich.

The researchers still have to overcome the obstacle of how to grow enough of the parasite for the demand (there is a huge volume of fish farms, each containing hundreds to thousands of fish). But for now, the mere fact that researchers have found a way to adapt a human technology for a lesser organism is particularly interesting.

Looks Like A Fish, But Its An Octopus

I found this interesting article in the BBC today about an octopus in Borneo that exhibits mimicry of certain fish. Researchers used a genetic analysis to study the behavior of the Indonesian Mimic Octopus (I know clever name, right?) What they found was that the octopus evolved the ability to mimic toxic fish, sea snakes, and other predators to help ward off its own.

Probably the most well known example of mimicry is in butterflies that exhibit the coloring or markings of other toxic species to keep themselves from being eaten by birds. Of course, I have an article about this: Genetic Hotspots Solve Mimicry Mystery from BioTechniques.

Is That A Tiger In Your Purse, Or Are You Just Scamming Security?

You've got all your liquids and gels in 3oz. bottles sealed in a clear plastic bag, you've stowed all your electronics in the same place for easy scanning, you've removed your laptop from its case, and taken off your shoes, now all thats left is the small issue of the tiger cub in your bag, and you'll be ready for take off.

The BBC recently reported on a woman in Bangkok who tried to board a plane with a tranquilized tiger cub in her checked bag. She placed the cub in among stuffed tiger toys to try to hide it. Needless to say the live tiger cub showed up when the bag was scanned, and the woman was arrested for attempted animal smuggling. She was trying to take it to Iran.  

Really? It astounds me how brazen some criminals are. Its a sad state of affairs when criminals think so little of the authorities that they attempt such things. I have to think that this woman can't be the first to ever smuggle an animal in her luggage. What I'd like to know is what can be done about it?

I know I keep relating current issues to past articles I've written, but this incident reminded me of an article from earlier this year on using genetics to crack down on chimpanzee trafficking in Africa. Essentially, the researchers genetically map the animals rescued from poachers to determine their family lines, and definitively say what regions that poachers are getting the animals from, to give the authorities a better idea of where to increase their presence. 

When Clinical Trials Go Awry

The New York Times' Gina Kolata recently reported on clinical trials and what researchers can or should tell patients and their families when the results aren't what everyone had hoped for. Interesting information and a point of view that I think most people who reflect on scientific research wouldn't necessarily consider.

Yale Lab Heist Story Continues

Over the summer I reported on a story out of Yale University about a researcher who was accused of stealing laboratory equipment as part of his divorce proceedings. The New Haven Register originally reported the story, and it was slanted at best because they only based their story on public record (police reports, the divorce proceedings) and the opinion of the researcher's ex-wife.

I did a follow up to the Register story, and got the researcher to comment easily. He replied to my email right away and thanked me for the opportunity to get his side of the story. According to him, no other news source had ever contacted him directly for an interview. So I find the Register and The Yale Daily's News' claims that he didn't return repeated requests for an interview sort of suspect. I think they tried to contact him... but his Yale contacts are long defunct. His gmail is available on the web very easily if you search his name.

But anyway, the Yale Daily News did a follow up on the story based on the Register and they do mention BioTechniques and a quote that the researcher gave me, so that is sort of cool.

The Yale Daily News:
http://www.yaledailynews.com/news/university-news/2010/08/27/yale-scientist-suspected-stealing-lab-equipment/

The New Haven Register:
http://www.nhregister.com/articles/2010/06/29/news/new_haven/aa1_tue_nelars062910.txt

My BioTechniques Story:
http://www.biotechniques.com/news/22K-worth-of-lab-equipment-seized-from-former-Yale-researchers-home/biotechniques-299798.html?autnID=288841

Wheat Genome Adds to Available Draft Sequences

Scientists have released the draft sequence of the wheat genome. There are new draft sequences being released all the time as genome sequencing capabilities have increased. While they are all important because they increase researchers' overall knowledge of the organisms that have been sequenced and how all organisms interact and are interrelated, some sequences have a far greater impact than others.

I've written about a few genome sequences that were released in the last year for BioTechniques, but I thought the wheat genome was worth mentioning because of the obvious impact it will have on the food industry. Whenever a staple crop is sequenced it adds to researchers abilities to tackle issues like world hunger by making super foods, but that is an issue which is controversial in and of itself. The more we learn, the more we can do. But just because we can make genetically modified foods that thrive in unconventional climates, should we?

Also just a note about why it is called a draft sequence and not just the sequence: every genome that is sequenced starts as a draft, when researchers sequence a genome there are parts of it that they either don't understand the function of, or that they haven't been able to unravel. So, the working genome that researchers use is a draft, it is what researchers will use compare their own sequencing work with that organism, to check for accuracy. But it is just a draft, drafts can be amended later if need be. Essentially, it goes back to the main nature of scientific exploration: researchers are constantly building on their knowledge base, which is why most scientific findings are left open to be improved upon as researchers learn even more.

Draft sequences I've reported on in the last year:
Horse Genome
Corn Genome
Hydra Genome
HIV Genome
King Tut's Genome

Top Ten Invasive Species

My mom (who gets all of her news from AOL, we'll forgive her though) sent me this article about the top ten invasive species in the United States. The species were ranked based on the financial impact they have on the United States each year, but I think invasive species are interesting because of the environmental questions they raise.

What constitutes a truly natural environment?
Are all invasive species bad?
How do ecosystems interplay with each other?
How do humans affect wildlife through other organisms?
What kind of legacy has the presence of humans left the world?

Things to think about, if you like that sort of thing.

The Battle Over Stem Cells

Stem cells have always been a controversial issue, but for a while it seemed that the Obama administration had brought some kind of direction to the issue by allowing federal funding of research based on embryonic stem cells. But recently, stem cells have been back in the news because a US district court filed suit to block the Obama administration's attempts to provide more funding for embryonic stem cell research.

Reporting on the issue by the BBC has been informative. I think giving the hard facts of the story in a way that doesn't entertain the emotional components and personally held beliefs (on either side) is really necessary. I think their reporting on the issue does just that.

One component of the story that I do want to comment on is the argument that limiting federal funding for embryonic stem cell research won't be detrimental to the research. The National Institutes of Health (NIH) is the largest funding organization in the United States. The amount of funding that private institutes can provide is completely dwarfed by the NIH.

Restricting funding on embryonic stem cell research in the United States will be detrimental to our progress, that is why under the Bush administration we lost researchers to other countries in Europe and Asia where that research is supported.  The research that took place during those years is indicative of what we'll accomplish under a new ban. Personally, I am glad the White House is fighting this. When religious beliefs start to take a role in shaping policy it can become incredibly dicey.

I do think that adult stem cell research has value, and research into induced pluripotent stem (iPS) cells has made tremendous progress, but researchers do still need to study pluripotency and iPS cells aren't an adequate model yet. I don't think you can replace one avenue of research with another, they just aren't the same no matter how much we might wish that they were because it would eliminate the ethical issues.

Here are a few highlights of articles that I wrote for BioTechniques recently on Stem Cell research:

Vatican to support international intestinal stem cell consortium
Induced pluripotent stem cells create first living animal
The shape of things to come: helping stem cells shape their future
iPS cells still fall short of embryonic capabilities
Are iPS cells a thing of the past?

Wisconsin & Writing

Today I ran a bunch of errands around the UW Campus. I got my student ID, got my bus pass, set up a bank account, got groceries, found my classes etc. According to my Mom my ID picture makes me look homeless. I guess its a winner. Today was my family's last full day here, they leave for the airport tomorrow at 4pm. I'm really glad they came out here to help me get settled but I think it will be good for me to just wander around a little by myself to get my bearings.

Tomorrow my article on genome wide association studies and technologies for finding rare variants is due for BioTechniques. I'm still waiting on one last interview, so fingers crossed that will come through tomorrow morning. Otherwise, I'm not sure what I'll do, quote from papers probably. I did get four other interviews so its not terrible, but they asked for five so I'd really like to deliver. Its not my best work, but given that I only had two weeks, and that I moved and have been with my family non-stop for one week of that I'm proud of myself for the progress I've made.

In other science writing news, Harvard recently found Marc Hauser guilty of misconduct. I mentioned in an earlier post that the New York Times had reported on the alleged misconduct. I thought their reporting on the case was relatively balanced, so I figured it was worth mentioning.

Junk DNA & A Wisconsin Update

I saw this article in the New York Times today, and it got me thinking about how misleading the concept of "junk DNA" is for the general public. It isn't really a good descriptive term because junk signifies that the DNA isn't needed, when really researchers just don't yet know what that DNA does. It isn't part of the exome (part of the genome that codes for proteins - which make all the substances of your body) but that doesn't mean that it doesn't have a role. I think its a term that people should avoid using because I think it causes more confusion than it does good.

In other news, today was my first full day in Wisconsin. I saw my apartment and met my roommate Francis, and she seems really awesome so that was exciting. I spent all day waiting for my boxes to come from UPS (which arrived at 6:45pm and ripped open, of course) but they finally came so that made me happy. Tomorrow we'll try to actually set up the apartment since my stuff is literally just dumped out all over the place. There is a definite lack of storage so we'll have to try to fix that, but overall the apartment is really nice and in a great location.

Hello, Wisconsin

Today I flew with my family to Wisconsin where I'll be starting grad school in a little over a week. The flight was less than stellar, but we made it ok, and the airlines even managed to get all my luggage here in one piece. We didn't get a chance to do much, but we did drive around Madison a little bit to show my brother the city (he's never been here but I visited with my parents in March).

Tomorrow we'll actually see about setting up my apartment, which is in a really awesome location. Its only a block from the Journalism/Communications department. I'm thinking that will be really nice during the Wisconsin Winter. Tomorrow I also get to meet my new roommate, the apartment building matched us up so we've never met. She moved into the apartment on Sunday when the lease started, so I'm excited to get to the apartment and start settling in myself.

Hard At Work

I spent all day today working on a new article for BioTechniques. The editor in chief of the journal offered me a freelance job, which is awesome, but the stipulation was that I had to get it done in two weeks. We're now at the one week mark, and I've now got a working draft, so I'm happy with that progress.

I got to interview David Goldstein from Duke University today for the article, which was pretty cool... even if he only gave me 15 minutes. The article is about the hunt for rare variants and how genome wide association studies were never intended to find rare variants, only common ones. Its slated to run in BioTechniques print edition in October. It still needs a few more sources, and some editing so hopefully in between moving (tomorrow!) and settling in Wisconsin I'll have the time to do more interviews... I better find the time.

Reporting on Science Misconduct

I usually prefer to read the BBC for science news (and all other news for that matter) because I find their reporting, especially only US Politics, to be fairly balanced in the grand scheme of journalism. But,  as a NJ/NY native, I can't help but check out the New York Times everyday. That is where I found this article on a case of alleged misconduct at Harvard that is still under investigation, but may have a trickle-down affect to various fields that the PI worked in, and students that he worked with. 

I always found it very interesting that when we ran stories at BioTechniques about cases of scientific misconduct, they caused a huge jump in hits to the website. People love gossip, and they especially love hearing drama about their colleagues. I guess its an old journalism standard that juicy stories usually win big, even in a field that can be dry (when not done right!) like science writing. Stories about misconduct feel a little cheap to me, almost like they belong in the Star magazine of the biological research community. But, then again misconduct is a huge issue that does need to be reported on.

Integrity in any field is important, but for researchers, the "publish or perish" adage adds to the pressure to get results no matter what the cost. Conducting research requires a lot of overhead, in addition to the time and energy of students, post docs, and technicians. When a PI choses to alter their data to get more favorable results it does have a huge affect on the other members of their lab, and can tarnish their careers even if they were unaware of the misconduct. Hopefully that case at Harvard won't derail too many promising careers. 

Since When do Journalists Need Grad School?

Most people agree that what counts most in creative fields, like journalism, is experience. However, in a field like science journalism there is a certain expectation that a writer will have extensive credentials, including a higher degree. When I interview scientists I have to hold my own with incredibly intelligent and accomplished people, all of whom have their Ph.D., and usually I do just fine, but they often ask me what my Ph.D. is in. Imagine their surprise when I tell them that I don't have a Ph.D. or even a M.A. (my B.A. in Science Writing is from Lehigh University.)

In my year at BioTechniques, I worked with several interns, three of whom moved on to full-time positions at NPR's Science Friday and Genome Web. What these writers had that I don't was a Master's Degree in Journalism. I've always wanted to pursue a graduate degree, so it just made sense for me to apply to grad school for science journalism. I start at the University of Wisconsin-Madison in September.

Part of my reasoning for starting this blog, in addition to wanting to constantly write about science and needing a new venue, was to chronicle my grad school experience as I try to make a name for myself as a science writer. So hopefully this blog will become a mix of personal stories, observations about science, and a few adventures (and I'm sure stumbles) as I chase that dream.

Science Writing Highlights

For the last year (2009-2010) I've been writing for the journal BioTechniques. In that time I've written way to many articles to post here, but here are a few favorites from Spring/Summer 2010:

"Ending cell line contamination by cutting off researchers" is my most recent piece, about how the biological research community can end the widespread use of contaminated cell lines for published (and peer reviewed) research. New York Times bestselling author Rebecca Skloot (who literally wrote the book on HeLa cell contamination) posted a link to the article on her Twitter.

"Fastest case of adaptation documented in Tibetans" reported on (what I think is) a really interesting development in the study of human genetic adaptation to environmental conditions. Basically, Tibetans adapted rapidly from Han Chinese to thrive in low-oxygen environments.

"The sequencing race: the home stretch" was a follow up to an article that I wrote that appeared in the February 2010 print edition of BioTechniques. The whole suite of articles reports of the progress that has been made (and is anticipated) in the field of genome sequencing technologies.

"Plant biology blasts off: shuttle missions explore biofuels" reported on experiments featured on the last few NASA shuttle missions exploring the affects of zero-gravity on possible new biofuels.

"Facial expressions quantify pain in lab mice" is about a method to quantify whether or not laboratory mice are experiencing pain due to their role in an experiment based on the way the features of their face change, indicating pain. It raised some important issues about animal rights, specifically what constitutes suffering and whether the animals are aware of what is happening to them.