Category: Genetics

Chocolate Genes

Genetics, Good Writing, Sequencing, ,

A science news story that has been circulating in the media this week is the sequencing of the chocolate genome. I know I’ve already talked about genome sequences and why I think some are more important and interesting than others so I won’t bore you with that. But, I did want to put up links to a couple of different articles on the subject because I think it is interesting to compare and contrast the headlines and leads in terms of who went for the cheesy chocolate jokes, who worked the chocolate in a subtle way, and who went for a strictly hard news angle.

800px-Cacao-pod-k4636-14There is value to all of the approaches, so my mind isn’t made up yet on what I favor. I think if I had to choose I’d go for middle of the road approach (which is usually a pretty safe place to be) and say that you have to work the chocolate in, in some way because its what makes the story fun, but that you don’t have to get ridiculous with yourself and lose the science and the purpose of the story.

CNN: Sweet scientific discovery in the world of chocolate
ScienceDaily: Sequencing of cacao genome to help chocolate industry, subsistence farmers
GenomeWeb: Consortium Using 454, Illumina Sequencers to Decode Cacao Genome
US News and World Report: A Taste of the Chocolate Genome
SiFy News: Cacao genome sequencing a boon to chocolate lovers
CBS News: Sweet Science Cacao Genome Map Completed
Scientific American: Candy-maker releases cacao (coco) genome sequence online
Reuters: Scientists Unlock Coca Genome, Release to Public Domain
New York Times: Rival Candy Projects Both Parse Cocoa’s DNA
AOL News: Wunderbar! Scientists Crack Chocolate’s DNA Code

Overall, I think that all these articles (which are just a sampling of what is out there) have interesting differences in the way they handle the headlines and even the rest of the body of the story. It might all be about chocolate, but each news organization definitely puts on their own spin.

J. Craig Venter: Portrait of a Businessman

Genetics,

The New York Times’ Andrew Pollack just published an interesting article on J. Craig Venter, the scientists and businessman who became a household name (at least around geneticists’ dinner tables) by competing with Francis Collin’s federally funded team to complete the Human Genome Project.

Venter’s company Synthetic Genomics created a sensation in May when they announced the creation of the first synthetic organism. I covered the finding for BioTechniques: Venter Creates First Synthetic Life. Recently Venter has focused on his efforts to use algae as a biofuel. Despite receiving funding from companies like Exxon Mobil and BP, Venter’s algae efforts have generated far less of a media frenzy.

The article takes a look at why Venter’s more industrial aims haven’t generated the kind of success that his research and science based work has. It also gives some interesting insight into Venter himself.

Wheat Genome Adds to Available Draft Sequences

Genetics, Past Articles, Sequencing, ,

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

Junk DNA & A Wisconsin Update

Genetics, Grad School, My Personal Life,

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.

Hard At Work

BioTechnology, Genetics, Past Articles,

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.