Genome Blog

How Carrots Won the Trojan War – a review

Thu, 17 May 12 17:00:00 UT

You probably knew that some of the vegetables that we eat are, from a botanical perspective, fruits. Did you know that it took a U.S. Supreme Court decision in 1893 to define which fruits are vegetables?

If there were a form of analytics on my television, it would discover that I watch a lot of science programs. I don’t know which station gets most of my attention, but I certainly like PBS, Discovery Channel, National Geographic channel and Space. If I’m not watching the science networks, then my television is tuned on to the History network. I also have some favourite shows on Food Network as well. You can imagine my excitement, then, as I found all the elements of science, history, gardening and food in Rebecca Rupp’s How Carrots Won the Trojan War.

In 20 entertaining and informative chapters, Rupp takes us on a journey through history, botany, genetics, culture and cultivation of the vegetables we eat. She lists over a hundred General Sources, and the Notes section contains many pages of specific references and additional information. It is an academically researched book, yet Rupp writes in a very entertaining and engaging fashion. Her sense of humour, suggested in the title, comes through on every page. Almost all chapter titles are alliterations, plus a small series of simple snippets suggesting several sidebars.

Rupp takes us on a historical journey reaching back to Neolithic times and the original cultivation of the vegetables. We visit the gardens and kitchens of ancient civilizations such as the Egyptian, Roman, Aztec and more, and move into modern genomics and the introduction of new crops. As a Canadian, I found some of the cultural and historical references in Rupp’s book may be more familiar to an American reader. That is certainly not a big enough impediment to prevent me from highly recommending this book as a great read.

Click here for a complete list of the books I have reviewed.

Twitter Snips for May 16th, 2012

Wed, 16 May 12 16:30:00 UT

A day on the Internet sees enough information to fill 168 millions DVDs being sent around the world. We send 294 billion e-mails and you're reading one of the 2 million blog posts written every day. @GenomeAlberta and @mikesgene are just two of the 40 million people who view Twitter every day so this collection of Twitter posts is a very, very, very small bit of theinformation available to us each and every day.
However we choose these posts to share with based on the people and organization we have come to know on Twitter and who we feel can inform you and occassionally even entertain you.
The links are safe for you to view so be sure to check out a few of them - or take your chances on randomly choosing from the 200 million tweets posted in a day.

@BloombergTV Facebook will offer 421.2 million shares, meaning the social network could raise as much as $16 billion http://bloom.bg/JG8rZB #FacebookIPO

@bmahersciwriter Jeffrey Taubenberger found a new ORF in the 1918 influenza genome!? Amazing that genes could be hiding in a genome that small for so long.

@boraz All A'Twitter: How Social Media Aids in Science Outreach http://bit.ly/M8hZPp by @CaitlynZim #SITT #scio13

@Cambridge_Uni A new era for personalised medicine. http://bit.ly/K6yp6E

@DKFZ Turning on genes by a circuitous route http://bit.ly/KEWt5s

@dgmacarthur A personal look at the past, present and future of the Personal Genome Project by @genomicslawyer: http://bit.ly/JjOndm

@Disalmanac Today is National Chocolate Chip Day, the day we remember all the chocolate chips that died in the Great Cookie Wars

@GENbio We're all mutants now: http://bit.ly/ITSjQY

@genome_gov New Genome Advance of the Month: Harnessing the full 'omics potential of personalized medicine http://qoo.ly/3tkx

@genomicslawyer Jim Watson on his fav gene: "It’s the only gene I know whose very structure is an implicit biological message": http://onforb.es/IuMJd9

@gwardis Genome of melanoma an aggressive and frequently fatal form of skin cancer, sequenced. http://yhoo.it/JQE2Z9 #scichat

@HollyDunsworth How to rid the world of genetic determinists? DTC for all, imho. http://genotopia.scienceblog.com/151/genetic-determinism-round-up/

@IAmBiotech Ten-Year Study Demonstrates Safety of Retroviral Gene Therapy Using T-Cells http://bit.ly/K6Ttd9

@jranganathan Survey in PLoS ONE: "science outreach is a bleak prospect with limited room for improvement" - #scio13 is solution! http://bit.ly/KNfGiw

@Lynwhit Countdown to #AskPeter TweetChat Join at noon for CEO @PeterASinger on his report @gchallenges progress http://bit.ly/IMCKtv

@mkonnikova Great interview by @BoraZ on promoting the work of young science writers--but equally applicable to non-science http://bit.ly/K26rcb

@sciencemagazine What's a genome worth in the clinic? #SciTM http://scim.ag/Kiqk0r

@wellcometrust Maximising health benefits of genetics & genomics. Includes @WellcomeLibrary's Simon Chaplin on digitisation project. http://wellc.me/KO5fvc

Tweets came to you courtesy of these people and organizations:

Bacon and Eggheads with Steve Larter

Thu, 10 May 12 21:30:00 UT

On May 3^rd, Stephen Larter presented to the Bacon and Eggheads breakfast in Ottawa. The series brings together Parliamentarians with experts from across science and engineering to show off Canadian research. The prestigious forum is a unique opportunity for scientists to communicate important findings to an influential audience.
The series is organized by the Partnership Group for Science and Engineering which is an umbrella group of 25 + science and engineering organizations.
Stephen Larter is one of the Co-investigators in our Hydrocarbon Metagenomics Project.
Stephen spoke about " Alternate futures for the oil sands industry: from the age of steam to the age of biology" and here is an abstract from his presentation.

"Underground steam injection has made in situ recovery of oil sands bitumen possible, but it comes at a high cost. The boiling of water consumes energy and can create significant carbon emissions of its own. In the quest for a better extraction technology, researchers are now drawing inspiration from the abundant microorganisms that produced the bitumen in the first place. Our speaker will introduce Canada’s role in the biotechnological revolution driving this quest, and the likelihood of implications far beyond the oil sector. Stephen Larter will also discuss more generally current Canadian research in technologies to manage better the carbon footprint of the industry.

Dr. Larter is the Canada Research Chair of Petroleum Geology at the University of Calgary and the Scientific Director of Carbon Management Canada Inc.—a federal Network of Centres of Excellence. He has worked extensively on technologies for reduced emission recovery from oil and gas fields and novel schemes for capturing and sequestering carbon. Dr. Larter has co-founded several energy technology companies and has won several academic, commercial and civil awards including the Friendship Medal of the People’s Republic of China. He is a Fellow of the Royal Society and a Foreign Member of the Norwegian Academy of Science and Letters (Det Norske Videnskaps-Akademi)."

Genome Alberta Award Winners - Science Fairs 2012

Thu, 10 May 12 17:00:00 UT

Both the Super Bowl and the Grey Cup of Science Fair season are happening this coming week. The Intel International Science and Engineering Fair (Intel ISEF) will take place in Pittsburgh, Pennsylvania, from May 13 – 18. The Canada-Wide Science Fair (CWSF) takes place in Charlottetown, PEI the same week. Students who participate in the CWSF are called finalists since they qualify by already winning at their school and regional level. Students must already have been CWSF finalists to be considered for Team Canada ISEF. Only 18 students make up this team.

Genome Alberta sponsors awards in all 10 Alberta regions. Many of the Genome Alberta award winners will be representing their region with competitive projects at the CWSF next week. We support independent research project-based learning and we are very proud of the outstanding students who are recipients of this year’s Genome Alberta Awards.

Here is a list of the Genome Alberta award winners.

Alberta Central East Regional Science Fair

Madison LaClaire,
Nicole Larson

Calgary Youth Science Fair

Brenden Hiebert,
Ankita Saxena,
Sarah Hyslop

Canadian Rockies Regional Science Fair

Reed Godfrey
Sam Hendry

Central Alberta Regional Science Fair

Ward Marshall
Derrick Holsworth
Leah Brunner

Chinook Country Regional Science Fair

Aisha Lillywhite

Edmonton Regional Science Fair

Yusra Hagi
Aaima Azhar
Diana Bark
Neesha Persad

Kiwanis Southeast Alberta Regional Science Fair

Alishah Gangji
Karima Gangji
Surina Grover

Sci-Fusion – The Lethbridge Regional Science Fair

Quentin Golsteyn

Peace Country Regional Science Fair

Christina Petluk

Wood Buffalo Regional Science Fair

Monica Montgomery
Destiny Noble

Government and Social Media - Arlington

Fri, 04 May 12 03:15:00 UT

I was speaking at a Government Communications Conference in Arlington, Virginia today and as is often the case, I find the U.S. government take on communications to be more sophisticated than we generally see up here.
A bit of a surprise for Canadians who often see the elephant to the South trying for world domination at any cost. Okay, maybe that is the goal, but they sure won't achieve it with such an enlightened communications community. Whatever they may think of his policies or politics, Obama's call for a more transparent and open government seems to have been embraced at the individual, departmental and agency level. In fact at times my perception is that there was a sigh of relief from many government employees who believe strongly in what they do in their jobs and were just waiting for someone to tell them it was okay to talk about it.

Take the U.S. Department of Transportation IdeaHub for instance. Deb Green (@Deb_Green) led the development of the DOT IdeaHub program taps://www.dotideahub.gov or http://www.nextgov.com/technology-news/wired-workplace/2010/08/dot-launches-online-ideahub/53643/ The goals were to give employees a voice, engage them, acknowledge their efforts, and give them a place to collaborate. What started as a more limited FAA initiative grew into a DOT wide program.

Captain Joseph Smart (@capster9) from the U.S.Navy Medical Department pointed out that U.S. Navy Medicine is a $6 billion dollar healthcare network covering 63,000 people around the world. They use many aspects of social media for internal and external communication and re-purpose material across print, e-mail, social media and other channels to get the most bang out of every communication buck. He showed that 50 tweets via @NavyMedicine reached 63,000 people, and as many people in the room picked up on, also noted that content is king in making that happen. I've been on the speaking roster with Captain Smart before (sorry, may never be able to call someone Cappy!) and the openness that the U.S. Navy approaches their communications with never ceases to amaze me. As he also pointed out, they can't control the sea of public opinion but they can at least navigate it.

Donna Berry from the National Institutes of Health walked everyone through how the NIH is using Yammer http://yammer.com as an internal communications tool. It started as a skunkworks effort led by Donna and Sandra Scarbrough. Though Donna never came right out and said it, there seemed to be an element of do it and ask for forgiveness later if it didn't work. But it has worked and though it is still is considered a pilot project, the Facebook-like interface of Yammer has more than 700 NIH users, 4,000+ messages and 695 search queries.

The 2 day Advanced Learning Institute event also had speakers from the Centers for Disease Control, the FBI (sorry I wasn't able to catch that presentation!), the Smithsonian, the National Cancer Institute and a few more U.S. agencies and departments.
Canadian government organizations have come a long way in the last few years in their use of online tools and some of the efforts at a municipal level can hold their own on the North American stage. In general though we're still in a world where controlling the message is the primary goal. The wheels are turning over slowly but we are moving in the right direction. We'll see if we can catch up to the social media behemoth to the South.

Twitter Snips for May 2nd, 2012

Tue, 01 May 12 05:30:00 UT

Half a billion registered users who post in the range of 175 million tweets in a single day. It is now safe to say that Twitter has become more than an oddity when it comes to communicating online. It is well established and is probably here for some time to come. It is used in business, public relations, entertainment, education and just about any other sector or interest you can think of including science.
For an introduction to how you can use it in science you should check out this blog post from the ‘Happy Science’ blog. It will give you some good tips and ideas, and if you want to know what makes for a good tweet, the Harvard Business Review has some ideas for you.
Every 2 weeks we share some of the Tweets that have come to the attention of @mikesgene or @GenomeAlberta .
Check the tweetsm check the links, check the people and organizations behind the posts. Get to know Twitter and how our life science community can start to put it to use.

@agapow Comparing benchtop sequencers - Ion Torrent so-so, MiSeq best (unsurprising): http://bit.ly/IekQzI

@AudacityInc An App Store for Genomic Tools? It's Happening. http://onforb.es/JlFnSJ #genomics #genetics

@bigs I love that @geochurch talks about solving infectious diseases at a time most geneticists only look at 'genetic' disease. #GET2012

@bmahersciwriter Neat MT @Duncande: There are 120 people with complete sequenced genomes in this room at Harvard. A record? #get2012

@C_G_S @MaraHvistendahl's book "unnatural selection" is a finalist for the pulitzer! http://www.biopoliticaltimes.org/article.php?id=6184 #biopolitics

@DNA11 Catch @ChiefSciAdvisor Sir Peter Gluckman's DNA Portrait at the #NewZealand Portrait Gallery's Art of #Science exhibit ! http://ow.ly/avnAu

@DukeIGSP California Genetic Privacy Bill Moves Forward http://bit.ly/Idf1Xq

@IAmBiotech Research & study could be a bit of fun ;) Ice Cream Headaches Might Offer Clues to #Migraines http://bit.ly/I5YiXt

@idtdna Metabolomics: the final frontier? http://ow.ly/aBmEQ #omics

@iihlab How far are we before pharmacists do on site chip enabled tox testing? #get2012

@LIFECorporation Members of the public get a sequencing lesson using Ion technology on the #ionbus in #timessquare. http://ow.ly/i/AryN

@martinwaxman What makes a tweet worth reading? Study findings. http://hbr.org/2012/05/what-makes-a-great-tweet/ar/1

@medethicsandme “Are we extending life or just prolonging the dying process?” http://fb.me/1ScgzrULt

@MountSinai Lunenfeld director Dr. Jim Woodgett awarded Diamond Jubilee medal for his leadership in biomedical research. http://bit.ly/InswTH

@phylogenomics Report: "How hungry microbes could revive old oilfields" Me: A bit skeptical http://shar.es/rFEIu

@ShipLives Interesting findings for those interested in social networks and higher ed: http://bit.ly/JWh1mJ #scio13

These 140 character posts come to you courtesy of:

Call for Session Proposals Canadian Science Policy Conference 2012

Mon, 30 Apr 12 15:45:00 UT

Call for Session Proposals: Canadian Science Policy Conference 2012

TORONTO, ONTARIO--(Marketwire - April 18, 2012) - Canadian Science Policy Conference (CSPC) 2012 is inviting members of the science policy community to submit proposals for the conference program Nov 5-6, 2012 in Calgary, Alberta. All submissions must be received online by end of day June 8, 2012.

This year's conference sessions will be under the following 4 themes:

Innovating on energy supply and demand for more sustainable resource management: a critical test for the integration of science, technology and policy

Re-imagining Canadian Healthcare: How innovation in science and policy can contribute to a more sustainable system

Food, Fuel and Farmers: Agriculture at the convergence of multi-disciplinary science policy issues

Science-Technology-Society-Nexus

A New Industrial Oilseed Crop to Be Tested as a Biojet Fuel

Fri, 27 Apr 12 22:00:00 UT

Saskatchewan’s Prairie Gold Project Takes Flight

A new industrial oilseed crop to be tested as a biojet fuel

FOR IMMEDIATE RELEASE
April 26, 2012

Saskatoon, Saskatchewan – Agrisoma Biosciences Inc., in partnership with Genome Prairie and additional partners have announced a world-first series of biojet flight tests. In collaboration with Canada’s National Research Council (NRC) and Honeywell UOP Inc., Agrisoma has initiated test flights using a biojet fuel blend that was derived from Agrisoma’s new Brassica carinata variety ResonanceTM .The ResonanceTM oil feedstock was blended with petroleum-based jet fuel. These test flights will demonstrate fuel performance and also measure in-flight emissions in real-time during multiple flight segments. The ResonanceTM crop used for the biojet fuel was grown in Kincaid, Saskatchewan in the summer of 2011 and is being commercially contracted on significant acres in western Canada for the 2012 crop year.

The technological development of industrial carinata from the field, to seed crushing, to initial biofuel refining was supported in part by the Genome Prairie led “Prairie Gold” project, a $4.5 million initiative which received federal and provincial funding. The overall goal of Prairie Gold is to translate genomics-based discoveries to develop and commercialize industrial oilseed crops that will allow synthesis of renewable alternatives to existing petroleum products. One of these crops, Brassica carinata (Ethiopian mustard) contains an oil profile that is highly suitable for biofuel production. Although carinata is closely related to the highly successful Canola crops in Canada, it is a non-food crop that grows well on marginal lands with minimal inputs; making it an ideal choice for industrial applications.

ResonanceTM offers a strong rotation option for southern prairie growers. Recently, Agrisoma and Paterson Grain have announced a long term partnership agreement for the commercial contracting and distribution of ResonanceTM, a name that reflects the new crop’s energy connection. Under the agreement, Paterson will be the exclusive contracting partner for identity preserved production of carinata energy feedstock in Western Canada, and seed will be distributed through Paterson outlets.

Agrisoma President and CEO Steven Fabijanski stated: “The support of Genome Prairie and the vision behind Prairie Gold have been instrumental in the commercialization of ResonanceTM. This is the first industrial oilseed selected for energy applications that has been commercialized in Canada, meeting the vision of Prairie Gold for the development and renewable alternatives for energy. The commercial roll out of the crop is targeting the southern Prairies, providing Saskatchewan growers with a new cash crop, opening the way for enhanced agricultural production and adding to the local economy. The unique genetic profile of ResonanceTM enables this production and the unique oil profile provides for enhanced efficiencies for biofuel manufacturing, highlighting how genomics and genomic discoveries contribute to opportunities in agriculture.”

“This is a major step for Agrisoma, and Genome Prairie is pleased to stand shoulder-to-shoulder with them,” said Genome Prairie CEO Wilf Keller, “We look forward to helping them improve the oil content and profile of their new carinata varieties and refine their processing technologies which will improve the performance of future biojet formulations.”

“The number-one priority of our Government is creating jobs, growth and long term prosperity,” said the Honourable Lynne Yelich, Minister of State for Western Economic Diversification. “Our support for this project is helping to strengthen both the agriculture sector and the aviation industry in Saskatchewan.”

“The research into renewable alternatives to petroleum products is creating environmentally friendly economic opportunities for farmers here in Saskatchewan,” said the Honourable Jeremy Harrison, Minister of Enterprise and Minister Responsible for Trade. “Saskatchewan is a natural fit for the industrial oilseed research and we look forward to Genome Prairie and Agrisoma’s continued success.”

Peripheral nerve regeneration project heading for Intel ISEF

Wed, 25 Apr 12 16:45:00 UT

In January, I was pleased to highlight Calgary student Sarthak Sinha. He had provided me with a link to the video where he was talking about his upcoming project for the Calgary Youth Science Fair. At the fair held last week, it was announced that Sarthak is one of the eighteen top high school scientists selected by Youth Science Canada to represent Canada at the Intel International Science and Engineering Fair (Intel ISEF) from May 12-19 in Pittsburgh, Pennsylvania. Intel ISEF is the world’s largest science fair.

Sarthak told me that he “believes Genome Alberta does an amazing job spreading the work of high school students”. In thanking him, I indicated that I would be pleased to see something about his Intel ISEF project. He immediately sent me the following video description: Potential of Schwann Cells – a look at peripheral nerve regeneration.

We wish him well in his endeavors in Pittsburg and know that he will be a remarkable representative of Canada’s best student scientists.

Amorifix Chief Scientific Officer Receives Genome BC Award for Scientific Excellence

Fri, 20 Apr 12 20:00:00 UT

NEWS RELEASE
FOR IMMEDIATE RELEASE

AMORFIX CHIEF SCIENTIFIC OFFICER RECEIVES GENOME BC AWARD FOR SCIENTIFIC EXCELLENCE

TORONTO, Ontario – April 17, 2012 – Amorfix Life Sciences Ltd. announces that its Chief Scientific Officer, Director and Company founder, Dr. Neil Cashman, has been awarded the 2012 Genome BC Award for Scientific Excellence. This award is presented annually by Genome BC to recognize individuals who have made outstanding contributions to the development of British Columbia’s life sciences industry across all sectors which are critical to the economic future of the province and country. Dr. Cashman will receive the award at the Life Sciences BC annual awards gala on April 19, 2012 in Vancouver, BC.

Dr. Cashman is an internationally recognized expert in misfolded protein diseases and the lead inventor of the ProMIS™ discovery technology which is exclusively licensed to Amorfix and being used to identify disease specific epitopes for new therapeutic targets. Amorfix recently announced success in developing antibodies that only bind and kill ovarian tumor cells but do not bind to normal ovarian cells, validating the value of the ProMIS discovery technology.

“We are very pleased to have such a creative force as our Chief Scientific Officer and we are grateful to him for the many contributions he continues to make to our development programs”, said Dr. Robert Gundel, Amorfix President and Chief Executive Officer. “With Neil’s scientific expertise and guidance, Amorfix is developing an innovative product pipeline of diagnostics and therapeutics that could significantly help patients and their families suffering from diseases such as ALS, Alzheimer’s disease and cancer. We congratulate Neil on this well deserved honour and award.”