On our Scoop It between July 2nd and July 25th

These are links from our Scoop It page between July 2nd and July 25th:

Frontiers | A Vision for 21st Century Agricultural Research | From Rich Jorgensen

from Richard A. Jorgensen, Guanajuato, México
Let’s admit an unfor­tu­nate truth: agri­cul­tural research in most of the world is based on old mod­els that no longer serve us well in the twenty-first cen­tury as arable land dimin­ishes, pop­u­la­tions increase, and cli­mate is chan­ging. A dra­mat­ic­ally new vis­ion is needed in order to remake agri­cul­tural research, per­haps rad­ic­ally, to address the chal­lenges of the world we find ourselves in today. Here is an attempt to begin to develop such a vision.

(1) We must learn to value found­a­tional (basic) and applied research equally.
(2) We need much stronger Foundational Research than cur­rently exists
(3) Applied Science must be reor­gan­ized around major concepts

(4) To repeat and extend the first point above (because it is so import­ant), suc­cess requires that we foster devel­op­ment of new cul­tures and new com­munit­ies that are coin­cid­ent with needs, not tra­di­tion. The needs for new com­munit­ies are many and varied.

To achieve this vis­ion will require us to let go of habits and pre­con­ceived notions in order to work toward under­stand­ing the diverse cul­tures and com­munit­ies that com­prise research, exten­sion, and industry and to find new ways of bring­ing them together pro­duct­ively and cre­at­ively in order to cre­ate syn­er­gies and achieve effi­cien­cies. The spe­cific ways for achiev­ing this vis­ion will be many and var­ied, and will require the cre­at­ive efforts of sci­ent­ists, engin­eers, fun­ders, industry par­ti­cipants, and poli­cy­makers everywhere.

Where should we start? Three prin­cipal areas need to be dra­mat­ic­ally reor­gan­ized: the ways that we fund research, the ways that organ­ize our research insti­tu­tions, and the ways that we define suc­cess and eval­u­ate pro­gress toward the goals above.

Funding pri­or­it­ies need to be dra­mat­ic­ally refocused.”

Promusa — Mobilizing banana sci­ence for sus­tain­able live­li­hoods | The ‘best gen­om­ics Venn dia­gram ever’ decon­struc­ted : ProMusa blog

“It didn’t take long after the journal Nature put online the art­icle on the banana gen­ome sequence for blog­gers to start com­ment­ing on the Venn dia­gram fea­tur­ing a a bright yel­low banana. David Ng at Popperfont qual­i­fied it as, “quite pos­sibly the most com­plic­ated (and there­fore awe­some) Venn Diagram ever”. Jonathan Eisen, the sci­ent­ist who coined the term phylo­ge­n­om­ics, said that it was “per­haps the best gen­om­ics Venn dia­gram ever”, while Joe, of the It’s okay to be smart blog wrote that it is “a pretty genius way of deliv­er­ing a bunch of banana data all at once”. He added that it was the first time he ever saw a six-way Venn dia­gram. Joe is right to be impressed, but the truth is that this is not the first ever six-way Venn diagram.

As a graphic designer cor­rectly noted, the dia­gram was inspired by Edward’s six-set Venn dia­gram. I can con­firm this because the bioin­form­at­ics sci­ent­ist who did the num­ber crunch­ing and the Venn dia­gram for the Nature art­icle is a Bioversity colleague.

It says a lot about the banana that its dis­tinct shape would make people notice an oth­er­wise arcane diagram. ”

Promusa — Mobilizing banana sci­ence for sus­tain­able live­li­hoods | Blogging your way out of anonym­ity : ProMusa blog

Blogging your way out of anonym­ity — ProMusa blog… There are some not­able excep­tions, but most sci­ent­ists only exploit one way to share their research res­ults: they pub­lish a paper in a sci­entific journal. And these papers often tend to be … well, let’s admit it … quite dry, as Adam Ruben recently described it in his blog post about “How to write like a sci­ent­ist”. Aside from the occa­sional present­a­tion at a sci­entific con­fer­ence (which, unless the sci­ent­ist is an espe­cially good speaker or presents ground-breaking res­ults, are usu­ally read­ily for­got­ten), most of us don’t take advant­age of the wide range of other media that are avail­able these days, such as videos, status updates, blog posts, blog com­ments, inter­act­ive graphs and maps, tweets, etc.

It’s a shame. These media can help sci­ent­ists reach a lar­ger and more diverse audi­ence much faster than the long slog of sub­mit­ting a paper to a journal.

Obesity pro­duces dia­betes epi­demic in India — ABC News Don’t equate devel­op­ment with Western diet

PHH com­ment: Don’t equate devel­op­ment with Western diet.

India is bra­cing for a massive surge in type 2 dia­betes, with cred­ible estim­ates put­ting the num­ber of suf­fer­ers in the next 20 years at more than 100 million.

via Cathryn Weller

The Phytophactor: Hot sum­mer garden point­ers

Gardening tips from the Phytophactor, includ­ing what to water and what to leave alone. 

Arabidopsis con­fer­ence tweets as stor­ify #icar #ICAR2012

The International Conference on Arabidopsis Research was held in Vienna, Austria July 3-7th 2012. As usual it was jammed packed full of inter­est­ing talks. here are all the tweets brought together.

The evol­u­tion of the banana, star of the Western fruit bowl LA Times inter­view

Did you hear? The gen­ome of the banana has been sequenced, an import­ant devel­op­ment in sci­ent­ists’ efforts to pro­duce bet­ter bananas.

The banana (Musa acuminata) gen­ome and the evol­u­tion of mono­coty­ledon­ous plants

Bananas (Musa spp.), includ­ing dessert and cook­ing types, are giant per­en­nial mono­coty­ledon­ous herbs of the order Zingiberales, a sis­ter group to the well-studied Poales, which include cer­eals. here the com­plete gen­ome sequence is ana­lysed in com­par­ison with other monocots.

Fascinating case study — sci­ence and polit­ics of non-browing “arc­tic” apples

This is going to be an inter­est­ing case to follow.


The sci­ence — Agrobacterium trans­form­a­tion used to intro­duce a silen­cing con­struct (derived from the endo­gen­ous apple gene) to switch off the four apple poly­phenol oxi­dase (PPO) genes. PPO pro­duces quinones, that upon cell dam­age non-enzymatically pro­duce brown, lingin-like com­pounds (more sci­ence here http://​www​.aphis​.usda​.gov/​b​r​s​/​a​p​h​i​s​d​o​c​s​/​1​0​_​1​6​1​0​1​p​.​pdf).


The articTM apples were developed by a small Canadian biotech com­pany Okanagan Specialty Fruits Inc. (http://​www​.okspe​cialty​fruits​.com/).


Here’s a sum­mary of some of the issues sur­round­ing these biotech apples (http://​applied​mytho​logy​.blog​spot​.ca/​2​0​1​2​/​0​7​/​c​o​n​s​u​m​e​r​s​-​s​h​o​u​l​d​-​g​e​t​-​t​o​-​t​r​y​-​f​i​r​s​t​.​h​tml)


The US Animal and Plant Health Inspection Service (APHIS) is soli­cit­ing com­ments about the peti­tion by OSF for the apples to be gran­ted non-regulated status. They say, “We are par­tic­u­larly inter­ested in receiv­ing com­ments regard­ing bio­lo­gical, cul­tural, or eco­lo­gical issues, and we encour­age the sub­mis­sion of sci­entific data, stud­ies, or research to sup­port your com­ments.” (https://federalregister.gov/a/2012–17144).


As of today, 54 com­ments have been sub­mit­ted, and they are avail­able for any­one to read (top right of the fed­eral register page, under the green button).


It’s a great learn­ing oppor­tun­ity for stu­dents, and chance for them to see and par­ta­icip­ate in the inter­sec­tion of sci­ence, policy, and pub­lic opin­ion. I would recom­mend ask­ing stu­dents to draft and share their own comments!



Welsh bot­an­ists cre­ate plant data­base

Botanists in Wales have cre­ated a data­base of more than 1,000 plant spe­cies which they hope will help with con­ser­va­tion and health research.


Ann Bot is a gestalt entity who works in the office for the Annals of Botany.