What to do on 12/12/12

From The Tree of Life Blog by Prof. Jonathan Eisen (UC Davis)

Doomsday Debunked! Featuring Laura Lege (ARC Astronomy): my notes from the Physics/Astronomy lunch lecture

Here is my summary and links for Laura Lege's ARC Physics/Astronomy lunch lecture last week (December 5).

Genomic and Biomedical Advances - SAGRudd paper.li

ARC College Hour: Project Kaisei and the Great Pacific Garbage Patch

On November 13 Margy Gassel from Project Kaisei was the guest speaker for ARC College Hour. She described her voyage to the Pacific gyre swirling with plastic debris and the dangers this poses for the ecosystem. Project Kaisei aims to develop ways to solve this tragic pollution problem in the Pacific Ocean.  Below is a summary of her talk.

Mole kitchen lab - that's mole, as in chiles and chocolate, not the Avogadro's stuff

This past three-day weekend I was in the mood for mole, with its chile spiciness calmed by sweetness. This recipe is adapted from Mark Bittman's Turkey in Almond Mole recipe with chocolate and some extra spices added.

Recipe procedure:

Remove stem and seeds from 5 mild dried chiles (I used Guajillo chiles). Soak chiles in hot water until softened . Remove chiles after soaking and save soaking water for use later in Mole sauce. Coarsely chop soaked chiles.

Pan fry in unoiled pan to toast:

0.5 tsp whole coriander seeds

0.5 tsp whole cumin seeds

0.5 tsp whole anise seeds

0.5 tsp whole peppercorns

Remove toasted spices from pan and allow to cool. Then grind spices.

Pan fry in unoiled pan to toast:

2/3 cup almonds

Remove almonds and allow to cool. Then chop almonds and set aside.

Chop coarsely 3 to 4 wedges of Ibarra Mexican chocolate (roughly 35-45 grams) 

Chop 1 yellow onion and 1 fresh jalapeno pepper and saute.  When onions are browned add 4 coarsely chopped Roma tomatoes and simmer until tomatoes are soft. Add chile soaking water as needed. 

Add chopped soaked chile peppers, chopped almonds, and chopped Mexican chocolate. Add chicken broth and/or chile soaking water to desired consistency. Allow to simmer until chocolate is melted. Add raisins and allow to simmer until raisins are softened.  Allow sauce to cool and blend until smooth consistency is reached. Add chile soaking water to adjust consistency if needed. (I use an immersion blender directly in the cooking pan with sauce). Adjust taste with honey and lime juice. We avoid salt in this recipe, but you can add salt as needed.

Then I follow Mark Bittman's recipe to cook the turkey thighs and simmer with the mole sauce.

Calling on Twitter for help with lecture prep

Prof. Jonathan Eisen @phylgenomics calls upon Twitter for help preparing a series of fungus lectures for a UC Davis Intro Biology (BIS002C) class. Prof. Eisen blog post Thank you interwebs: help proving fungi are cool

Science Writers 2012 - eBook - caught on Storify

The National Association of Science Writers (NASW) held their 2012 Science Writers Meeting in the Research Triangle, North Carolina. One of the participants, Keith Eric Grant, compiled the tweets from the e-book session into a Storify, shown below. 

My tweet to Rick Topinka got caught in the story line:

The full Storify:

Our comrade at UC Davis, Denneal Jamison-McClung, co-stars in GMO explainer video!

Denneal Jamison-McClung, the Associate Director of the UC Davis Biotechnology Program, and I have worked for more than ten years together in various biotechnology education projects for high schools and community colleges. So I was thrilled to see her in this new video about GMOs (Genetically Modified Organisms) from The Center For Food Integrity. Here's the GMO 101 video:



For more information about the video, Colleen Cecil provides a behind-the-scenes story in her blog Growin a Home.

Managing the social media deluge - storify

Managing the social media deluge - a storify from science writer Emily Willingham. She compiled the tweets from the NASW #sciwri12. 

For more information:

Science Communication and Social Media wiki

The official hashtag for the National Association of Science Writers session that inspired this wiki is #sciwri12deluge.

Emily Willingham's blog Words, words, words 

Organic tomatoes are killer tomatoes!

Yes, that's true - organic tomatoes are dangerous! If you think GMOs are deadly, compare them to what we know about organic tomatoes.

Thinking about the genetics of stupid - do mutations make you dumber?

David Dobbs writes about changing our genetic point of view on intelligence - instead of looking for intelligence genes, search for mutations that slow down normal brain development (aka the genetics of stupid)

His blog post: The Genetics of Stoopid in Wired Science Blogs | Neuron Culture (October 22, 2012)

His New York Times Science article: If Smart Is the Norm, Stupidity Gets More Interesting (October 22, 2012)

You can follow David Dobbs on Twitter @david_dobbs

NPR: Chasing Down Polio

Excellent three-part series last week on NPR: Chasing Down Polio:

Part 1 Wiping Out Polio: How The U.S. Snuffed Out A Killer

Part 2 Social Mobilizers Combat Polio In Pakistan's Slums

Part 3 With An Army Of Vaccinators, India Subdues Polio

MIT's Sherry Turkle, author of Alone Together, on our fear of conversation

MIT Professor Sherry Turkle was interviewed on NPR's Fresh Air,  and she explained why teenagers and adults now favor texting over face-to-face conversations. During her interviews they point out  that when face-to-face

you can't control what you are going to say, and you don't know how long it's going to take or where it could go.

But that's precisely the purpose of real conversation, to learn how to read each other's emotions and develop the give and take needed for a meaningful relationship. A danger of technology is that we are losing our ability to connect with one another.

Turkle explains that face-to-face conversation teaches

skills of negotiation, of reading each other's emotion, of having to face the complexity of confrontation, dealing with complex emotion.

From a different perspective, educator Steve Wheeler in his Learning with 'e's blog post notes:

When I share my slides and blogposts under a Creative Commons licence that enables repurposing, somewhere, someone has translated my content into Spanish, opening up a huge new audience for me in Latin America. None of this would be possible without social media.

Wheeler relates his experience to what Clay Shirky in Cognitive Surplus* emphasizes - social networking technology connects people productively:

When we use a network, the most import asset we get is access to one another. We want to be connected to one another, a desire that ... our use of social media actually engages.

Optimally, both face-to-face conversation and social media can be effective tools to connect and collaborate with one another. 

*Shirky, C. (2010) Cognitive Surplus: Creativity and Generosity in a Connected Age 

Pre-med student reality check

One of my former students, now at UC Irvine, reports on a conversation she overhears outside her organic chemistry class:

Oh my God, I totally thought I wanted to be a doctor because I watch all of those tv shows and stuff. I thought it would be really easy, but then I found out I had to take all of that science stuff. I was like, no. Why can't it be like 'Grey's Anatomy?'

The Story of Stuff - Allison Cook, Special Projects, at ARC

Allison Cook was on the ARC campus to talk about the Story of Stuff Project. Creators of one of the most watched environmental movies of all time, the Story of Stuff Project makes short, new media pieces that explore some of the key features of how we make, use, and throw away Stuff and the social and environmental impacts along the way. In addition to its movies, the Story of Stuff Project develops free, interactive educational resources and programs for everyone from teachers and people of faith to business and community leaders to support the learning and action of the over 250,000 members of the Story of Stuff community for a healthy, sustainable and just planet.

Learn more: The Story of Stuff website http://www.storyofstuff.org

Outreach: CareerGPS at Cal Expo

The North Valley Biotechnology Center team was at the CareerGPS event on October 10-11, 2012 http://leed.org/programs/careergps/

Follow-up to Seralini GM corn and cancer study

This post also appeared in my Wordpress blog

I posted my concerns about the Living on Earth segment on the new Seralini study linking GM corn to cancer http://goo.gl/uKI9v 

As a postscript, the European Food Safety Agency (EFSA) issued an October 4, 2012 statement rejecting the validity of the Seralini GM corn study. My perspective throughout this affair has been that this study should be approached with ample skepticism, and this new statement from EFSA validates my concerns.

The EFSA statement points out the concerns regarding Seralini's study

• The strain of rat used in the two-year study is prone to developing tumours during their life expectancy of approximately two years. This means the observed frequency of tumours is influenced by the natural incidence of tumours typical of this strain, regardless of any treatment. This is neither taken into account nor discussed by the authors. 
• The authors split the rats into 10 treatment sets but established only one control group. This meant there was no appropriate control for four sets – some 40% of the animals - all of whom were fed GM maize treated or not treated with a herbicide containing glyphosate. 
• The paper has not complied with internationally-recognised standard methods – known as protocols - for setting up and carrying out experiments. Many of these procedures are developed by the OECD (Organisation for Economic Cooperation and Development). 
• For a study of this type, the relevant OECD guideline specifies the need for a minimum of 50 rats per treatment group. Séralini et al used only 10 rodents per treatment set. The low number of animals used is insufficient to distinguish between the incidence of tumours due to chance rather than specific treatment effects. 
• The authors have not stated any objectives, which are the questions a study is designed to answer. Research objectives define crucial factors such as the study design, correct sample size, and the statistical methods used to analyse data - all of which have a direct impact on the reliability of findings. 
• No information is given about the composition of the food given to the rats, how it was stored or details of harmful substances – such as mycotoxins – that it might have contained. 
• It is not possible to properly evaluate the exposure of the rats to the herbicide as intake is not clearly reported. The authors report only the application rate of the herbicide used to spray the plants and the concentration added to the rats’ drinking water but report no details about the volume of the feed or water consumed. 
• The paper does not employ a commonly-used statistical analysis method nor does it state if the method was specified prior to starting the study. The validity of the method used is queried and there are questions over the reporting of tumour incidence. Important data, such as a summary of drop outs and an estimation of unbiased treatment effects have not been included in the paper. 
• Many endpoints – what is measured in the study – have not been reported in the paper. This includes relevant information on lesions, other than tumours, that were observed. EFSA has called on the authors to report all endpoints in the name of openness and transparency.

Rick Topinka's Seaweed T&L talk in Storify

Re: Living on Earth: New Study Links Genetically Modified Corn to Cancer

My tweet:









After listening to this Living on Earth segment I went nuts (and not in a good way), so I posted my concerns about this study:

This segment, unfortunately, downplays the serious concerns from many scientists about the validity of the Seralini study. Since the announcement of this study, countless articles have appeared to expose the scientific shoddiness of this research. I refer to two articles as examples:

In New Scientist http://bit.ly/SutEWB - a few of many concerns raised about the Seralini study:

• "the strain of rat the French team used gets breast tumours easily, especially when given unlimited food, or maize contaminated by a common fungus that causes hormone imbalance, or just allowed to age. There were no data on food intake or tests for fungus in the maize, so we don't know whether this was a factor."
• " Five of the 20 control rats – 25 per cent – got tumours and died, while 60 per cent in "some test groups" that ate GM maize died. Some other test groups, however, were healthier than the controls."
• In Forbes (in a special article by two recognized scientists) http://t.co/dPJBjpgh - a few of many concerns raised about the Seralini study:
• "the statistical methods employed were unconventional and appeared to be selected specifically in order to give a certain result. Tom Sanders, head of the nutritional sciences research division at King’s College London, called the treatment of data 'a statistical fishing trip.'"

And of special interest to your listeners...

• "inappropriate, unnecessary suffering of the rats, which should have been euthanized long before the tumors became so huge – an especially egregious ethics violation given that the study is, in any case, worthless."

There have also been concerns about how the Seralini team released their findings, in which they refused to allow journalists to show their findings to scientists before their release. This prevented a scientific expert review of the study before journalists published their news. Science writer Carl Zimmer has denounced this suspect practice http://t.co/H9nEF2EO

In addition, it should be noted that Seralini's earlier GMO corn study was discredited for scientific validity by the European Food Safety Authority (EFSA) several years ago  http://bit.ly/QCAZHt - this is particularly noteworthy since the EFSA is certainly no friend to GMOs.

You can review the numerous articles describing the concerns about the new Seralini study for yourself - the links have been provided by VeganGMO http://bit.ly/PBSzZv

Taken together, the new Seralini study should be approached with ample skepticism, a point of view not taken in this Living on Earth segment.