classroom

GENOMIC DNA EXTRACTION IS ABOUT THE PLAYING

By | archive, classroom, impressions

We are grand father-grand son duo emotionally intertwined like the two complementary strands of a DNA duplex. Unlike the weak H bonds in the biomolecule, our attachment is due to divine bonds strengthened by a friendship extraordinaire.

Farzaan, eight-year old grandson of the senior author, is a regular viewer of ‘Backyard Science’ shows on television. Some months ago he dared his grand father, a university teacher of plant cytogenetics to coach him perform molecular biology experiments in their home in Kolkata, India.

The kid had jeered at his friend-grandpa: “You bore me incessantly with your books and bla bla about ‘jeans’ (genes), ‘Diana’ (DNA), ‘rana’ (RNA). C’mon, shut up and play with me now”.

Grandpa couldn’t figure out the course of action; he didn’t want to distance himself with either Farzaan or DNA. Could DNA be a kid’s play, the Professor wondered! The oldie knew to perform experiments only in well-equipped labs! He was neither trained nor did he ever train his students for molecular experiments outside the laboratories.

It was a virtually impossible challenge for the professional cytogeneticist@ until he stumbled upon ‘The MacGyver Project: Genomic DNA Extraction and Gel Electrophoresis Experiments Using Everyday Materials’ [1] through a Google search of Do-It-Yourself (DIY) sites. “Oh, no that cannot be true”, was the professional’s first reaction.

He hesitantly tried the procedure and, it did happen. Wow, it could be play! He then, successfully extracted genomic DNA from a leaf of betel (Piper betle L.) known as paan chewed by many Indians including himself. Once successful with the MacGyver protocol, the present authors began playing the DNA game. Both were happy with the novel eduplay.

They found the MacGyver extraction procedure to be the most handy and amenable to home-kitchen experiments among several inexpensive protocols available online.

A bulb of onion (Allium cepa L.) is a preferred material for demonstration of genomic DNA extraction in most protocols. The duo thought of doing something different. They used an onion flower-bunch known as inflorescence instead and obtained a substantial yield of DNA .

Protocol

The experimental details are essentially and fundamentally similar to many other procedures already out there. However, items available at home and indigenous materials available in the local Indian market were used.

Procedure

All items i.e. material, brass mortar-pestle, Aquaguard®-filtered drinking water, Vim® liquid dish washing soap, propanol or ethanol, homoeopathic vials etc, were pre-chilled in the icebox of a refrigerator.

Onion inflorescences attached to long stalks were purchased from a local vegetable vendor. The spathe (leafy wrap around the inflorescence) was removed. Flowers were, then, scraped from the tip of the stalk and put in a brass pestle for grinding.

One teaspoonful of water and a pinch of Tata® iodised table salt were added to flowers. The flower tissue was crushed by grinding and pulverised to make a viscous solution.

Two drops of Vim® detergent were added. The mixture was stirred gently with plastic ice-cream spoon for a few minutes.

The mixture was carefully poured in to a homoeopathic vial. Isopropanol, the rubbing alcohol, was slowly poured in the vial with an injection syringe to avoid disturbing the tissue suspension. Bubbles started rising almost immediately and in about ten minutes the DNA-cloud was seen between the mucky stratum of tissue-salt-soap mixture below and the clear alcohol layer above. DNA did not float as expected.

Absolute ethyl alcohol was added in place of isopropyl alcohol in our repeat experiments taking due care that all other steps remained unaltered.

A fascinating result was obtained (see figure below). Three vials represent the stages of precipitation and floatation of DNA.

Epilogue

The duo embarked upon a series of genomic DNA extraction experiments with whatever uncooked live eatables they could lay hands on. The two generations, separated by 55 years, enjoyed every bit of what they did. It was another matter that each experiment left the home kitchen messier and the ladies angrier. It was play!

Both are now among the growing crowd of MacGyver Project-inspired scientists keen to wipe the psychological fear of Molecular Biology from the minds of all interested persons in homes, students in schools, young freshers in colleges and enterprising researchers in small-time developing laboratories anywhere in the world.

As well, the senior author has since standardized the protocol and has shown (in to-be-published work) that genomic DNA as obtained shows exact banding when electrophoresed alongside DNA obtained by standard ‘professional’ protocols and is of equal PCR quality. He is aware of the ethical debates about DIY Molecular Biology by anyone interested anywhere. However, he firmly believes that the outreach of Molecular Biology to outside of costly laboratories, as is the case with agricultural technology and information technology, shall attract billions of minds to understanding and application of New Biology to the well being of global citizens at low costs. He is including the inexpensive procedure in course curriculum and research project work of his current students. Good luck to all MacGyverites!

References

1. Yas Shirazu, Donna Lee, and Esther Abd-Elmessih (2009) The MacGyver Project: Genomic DNA Extraction and Gel Electrophoresis Experiments Using Everyday Materials. Accessed here.

About S.K.T. Nasar and S. Farzaan D. Nasar

S.K.T. Nasar is presently a Professor in the Department of Biotechnology of Bengal College of Engineering and Technology at Durgapur and continues to be an honorary Vice-President of Maromi Human Resource Development Society, an NGO, based in Kolkata. S. Farzaan D. Nasar is his eldest grandson. It was when he turned eight in 2009 that "grand papa" was challenged to play science with him.

DARWIN’S STRANGE INVERSION OF REASONING (VIDEO)
DANIEL DENNETT
JANUARY 14th, 2009

By | archive, classroom


“Darwin’s Strange Inversion of Reasoning”
(January 14th, 2009, Frederick Wood Theatre)

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One of Darwin’s earliest critics noted his “strange inversion of reasoning: in order to make a perfect and beautiful machine it is not requisite to know how to make it.” This is indeed a counterintuitive idea, but it is central not just to biology but to computer science and, indeed, all of science.

Resistance to this ‘strange inversion’ is at the heart of popular discontent with both evolution by natural selection and computer models of the brain and mind. It helps to understand some of the controversies surrounding theories of consciousness to recognize that some of the participants are “mind creationists” who cannot accept Darwin’s inversion when applied to minds.

Sponsored by the Canadian Institute for Advanced Research and the Vancouver Evolution Festival. Video filmed by the UBC Terry Project.

About Daniel Dennett

Daniel Dennett is a prominent American philosopher whose research centers on philosophy of mind, philosophy of science and philosophy of biology, particularly as those fields relate to evolutionary biology and cognitive science. He is currently the co-director of the Center for Cognitive Studies, the Austin B. Fletcher Professor of Philosophy, and a University Professor at Tufts University. Dennett is a noted atheist and secularist as well as being a prominent advocate of the Brights movement.

INTRODUCING THE PHYLOMON PROJECT! KEYWORDS POKEMON AND BIODIVERSITY

By | archive, classroom, creative, visuals, web experiment

(From http://phylomon.org)
(Facebook group: link)

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“When you have seen one ant, one bird, one tree, you have not seen them all.”
~ E. O. Wilson.

animalcard

Well 2010 is here, a.k.a. the International Year of Biodiversity, and to us at the SCQ, it means that we’re finally ready to go ahead with our long awaited phylomon project. Please repost, reblog, retweet, phone a friend – whatever you can do to spread the word.

WHAT IS THIS?

Good question. Well, it’s an online initiative aimed at creating a Pokemon card type resource but with real creatures on display in full “character design” wonder. Not only that – but we plan to have the scientific community weigh in to determine the content on such cards (note that the cards above are only a mock-up of what that content might be), as well as folks who love gaming to try and design interesting ways to use the cards. Then to top it all off, members of the teacher community will participate to see whether these cards have educational merit. Best of all, the hope is that this will all occur in a non-commercial-open-access-open-source-because-basically-this-is-good-for-you-your-children-and-your-planet sort of way.

WHY ARE WE DOING THIS?

Well, it was conservationist Andrew Balmford’s letter (Why Conservationists Should Heed Pokemon, Science. 2002 Mar 29;295(5564):2367.), published in Science, that provided the proverbial kick in the pants. Essentially, he did this eye opening study to show that children as young as eight had the remarkable ability to identify and characterize upwards of 120 different Pokemon characters. However, when the same rubric was applied using photos of “real” flora and fauna (animals and plants that lived in the children’s back yards) the results were simply horrendous.

“Our findings carry two messages for conservationists. First, young children clearly have tremendous capacity for learning about creatures (whether natural or man-made), being able to at age 8 to identify nearly 80% of a sample drawn from 150 synthetic “species.” Second, it appears that conservationists are doing less well than the creators of Pokemon at inspiring interest in their subjects: During their primary school years, children apparently learn far more about Pokemon than about their native wildlife and enter secondary school being able to name less than 50% of common wildlife types. Evidence from elsewhere links loss of knowledge about the natural world to growing isolation from it. People care about what they know. With the world’s urban population rising by 160,000 people daily, conservationists need to reestablish children’s links with nature if they are to win over the hearts and minds of the next generation.”

In effect, Andrew asked, “Can we do whatever Pokemon does so well, but with the reality of biodiversity and ecology providing the content?” With this brilliant seed of an idea, the folks behind the SCQ have been wondering whether the ideals of this thing called “WEB 2.0” can work towards Andrew’s suggestion. And with his blessing, we are now ready to pursue his idea full heartedly, optimistic that the good old internet, its social networking ability, and its often wonderfully active and engaged citizens will deliver something amazing.

animalcard

HOW WILL THIS HAPPEN?

Well, as we speak, a website is being carefully developed, but more importantly, it is being programmed using the nuts and bolts of the open source WordPress software and the remarkable image organizing prowess of Flickr. The idea here is that whatever template is produced, it will be relatively low maintenance to use and to look after, and that there will be ample opportunity for others to use it in their own locales, and for it to be tweaked, improved, for further use. If you’d like to see the initial layout for this website, you can download this pdf which includes the general logistics and rough design schematics. At this point, we are planning to launch the website at phylomon.org sometime in late February, early March 2010.

BUT WHAT CAN I DO RIGHT NOW?

In a nut shell, our first order of business is to drum up enthusiasm from the graphic design and illustration community. We’re actually hoping for something wonderful (and a bit viral) like the 700 Hoboes Project (another great web based art collaboration). In this respect, here are a few things you can do to help:

1. You can spread the word to as many folks as you can. In particular, any courting of the character design community to play would be brilliant, although any word of mouth is also greatly appreciated.

2. As images begin to come in, feel free to comment at the Flickr group site. It is this sort of feedback that will help guide our choices for images used in the actual cards. We’re actually quite curious what type of imagery will be presented (will it be ultra realistic, more character design focused, something in between, or a bit of everything)

3. Better yet, if you are an artist, or just someone who is intrigued, then do submit a picture. If so, here are a couple of things to consider.

FIRST: whatever image you provide, the copyright will still remain with you, the artist. What you agree to, is allowing us the use of the image in a non-commercial educational format specifically for the home printing/production of phylomon cards.

SECOND: the image you supply would only need to be given at relatively small dimensions (150dpi at 2.4 inches x 1.5 inches or 360px X 225px). This is done on purpose so that the small size of the image limits its usefulness for the more unscrupulous folks out there. As well, attribution and linkage to the artist’s personal website will be provided throughout the process. This way, if a viewer loves the artist’s image, and, say, wants to buy it full size, or wants to inquire if it’s available as a t-shirt, he/she will have the option to follow up on to the artist’s personal URL.

THIRD: Submissions will occur via a Phylomon Flickr group (links provided below). Full submission details (i.e. specific size of images and tags to include) can be found at the Flickr group pages. As we plan to incorporate a variety of communities in this project, we will start by creating three Phylomon submissions groups. One for the graphic design/illustration community, one for the photography community, and also one for the school community (i.e. kids and students can play too!). We do plan on initially focusing on the illustration elements (where perhaps reality can be embedded during gameplay – i.e. the card can do extra when coupled with a photo brought in by the child), but go ahead, check them all out below and submit away!

- Phylomon submissions (Graphic Design and Illustration Community)

- Phylomon submissions (Photography Community)

- Phylomon submissions (School Community)

FOURTH: It is hoped that a large repository of great images will collect over time. From these pools, specific images will be chosen for card production. This will involve our team contacting the artist for permission to include the image in the main Phylomon flickr account to create a “card queue” which in turn will be worked upon by a community of biodiversity scientists (graduate and undergraduate students, with some oversight from Faculty/Research Scientists) who will be assigned the task of providing scientifically literate content for each card. This content will also provide and inform logistics for gameplay design.

animalcard

Anyway, if you have any questions about the project please do contact me via email or twitter. I would love to hear feedback and your ideas!

Cheers
Dave Ng
Michael Smith Laboratories, University of British Columbia
Vancouver, BC, Canada (11/01/2010)

Big thank you to Randy Laybourne, Colin Moore, and Ele Willoughby for use of their awesome images; and, of course, to Andrew Balmford and his colleagues for the wonderful idea.

About thesciencecreativequarterly

THE RECEPTION TO DARWIN AND THE MYTH OF CREATIONISM

By | archive, classroom, textbook

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Presented on March 10th, 2009 at the Second Annual Most Exceptional Escapades in Science (This Time Also Darwinian) High School Student Conference, Michael Smith Laboratories, University of British Columbia.

About Keith Benson

Dr. Keith Benson is a historian and retired professor at UBC. “I became interested in biology as a result of a high school internship in a marine biology laboratory. While there, I also learned about the importance of the humanistic part of science, since the director of the laboratory was the editor of a book about seashore life, written by John Steinbeck’s closest friend, Ed Ricketts. These early interests are still part of my research career, thus emphasizing how important it is to become exposed to the sciences and the humanities.”

TERRY TALKS VIDEO: TIFFANY TONG – REDEFINING BOUNDARIES, URBAN AGRICULTURE

By | archive, classroom, textbook

(From Terry talks, November 22, 2008)

How often do we connect the words “urban” and “agriculture” in our brains? The word “urban” conjures up a concrete jungle where skyscrapers dominate the grey sky. The word “agriculture” makes me see rows after rows and fields after fields of green crops and livestock dotting the landscape. These words seem to be an unlikely duo to be integrated and be able to produce surprising benefits. But they do. According to the International Development Research Centre, 15% of all food eaten in cities world-wide is grown by city dwellers. Urban agriculture actually provides many who spend more than 40% of their income on food a much needed safety net. But we should keep in mind that by 2030, 60% of the world’s total population will live in cities. The costs and challenges of importing so much food into cities to feed the burgeoning population will rise exponentially. What would happen to food security, food safety, and other concerns?

I will lead the audience through a brief story of the global food system and urban agriculture intertwined with my own discovery of the importance of food. Growing up as a normal urbanite, I never gave the question “how my food reaches my lunch box” any deep thought. What made me change? Finally, I will offer the inspiring stories of best practices and victories of urban agriculture around the world, based on research I am currently doing for the NGO International Centre for Sustainable Cities. Of course, we must not forget the incalculable value the UBC Farm, the only working farm in Vancouver, provides to us urbanites.

One of my dreams is to see most of the lawns of Vancouver turned into productive edible gardens that reconnect people to their food, enhances food security, and makes our city more sustainable.

About terry

What is Terry? Terry is a website that aims to collect prevalent (as in academic, educational, or critical) as well as esoteric (as in creative, humourous, or surreal) pieces that look at pertinent global issues. Plus, it has a kick ass speaker series.