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 .

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.

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.

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!

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.

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.

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.

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.

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.

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.

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 (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.

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.

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.

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.

Anyway, for those of you who have an annual tradition of putting together a gingerbread house, why not do it this year with a sustainability twist?

That’s right! our sister site’s own “Bake for a Change” is a contest where you, as the submission details say, apply sustainable building design practices to a gingerbread house.

Anyway, those details in full are presented here, and you can see last year’s entries by checking through this Flickr group. If you do check the flickr page out (and this highly recommended since it’s really cool), then you’ll note that we’re happy to see all sorts of entries, from the fun to the fancy. Seriously, winning really isn’t the point – it’s more about creative (and in this case, edible) ways to think about sustainable practices.

Mind you, as you can see from our last year’s winner (above), things can get pretty elaborate. Anyway, game on! Sounds like this year, we may even have some architecture schools on board, as well as some sustainability related highschool and university classes.

Dr. William Rees.
Professor, School of Community and Regional Planning.
October 24th, 2008
“It’s Your Experiment!” Science Teacher Conference.
Michael Smith Laboratories, UBC

Description: A 30 minute lecture looking at whether science is enough. And if not, what elements of human behaviour are dictating or thwarting our efforts towards a sustainable future.

Prof Rees’ teaching and research focus on the public policy and planning implications of global environmental trends and the necessary ecological conditions for sustainable socioeconomic development. Much of this work is in the realm of human ecology and ecological economics where Prof Rees is best known as the originator of ‘ecological footprint analysis.’

This workshop aims to teach environmental and social responsibility while exercising student empathy by having students write letters from the point of view of inanimate objects or animals. Coincidentally, good writing habits and understanding of narrative techniques are developed in the process (but don’t tell them.)

Who cares about the ecosystem? It’s boring. And it just sits there.

It’s quite undeniable at this point: we’ve messed up the Earth pretty good in our time here so far. There’s carbon in the air and chemicals in the ocean. Animals are going extinct and the planet is heating up like a big toaster oven. How did we ever get so terribly out of touch with the Earth and our terrible impact upon it? Well, it’s not that we don’t care…it’s just that…well…it doesn’t affect us.

If that’s true, what could we do to put us, and others, in touch with the Earth? Clearly running outside and rubbing dirt on our faces is not the answer. Then what are we to do?

I can’t hear you!

Maybe we’ve been so neglectful simply because our planet, the ecosystem, and everything in it hasn’t been able to speak for itself! It’s hard to know someone is unhappy if they don’t complain, right? Perhaps if the ecosystem could tell us what it needed or more importantly, how it really felt, then we’d feel bad for it, have more empathy for it, and take better care of it in the future.

Fiction writers have been using this trick for years: Anna Sewell wrote her book Black Beauty in the person of a horse and Barbra Gowdy’s White Bone was written from the point of view of an elephant thus creating all kinds of empathy and understanding for these, and all animals, in the minds of young and old. The old cliché: To know someone, you have to walk a mile in their shoes, is a cliché because it’s true. The reason fiction is fun is because you get to be someone else for a while, feel what they feel, think what they think.

Envelopes everywhere.

What if you were on your way to school and you found a tiny envelope on the sidewalk. You opened it and discovered it was from a squirrel who lives in a tree on your block. What would the letter say? Is the squirrel happy? Does it like people? Or does it simply tolerate them, counting the laborious seconds until people are extinct and the squirrels can finally take over?

Letter writing also has a long history in literature: writers such as Alice Munro, Dave Eggers, Nikolai Gogol and Jonathan Safran Foer have used the technique with hilarious and heart wrenching results.

So. What if everything on Earth, each part of the ecosystem, had the ability to write a letter? What would those letters look like? What would they say? Would they change how we and others thought? Could they? Let’s try.

The Fun Part – Writing Your Letter.

The first thing to do is to decide who your letter is from. Who (or what) are you going to be while you write. You could be an animal, like a cricket, a parakeet or a muskox, Or you could be a thing,something nice like the ocean, clouds or a forest, or even something nasty like plastic, crude oil or gasoline.

It can be anything you’d like. Just try to pick something you imagine has a lot to say (be it good or bad) but just hasn’t had the chance (or the writing skills) to say it yet.

The letter can be a one-pager or longer if you find yourself with lots to say.

Some things to think about while you are writing:

• Who is it addressed to? This is important. Do you talk the same to your friends as you do your parents or teachers? No? Good. In writing (especially letter writing) you have to know your audience. So your letter could be addressed to the Prime Minister or your best friend, it could be a letter that’s going to be read to everyone on the planet in every language all at once or one that only one person is supposed to read. It’s up to you.

• This person you are sending the letter to, have you met this person before? If so, where? How long has it been since you last spoke? What has happened to you since then?

• Why are you writing? To ask a question? To transmit information? To get something? A job? Some money? Or are you trying to scare them? Or warn them of danger? Or is it all of the above?

• What do you think is important for the person to know about you? What do you do with your time, eat, think? How do you really feel?

• How will you end your letter? What ideas do you want to leave the recipient with? How will you sign your name? What is your name anyway?

This exercise can take up to an hour. You are allowed to write multiple letters or work on perfecting one. When finished, students have the opportunity to read their letters, or parts of them, to the class who will almost definitely meet them with applause, admiration, laughter, cheers and tears (if appropriate).

NOTES:(From left to right), [1] “Shrimpy’s New Home”; (shrimp names) Flipsy, Zippy; (smail names) Floaty, Gary, Boulder. [2] “Biosphere EJKKPPLF”; (shrimp names) Thumper, Jumper; (snail names) n/a; [3] “Schnomadome”; (shrimp names) John Doe, Boe Doe; (snail names) Roman, Yanderbin, Noma, Hair.

Some concern about floating snails (are they alive?). Amphipod counts could be low (~2 to 3 per biosphere). Water is cloudy due to oyster shell Calcium Carbonate.

NOTES: Order change [1] Biosphere EJKKPPLP, [2] Schnomadome, [3] Shrimpy’s New Home.

All shrimp look good No more snail “floaties.” Calcium Carbonate has cleared, so biospheres look quite pretty right now.

NOTES: Order [1] Biosphere EJKKPPLP, [2] Schnomadome, [3] Shrimpy’s New Home.

All shrimp still accounted for, and generally have increased in size by about 50%. Generally, they look happy and are still swimming happily around. Shrimpy’s New Home is fast becoming Snails’ New Home as it has a lot of new “baby snails.” Don’t see this so much in the other biospheres.

MOLECULAR BIOLOGY TECHNIQUES WORKSHOPS (SUMMER 2008 PROGRAM):

Now accepting registration
To register, please contact Dr. David Ng at db@interchange.ubc.ca

(1) ONE WEEK VERSION
Dates: July 21st – 25th, 2008
Price: CAN$1250 (does not include room or board)

Reviews and Testimonies
Can be found here.

INSTRUCTOR: Dr. David Ng
DESCRIPTION: This intense one week workshop will focus on a myriad of different techniques used in the molecular manipulation of DNA, RNA and protein. Primarily aimed at researchers who are new to the area, or familiar but require a quick updating. Procedures that will be covered both practically and theorectically can be seen in the table of contents of our lecture notes Note that there will be some modification to the content as we update our syllabus for the July session:

ONE WEEK WORKSHOP LECTURE NOTES (previous pdf lecture notes available):
(previous pdf for 1 week lab manual also available)

CONTENTS: (note that the order is due to experiments).

1.1 DNA: Your Friend.

2.1 GENOMIC DNA: What and Why.
2.2 GENOMIC DNA: Cell Lysis.
2.3 GENOMIC DNA: DNA Purification.
2.4 GENOMIC DNA: DNA Precipitation.

3.1 MORE ON DNA: Quantitation.
3.2 MORE ON DNA: AGAROSE GEL ELECTROPHORESIS.
3.3 MORE ON DNA: NUCLEIC ACID PURIFICATION KITS

4.1 Cloning: What is a Vector All About?
4.2 Cloning: Which Vector Should I Use? (Part 1)
4.3 Cloning: Which Vector Should I Use? (Part 2)

5.1 ENZYMES: Restriction Endonucleases (Part 1).
5.2 ENZYMES: Restriction Endonucleases (Part 2).
5.3 ENZYMES: Ligases and Phosphatases – The Jist.

6.1 Transformation/Transfection: Getting DNA into your host.

6.2 PLASMID PREPS.

7.1 PROTEINS: Your “High Maintenance” Friend.
7.2 PROTEINS: The Western Blot – Part 1.
7.3 PROTEINS: The Western Blot – Part 2.

8.1 RNA: Your “unreliable” friend.
8.2 RNA: Isolation and Purification.
8.3 RNA: Gene Expression.

9.1 POLYMERASE CHAIN REACTION – The Jist.
9.2 PCR – A brief tour of the reaction specifics.
9.3 PCR – A brief tour of troubleshooting options.
9.4 REAL TIME PCR.

APPENDIX A: Replication, replication, replication…
APPENDIX B: Hybridization and Stringency for Dummies.
APPENDIX C: A Selection from the Merck Manual.

LOCATION:
Located in the heart of the UBC campus, the Michael Smith Laboratories is a testament to the vision of its founding Director, Dr. Michael Smith. Under his leadership, a gifted team of young scientists were recruited. These scientists have gone on to develop internationally renowned programs of research and training. The second and third floors of the new building are dedicated to the research facilities of the former Biotechnology Laboratory. The Stewart and Marilyn Blusson Education Forum is located on the ground floor and is open to the public. The molecular techniques workshops are held in the teaching lab,room 105 of this forum.
(click here for detailed directions)

REGISTRATION DETAILS:
Registration is essentially through first: an email inquiry for space (db@interchange.ubc.ca), second: a verbal commitment and then third via payment. Your place is essentially secured with payment, which more or less equates to a first come first serve mechanism. This payment would be a CAN$1250 cheque (or equivalent) payable to “The University of British Columbia” and sent to

Dr. David Ng
Michael Smith Laboratories
301-2185 East Mall,
University of British Columbia
Vancouver, BC, CANADA V6T 1Z3

If you prefer us to send an invoice, please let us know and we can arrange that accordingly. Note that we can accommodate a maximum of 16 clients, but on occasion up to half of these spaces are already reserved for predetermined group clients. Therefore, it’s best to put your name down as soon as possible if you are interested in the workshop.

REFUND POLICY
Your spot in the workshop is secured when we receive your payment. The deadline for receipt of payments is 3 weeks prior to the workshop start date. Unfortunately, we are unable to issue any refunds after this deadline has passed.

DAY TO DAY SCHEDULING DETAILS:
Workshop will begin each day at 9am sharp and usually end around 5:30pm. A detailed final schedule and syllabus will be released to clients as the date draws nearer.

MATERIALS:
All paper materials will be provided on the first day of the workshop. Downloadable versions will be available a week before the workshop begins. Whilst we do not require the clients to “study” these documents, we do ask that clients take a moment to peruse the first day practical materials. Please also bring a lab coat – if one is not available, please let us know and we will make arrangements accordingly. All other safety gear is provided at the workshop.

ACCOMODATIONS:
Here are some accomodation options that are basically on campus. Costs involved would vary (I think the most budget option would be the Vancouver Youth Hostel which is about a 15minute bus ride away). The closest would be those of Gage through UBC conferences. The others (except for point grey house) are all a relatively short walk away.

International Youth Hostel at Jericho Beach
UBC accomodations (on campus – note there are only 47 available)
St. John’s College (on campus)
Green College (on campus)
St. Andrew’s Hall (summer only)
Point Grey House (off campus, but only 10 minute bus ride away)

Alternatively, Downtown Vancouver offers a variety of accomodation options, but would entail about a 30-40minute bus ride each way. Depends on your preference since the Campus is pretty quiet at night time, whereas other areas would be more lively. Go to www.expedia.ca, and select:

hotel > near an attraction/vancouver > type in “University of British Columbia”

Usually the out of town clients make use of a little extra time after or before the workshop in visiting some of the sights Vancouver has to offer. I often strongly recommend this since the city and surrounding locale are really quite spectacular. In particular Whistler Blackcomb is a world famous ski/outdoor resort, and is only a 2 hour drive away. Ski season usually opens in mid November (click here for more info)