Sweetie DNA and Schoolkids: Genes and DNA for Year 3s

I volunteer with the STEM Ambassador programme in the north of England, and in preparation for a talk / hands-on session I was giving at a local primary school last week, I went in search of visual aids for DNA. The main focus of the event at the school was helping the kids of three Year 3 classes build models of DNA out of sweets (as described in this Guardian article). Before we got stuck into the gummy bears and liquorice, I wanted to give them a short introduction to DNA. I had discovered a lovely pattern for crocheting DNA, which I followed the night before the event, which worked out great (you can see the results in my other blog post about the crocheted DNA itself). After asking them to pass the “DNA” around and take a look, I got started on my talk.

I used the slides below to give them something to look at while we chatted about DNA. Getting them to try to pronounce “Deoxyribonucleic acid” was hilarious for all of us and got them engaged in what I was saying from the start.

After giving them an introduction, I stopped at slide 7 and showed them the sweetie DNA that I had made with my son over the weekend in my best “Here’s one I prepared earlier” style. They were very excited to be using sweets to build their models – I hope they were allowed to eat them at the end of the day!

They were already sitting about 5 to a table, so we handed out enough materials that each table could make one model. The sugar phosphate backbone was strawberry liquorice with sherbet inside, and the As, Ts, Cs, and Gs were gummy bears. They all worked together really well. The gummy bears were very colorful but quite firm, so it took quite a bit of effort for the kids to push them onto the cocktail sticks / toothpicks. However, we had only one poked palm (that I was aware of) – the kids were pretty dexterous. The kids made beautiful models, and it was loads of fun helping them. They were quite keen to show us adults their handiwork, too. They were rightly proud of their sweet-based masterpieces.

Once they finished building their models, we had just a few minutes left, so I showed them slides 8 and 9, which talked about putting genes from one organism in another. I told them to imagine me tearing out a recipe for fluorescence from the jellyfish recipe book and stuffing it into a bacteria’s recipe book. Then, you could create fluorescent bacteria! Slide 9 is a picture of an agar plate of fluorescent bacterial colonies with a difference: the researchers had made a beach scene with them! So, I asked the kids to draw “bacterial colony”pictures with chalk on black paper. They loved that as well: volcanoes, cheetahs, eagles, sharks, and more. One scientific soul even drew DNA and the bacteriophage from slide 2!

The kids were engaged throughout, providing loads of good answers to my questions and asking fantastic questions themselves. I visited 3 different classrooms, and they all showed such an interest in science. 8 is a fabulous age – all curiosity and interest. Thanks very much to the lovely teachers and staff, and of course to the schoolkids; it was fun hanging out with you all! …and thanks for letting me use your pictures of my visit. Thanks also to the STEM Ambassador programme for both organizing this visit and providing the sweets!

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Adventures in Crocheted DNA

I made some crocheted DNA this week, and I was so impressed with both the free pattern I found, and the result, that I thought I should share my experiences here.

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I volunteer with the STEM Ambassador programme in the north of England, and in preparation for a talk / hands-on session I was giving at a local primary school, I went in search of visual aids for talking about DNA. I was already planning to help the kids of three Year 3 classes build models of DNA out of sweets (as described in this Guardian article), but before we got stuck into the gummy bears and liquorice, I wanted to give them a short introduction to DNA. (I go into more detail about the actual presentation I gave, as well as how the sweetie DNA turned out, in my related post on Genes and DNA for Year 3s.)

So, how do you make crocheted DNA? Well, I had a vague recollection of a DNA scarf pattern that I had come across some time ago (and you can try your hand at too), but I knew that would take too long to make. Also, it didn’t really have the 3-dimensional look I was going for. The scarf is gorgeous and scientifically accurate, but it isn’t much better than a drawing or a video from the perspective of the kids; it doesn’t show them the shape of a double helix.

My Googling then took me to the Wunderkammer blog by Jessica Polka, where she had posted this free pattern for crocheted DNA. It was another happy convergence (as was true with the scarf) of science and wool. You should all visit Jessica’s blog post as it goes into detail about how, if you’re right handed, you end up with a left-handed helix for your crocheted DNA if you follow her pattern. While I appreciate chirality, I went with the simpler left-handed helix for my work this week.

Jessica, however, went the extra mile and crocheted both left handed and backwards with her right hand! I admire her dedication, but I didn’t have that kind of time. I thought it might be useful for others to see the fruits of my labor, and provide a few helpful details on the pattern for others.

Firstly, the original pattern allows you to choose your own length of DNA, which is helpful. However, I had no idea how long it would end up, so for other people looking to make this pattern, I made an initial chain of length 50. As you can see from the picture at the top of the page, the resulting length of DNA was about twice the length of a crochet hook, or about 30 cm, give or take. Your work will be longer than that if you pull it tight (as the natural double helix shape contracts the length somewhat), and shorter if you have an 8-year-old squashing it as small as she can in order to mimic how the DNA is stored in the nucleus 🙂

An important note at this stage is that the pattern is American, and if you’re used to reading UK patterns please replace any reference to “single crochet” with “double crochet”.

After you create the chain and start on the single crochets, then you start to see the single spiral / helix forming:

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It’s really quite magical, and I don’t mind saying I felt weirdly happy watching the spiral slowly (but neatly) curl behind the active part of the work. However, I didn’t really believe the second row of single crochets would work as nicely as the first – I figured some fiddling would be required. However, even the second (and final) row spiralled neatly behind the “active site” (I know, I should have been a comedian! Ha ha), as you can see from this picture, where the completed (left-hand) double helix is on the right of the image, and the incomplete single spiral on the left:

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Finally, I didn’t tidy away the ends of the yarn on either side of the completed work as it 1) allowed for a useful place to hold the DNA while twirling it, creating a pleasing spin to watch, and 2) it was just about right to tie the ends together and make a circle of DNA should you so desire!

It only took about 30 minutes (including interruptions). I gave the DNA to the school at the end of the STEM event, as the kids seemed enthralled by it. The major and minor “grooves” were clear – clear enough that I was able to point them out to 7 and 8 year olds, who were able to understand the difference. I was also able to flatten it and show its similarities with the “ladder” diagram that I had up on a slide to show them how they were going to build their sweetie DNA.

Kids playing with Crocheted DNA
Kids playing with Crocheted DNA

I made it almost as an afterthought, yet it was so beautifully tactile when held and elegant when spun that the kids really enjoyed it. One girl in particular kept on spinning and spinning it, making the 30 minutes of my effort well worthwhile. I’ll definitely be making more whenever I run a similar event in future. Perhaps I should start making a full set of human “chromosomes”? But what colors should I choose for each one? Thoughts in the comments please!

Reloaded…Again…Again, or Memories of ISMBs Past

Who out there remembers ISMB 2009? If, like me, you need a refresher then take a look at the ISMB 2009 Summary and Highlights article that I wrote at the end of it. We all enjoyed Sweden, and had a lot of fun. Due to an increase in my family size by two over the intervening years, and a concomitant switch to part-time work, I haven’t been back to an ISMB since. Shocking, I know! I love conferences, and hope to start going again soon, but until then, take a good long look at my badge-based blast from the past, pictured on the right.

Were you carbon based or silicon based? Do you still have your badge? Please let me know!
Were you carbon based or silicon based? Do you still have your badge? Please let me know!

Now, I’m pretty sure that this badge came from the conference party at ISMB 2009. Please can someone confirm this though, as clearly 2009 is a Very Long Time Ago.

…Anyway, at least I remember the party! As we came in, we were each given a pair of sunglasses and had to choose a badge. Carbon-based badges were for people who had studied the life sciences before they came to bioinformatics, and silicon-based badges were for those with a Computing Science background. I chose carbon based as my undergraduate work was in Biology, although all subsequent study was in bioinformatics.

Anyone remember ISMB 2009 and have any experiences they’d like to share, especially with regards to this badge? Were there better parties at other conferences? I’m pretty sure Tainted Love came up at one point while a large proportion of the delegates were dancing. But then, I may be confusing my conferences. Hmmm, must take notes on more than just the lectures next time!

When three scientists walk into a primary school…

Last week I had another volunteer session as a STEM Ambassador with a local primary school. I was one of three STEM Ambassadors (as well as the lovely STEM coordinator Catherine Brophy) who spoke for an hour with a variety of Key Stage 2 children (anywhere from around 7-10 years old I think) about being a scientist. They interviewed all four of us about what it means to be a scientist, why it is fun/important, and more. When I wanted to speak a bit more about what it means to “do biology with a computer”, I referred occasionally to these slides I had made for a similar purpose a few years back:

The slides are full of pretty pictures (the notes to accompany these slides are also available on my blog) and they gave me a way to focus the children’s attention. However, the kids last week really didn’t need much focusing, and asked lots of great questions. They asked if I had invented anything (does inventing biological data standards count? I think so…!), who my inspirations were (my high school Biology teacher of course, among others), if I had any pets (slightly off topic!), and what my greatest accomplishment was (my thesis – phew!). They all seemed really animated, which is one of the best perks of going to a primary rather than a secondary school. I love the fact that secondary school students can handle more complex discussions, but the enthusiasm of primary school kids is just stupendous.

This trip to a primary school was very timely, as I had recently been to a parents’ meeting at my own son’s primary school about the change in the English school system away from levels. The head teacher was fantastic at explaining the changes, but one of the things I noticed about the new system was a seeming lack of guidance for schools in the science curriculum. It worries me that primary schools are being edged away from teaching science due to a large emphasis on English and Mathematics.

However, this is an issue that the STEM network can help solve. As ambassadors, we can come into your school and talk about science, how we became scientists, and why we love it. Last week it was three scientists talking, but the STEM network can provide experiments and other visual aids too, as well as helping schools enter science contests and fairs such as the Big Bang.

We had fun last week. We had a chemist (with a background in maths) who brought props: a cow bone, jelly babies, hair dye and other things. She asked the kids what the cow bone and jelly babies had in common (gelatin!), and quite a few of them knew. The other biologist had done field work with butterflies, and had the children imagine how you could mark or safely trap them. I talked about the structure of DNA (one child knew the comparison with a spiral staircase!), and how science was great because you don’t have to accept what anyone says “just because”. You don’t believe them? Test it! Science is imagination, testing, and reproducibility.

You don’t have to take my word for it “just because” I say it’s great – become a STEM Ambassador yourself, and test my statement that it is a completely awesome thing to do 🙂

Back into data standards with BioSharing

biosharing-logoBy the end of last year, I had finished my work with both Manchester and Newcastle. Happily, I’ve found a new (working) home with Susanna, Philippe and the gang at the OERC in Oxford. I’ll be working part time on the BioSharing.org project, and will be doing all sorts of things related to biological data standards, policies, and databases.

I have a history in biological data standards and in developing community-driven standard formats, checklists and ontologies. I look forward to devoting some time to this collaborative, integrative project, and to helping people structure and manage their data well. To finish, here is a little bit about BioSharing, taken from the website itself:

“BioSharing works to map the landscape of community developed standards in the life sciences, broadly covering biological, natural and biomedical sciences. […] As part of the growing movement for reproducible research, a growing number of community-driven standardization efforts are working to make data along with the experimental details available in a standardized manner. BioSharing works to serve those seeking information on the existing standards, identify areas where duplications or gaps in coverage exist and promote harmonization to stop wasteful reinvention, and developing criteria to be used in evaluating standards for adoption.”

Image from http://www.biosharing.org/pages/about/
Image from http://www.biosharing.org/pages/about/

A Pause in Posting

You may have noticed a pause in my posts (here, and on Twitter, and on G+ etc. etc.) – this is due to an 8 lb 15 1/2 ounce (4.07 kg) bouncing baby boy coming into our lives this past July 🙂 So my apologies, I do plan to post more about bioinformatics and ontologies in the near future, but as this is a work blog (and not a baby blog!) there will be a little break now. Normal service will resume, eventually!

The reason I'm not posting to this blog at the moment :)
The reason I’m not posting to this blog at the moment 🙂

PhD Thesis: Table of Contents

Below you can find a complete table of contents for all thesis-related posts (you can also get to the posts via the “thesis” tag I have used for each). Enjoy!

Thesis Posts

And, if you’re interested in how I performed the conversion, I’ve written about that too.