‘Fold it’- protein puzzles for everyone.

This blog post is a re-blog of the “‘Fold it’- protein puzzles for everyone” which was originally posted during 2013 on another blog site, which is no longer operational. 

Fold it is an invitation to participate in science everyday. You don’t need to be a biologist or even a scientist to participate in this ground breaking research. All you need is to enjoy puzzles and games.
What started as a way for researchers from the University of Washington to access the hard drive of home computers to help generate more time solving the possible protein folding configurations, has now developed into a very successful, crowd sourced science research project. You can read more about the history of the project here: http://fold.it/portal/info/about, and about some of it’s successes here: http://www.scientificamerican.com/citizen-science/project.cfm?id=foldit-protein-exploration-puzzle,
http://www.scientificamerican.com/article.cfm?id=foldit-gamers-solve-riddle and in a journal here: http://www.nature.com/nature/journal/v466/n7307/full/nature09304.html.
If you happen to be a biologist, you will be aware that proteins are one of the foundation molecules that make basic cell function possible. Peptides (sub units of proteins) are joined in various ways, following the instructions from RNA. There are many combinations of peptides which lead to different proteins and a range of different functions within cells and organisms. Now, if you happen to be a Biology teacher, Unit 3 and 4 of VCE Biology require students to develop a working knowledge of proteins, their structure and function. One approach to teaching such ‘abstract’ concepts is to use modelling.
There are many modelling tools available to help students conceptualise the structure and function of proteins, these include Toobers: http://www.umass.edu/molvis/toobers/, Cn3D:http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml, bio-molecular 3D explorer: http://www.umass.edu/molvis/bme3d/materials/explore.html, and many resources at the Protein Data Bank (PDB) including the archive of molecule of the month: http://www.pdb.org/pdb/motm.do;jsessionid=D608F408EC87F4494ED671924DD998B8. Fold-it is another tool we can tap into.
Fold-it provides an opportunity for students (and teachers) to be directly involved in ground breaking research. In addition this game may help to develop a better understanding of the rules and nature of protein folding. It is a wonderful example of promoting the use of real life applications within, and beyond, the classroom. It is also a great way of promoting skills like problem solving and collaboration. So, will you and your students come and play?
Until next time,
Fiona T

Blog link: Moving beyond ‘because I said so’ – motivation for thesis writing

I have spent the last few months re-writing my thesis. I feel like I am in a bubble with work and family life squashed in around my writing. This post, sent to me by one of my supervisors, resonates with thinking about ‘post-thesis’ life…something that seems very far away at the moment. It might be helpful for you too:

Source: Moving beyond ‘because I said so’ – motivation for thesis writing

Until next time – happy writing

Fiona T

The PhD and side quests

A while ago I read a tweet http://researchblog.iclon.nl/phd-side-quests-teaching/  likening various distractions (like teaching) to a side quest in a multiplayer online game. Even though I’m part time on my PhD and full time teaching, I find this tweet still resonated with me. At present I feel very stretched- full time academic teaching load, additional (short term) administrative role, part time PhD student, and Mum- it’s always busy and every minute is precious in each role. When I do have blocked time for my PhD analysis and writing I feel like if I am not writing actual words into a chapter that somehow I am not working effectively enough, then I realised I had to change my personal PhD narrative if I was going to do this to the best of my ability. Let me explain…

A few weeks ago I was up to day 5 of what would be a 2 week lack of motivation for my studies. I felt tired, overwhelmed and frustrated that this sacred writing time was being wasted while I looked up new references, read over old data and tried to re-envision my literature review while writing a data chapter. I was thinking about changing the chapter structure of the thesis to follow themes rather than data sets, this was going to be a huge shift. There was textas, A3 paper, muttering and scribbling. Mendeley was getting a workout as I uploaded and annotated more articles. I was busy, but didn’t feel like I was making progress visible to anyone else. I briefly considered walking away from the PhD- but am so close to being finished I know I would regret it. By day 5 I realised the truth- I was caught up in a side quest! As my thesis links to games, learning and aspects of motivation, I realised I was living the kinds of scenarios I had been researching for the last few years; what motivates a person to push past this point, where it all seems too hard to manage? I looked to my data, and my own personal side quests- my craft and other blogs. If you follow these blogs : one mad tatter and My WISE Dolls, you may notice that my whole life in recent years is chipping away at various goals over a longer period of time. It isn’t about being motivated to complete a project in one day, and my thesis is another such project.  I realised that I needed to be my own advocate, and so I gave myself permission to just be- to leave the actual writing of my chapter for a few days and go on a side quest of reading and thinking. This took me another week or so, but after this time I felt again in a position to edit and write some more. Last week I sent the finished chapter to my advisory group for feedback- and it felt like an epic win!

The side quest was an important part of the journey, of narrowing down the new articles to those that could be used to support my data and the unfolding story in my thesis. The ‘re-envisioning’ of the thesis was also deemed a side quest, confirming that the chapter structure I have drafted over the last 2 years will work better for my thesis than the one in my clouded mind a few weeks ago. While these two processes didn’t make a visible difference to my writing and work so far, they have helped me to think through my options and make firm choices on the direction of my thesis, and so this clarity of mind makes the side quest worthwhile in my opinion. The PhD is as much about the thinking, pondering and analysing as it is about the written submission. I need to wander down some of the pathways to realise they are dead ends. And, even if I don’t feel like writing, there are lots of tasks to to that will contribute in different ways to the completed submission.

Some side quests might be setting up fonts, highlighting relevant data, creating images and labelling figures- they are important small tasks that support the end goal. These are what help build the thesis from the ground up, and no one else can do it for me; I have to own the whole quest, not just the fun bits 🙂 I need to remind myself of the work I have been doing towards this since 2011, for all intents and purposes I have done the hard yards; the planning, considering methodological protocols, completing ethics for university and education departments, approaching schools, and building relationships with principals, teachers and students in order to generate data on site. I have the conceptual framework in place and have identified the gaps in the research my study seeks to contribute to. I have come a long way in my writing and thinking, been supported by a fabulous team of family, friends and colleagues and really love my topic. With less than a year to go until submission, I need to remind myself “I’ve got this!” 🙂

I still need to recognise that some side quests are time sinks, and wont be helpful in the bigger scheme of things for the PhD goal. For example, my WISE Dolls site is exciting and will be great, but it doesn’t need to be the focus of my energy this year, it will be waiting for me to pick it up again next year. The same with some of my tatting design ideas and goals, these too will wait until I am on the other side of thesis submission. In recognising these as alternate side quests I can more easily make a clear decision to refocus my precious PhD time to the side quests really need my focus here and now.

So, it seems the side quest metaphor works for me, here is a link to a paper about such metaphors for PhD work (McCulloch, 2013)  http://w3.unisa.edu.au/researcheducation/contact/documents/mcculloch-2013.pdf
or perhaps the Map for the PhD student graphic (MGSE, 2012) http://education.unimelb.edu.au/__data/assets/pdf_file/0011/621929/Map_for_the_PhD_Student.pdf might resonate with you. Whichever you decide, make sure you can identify for yourself what will be a productive use of your time, and keep your eye on the prize- that PhD 🙂
Until next time, happy questing
Fiona T
NB: It was also confirmed by my Wonderful Husband that this post is ironic- it was a side quest too. Now I have blogged it, it is completed [Achievement unlocked: 1084 words posted on PhD Blog] and I guess it’s back to the data for me 🙂

Books to promote STEAM ideas with kids

This year has gotten off to a rocketing start –  I have been working on my PhD and getting back into the swing of my working year. Over the December holidays I also launched my new site: My WISE Dolls. This site aims to curate and share resources to support children(7-15) to up-cycle dolls to make “Working In STEAM (Science, Technology, Engineering, Arts and Maths) Enterprise” Dolls. I have made under and up-cycled one doll: Mini Fi, the science teacher 🙂 The next one I will do is a Computer programmer doll for my Son.

Being a science teacher, I really want to promote opportunities for all children to access an understanding of what STEAM (Science, Technology, Engineering, Arts and Maths) careers/interests can be. One aspect of this is though books, and I have been amassing a small collection of books that claim to address aspects of STEAM for this age group.  The blog posts over the next few months on mypaperlessphd will be short reviews of these books.

The first book I will review is Nick and Tesla’s High Voltage Danger Lab by “Science Bob” Pflugfelder and Steve Hockensmith. wp-1455419545895.jpgThis book would suit children aged 9-12 years old, and has an interesting mystery storyline that keeps the pages turning. There are accessible activities for children to replicate- with assistance from their Adult at times.  The story is made up of one part real science, one part mystery, one part adventure and one part MacGyver! The children in the story, twins Nick and Tesla are sent to stay with their Uncle for the summer. Their adventure starts right at the airport, and we get a sense that these two are very resourceful characters. As the first book in the series it gives closure on the first mystery, and sets up for a longer story line that will unfold over the coming books.

Here is the blurb from the website:

“Nick and Tesla are bright 11-year-old siblings with a knack for science, electronics, and getting into trouble. When their parents mysteriously vanish, they’re sent to live with their Uncle Newt, a brilliant inventor.

But it’s not long before Nick and Tesla are embarking on adventures of their own—and engineering all kinds of outrageous contraptions to save their skin.

In Nick and Tesla’s High-Voltage Danger Lab, we meet the characters and learn how to make everything from rocket launchers and burglar alarms to mobile tracking devices and more. Science has never been so dangerous—or so much fun!”

To read an excerpt pop over to the webpage: http://nickandtesla.com/book-1-high-voltage-danger-lab/.  This book can be read alone by children, but would be a lovely one to read aloud together too. It is also available as an audio book. As the main characters are a boy and a girl, this is a book promoting that science is accessible to everyone. I recommend it highly, and have just ordered the next in the series 🙂

I wonder if you have a STEAM book you would like to review- or would like me to review. Please let me know through the comments below, or through the facebook page.

Until next time

Fiona T

*All opinions are my own, and are unsolicited. I personally purchase all items reviewed on this blog and have received no payment from any supplier for promoting their goods. I am a student/teacher/academic and have no personal business affiliation or business motive on this blog. Opinions expressed are my own, and are not necessarily endorsed by my employer.

Tinker tailor: up-cycling, problem solving and learning

This past week I was lucky enough to be able to run a ‘maker movement’ workshop with my students (who are adults training to be teachers 🙂 ). My inspiration came from the following sources, as indicated below in my blurb for the workshop:

The maker movement is gathering traction in the US and internationally: https://www.techopedia.com/definition/28408/maker-movement. It recognises the need to have young people explore technology by taking it apart, finding out how it works and redesigning the technology to make some thing new. There are strong Science, Technology, Engineering, Art and Math (STEAM) links here that we can harness in schools, either as part of formal curriculum, or as an extension/engagement opportunity. We will be deconstructing McDonalds toys (which can’t go to landfill) and up-cycling them to make artistic posters OR redesigning them to make a new toy/item- It is up to you. Examples: http://www.telegraph.co.uk/culture/art/art-news/7675915/Artist-builds-sculptures-from-circuit-boards.htmlhttp://www.sodapopgirl.net/art/disassembly/ and http://www.toddmclellan.com/commercial#5 .

The purpose of the workshop was for them to experience first hand the wide educational potential of an open ended invitation to up-cycle some old McDonald’s toys. Why McDonald’s toys? When my son, Little Tacker (LT) was younger we would have McDonald’s as a semi-regular treat, and very quickly accrued a pile of plastic single purpose toys. When he was about 5 I cleared out his room and found we had heaps, and the problem became how to dispose of them. The toys are plastic and often have batteries in them, meaning we can’t put them into the plastic recycling bins or landfill. So I finally had an opportunity to use them with a class and see how creative we could be.

Unfortunately many of these toys have (what I now know to be) Security screws that need a specialist triangular bit to undo them….and I had bought a few sets of small Phillip’s head and flat head screw drivers for my students to use- Whoops! Fortunately this was only a hiccup for a short time in the workshop and my students were able to problem solve and figure out different ways of opening the toys and re-purposing them. Below are some pictures of the ‘end products’.

Inside a clock work smurfThis was a clockwork Smurf toy- it ‘laid down’ and rotated on a ball attached to it’s feet and would intermittently turn to balance on it’s elbows, then go back to rotating on the ball. After much perseverance the student with this toy was able to break away part of the body and remove the cogs that performed the motion.  The two cogs had different arrangements of teeth which gave rise to the ‘intermittent’ movements we observed int he working toy. This lead to a small group discussion about one of the earliest forms of programming being the Jacquard Loom. A very interesting discussion that created curiosity and a few email discussions after the session too. Inside a pop up toy smurf

This student had a ‘pop-up’ present Smurf, and was able to reassemble her toy as a 3D item to display the inner workings.

Up cycled mobile

This student made a ‘superhero mobile’ – pictured flying over Melbourne 🙂 Upcycled ringA couple of students up-cycled their toys into Jewellery- Ninja Turtle rings anyone?

This workshop was great fun and highlighted an opportunity to engage students in a STEAM (Science, Technology, Engineering, Art, Math) experience. It also created a high level of cognitive engagement and curiosity in the group- me included! I have now found the screw drivers we need on ebay – so will source some before I run this workshop again next year. I would like to thank my students for agreeing to let me use photos of their creations and share their stories here too.

Until next time- happy tinkering.

Fiona T






Neural Knitworks- the maker movement and crowd sourcing meets Science week

This year I have embraced Neural Knitworks again, and with a more timely introduction for my students we have had a good response this year. Today I finished hanging our display in our Science Foyer, and am excited to share this with you. Thanks to the students and staff who contributed- one learning to crochet to participate! If you would like to see what is happening on a bigger scale, or participate- here is a link to the Neural Knitworks site- and it’s call to crowd sourced making to improve our understanding and skills 🙂

2015-08-21 11 36 02 neural knitwork wall

This kind of hands on project and modelling of Biology can be a welcome invitation for teachers and students alike to develop new skills and contribute to a community project. There are no-knit options too, so there are differentiated entry points for anyone willing to give it a try.  Oh- and it is fun too!

Until next time, happy crafting and making.

Fiona T

Games and toys that promote creativity and thinking (Part 6.1) More on Goldiblox

A quick update for you all:

Lately I have been thinking more and more about STEM (Science technology Engineering and Math) promotion in schools and homes with our Children. While researching STEM and girls education for an upcoming workshop I found reference to the Goldiblox game and the now growing company promoting a wider range of toys for children to explore STEM ideas in fun ways. I was really pleased to see expansion packs too, that could be paired with any of the games to provide the much needed extension I thought was lacking in the first game.  Here is a link to the store: http://www.goldieblox.com/ and a link to my original blog about the first toy in the series.   I wonder if you have any STEM toys/games you think are a valuable part of your classroom/home? Please feel free to share them in the comments below.

Until next time

Fiona T

*All opinions are my own, and are unsolicited. I personally purchase all items reviewed on this blog and have received no payment from any supplier for promoting their goods. I am a student/teacher/academic and have no personal business affiliation or business motive on this blog. Opinions expressed are my own, and are not necessarily endorsed by my employer.

Healing blade- a biology card game.

This story started in 2011, when I first read about the “Healing blade card game” From Nerdcore in this blog: https://drottematic.wordpress.com/2011/08/11/review-healing-blade-the-infectious-disease-card-battle/.    I began to search for this game, knowing it would probably be too advanced for the VCE (Victorian Certificate of Education- Year 12) course I wanted to use it for. Healing blade was developed for Medical students to use as a learning tool- and this is what intrigued me the most, the information within this game wouldn’t be “dumbed down” or incorrect. To me, accuracy is a very important aspect of any game I would want to use as a learning tool.

Unfortunately, the game had a small initial print run and it took me quite a while to find out about the kickstarter movement and track down the print and play version. Late last year I received the newest version of the downloadable file. I was impressed with the quality of the card fronts and really wanted to print these out on card stock for my classes to work with. The months flew by, and the printing of the cards was pushed on down the priority list. Then the sudden realisation that I need the cards for my class this week hit me! So, I have compromised and printed out my card set on a normal photocopy paper. I spent a couple of hours yesterday cutting up the paper cards and backs and sliding them into plastic card holders (Thanks MindGames on Swanston St for your help in sizing the right ones).

Sometimes the work of teaching is ‘making’ the resources 🙂

Healing blade pic for blog

Now the game is ready to play.

Along with 6 other Biology based games, Healing blade will be considered by my students this week, and critiqued as a possible classroom tool.

I hope, in the coming weeks, that I will blog about our impressions of each of the 7 games we will critique, so stay tuned 🙂 (or link the RSS feed to your email, so you don’t miss out!)

Until next time,

Fiona T


Re-blog: The Happy PhD Zone: How To Maintain A Work-Life Balance In Academia – Next Scientist

I recently read this post over at Happy PhD zone, and it made me laugh, and think about my priorities at the moment too. I am trying to balance my time on weekends to make sure I recharge and spend time with my beautiful family. The PhD and a full time teaching load make for very busy week days. So, this blog is worth a look 🙂

The Happy PhD Zone: How To Maintain A Work-Life Balance In Academia – Next Scientist.

Until next time,

Fiona T

Re-Blog: 7 Smart Ways To Use Evernote For Research As A PhD – Next Scientist

OK- I still Love, Love, Love Evernote. It is one of my 3 technology saviours for my PhD and academic work (the other two are Dropbox and Mendeley) Here is a blog I read a while ago with some great tips for using Evernote to better organise your research. They had me very early on with the comparison to a ‘swiss army knife’… read on and enjoy 🙂

7 Smart Ways To Use Evernote For Research As A PhD – Next Scientist.

Until next time,

Fiona T

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