Sparks – Malta Genome Project

Hi and welcome to this post which is part of my series on the Sparks exhibition currently hosted at Esplora in Malta until the 2nd week of September 2017. You can read the rest of the series by viewing the Sparks category.

As the Sparks exhibition tours Europe, each host country also creates a local exhibit featuring a local example of citizen science.

In our case, Malta’s featured exhibit is about the Malta Human Genome Project.

Your genome is the list of instructions that tells your body how to build itself. There’s a copy inside every cell of your body, and it tells what colour your hair and eyes should be, your height, your gender, and lots of other things.

A person’s genome can also contain mutations (changes) that cause diseases such as breast cancer or thalassaemia. Unlike catching a cold, which is caused by a virus entering your body, these diseases are caused by “mistakes” in your genetic instructions.

The idea behind the Malta Human Genome Project is to create copy of a reference (typical) genome of a Maltese person, and then any other Maltese person’s genome can be compared to the typical copy, to see if there are any important differences. Spotting these differences can reveal a lot about a person, including providing clues about whether that person is vulnerable to certain types of genetic diseases.

The reference genome needs to be based on the Maltese population, because typical genomes are different in different parts of the world. For example a typical Maltese genome builds a person who is short with brown hair and eyes, while a typical Scandinavian genome builds a person who is tall, with fair hair and light-coloured eyes. Just as our physical appearance differs, so to the genetic diseases to which we are susceptible (for example the incidence of pernicious anaemia is relatively high in Scandinavia).

If a person has already been diagnosed with a genetic disease, then comparing their genome to the typical genome can provide clues about which particular genes can cause that type of disease.

The Sparks exhibition is all about citizen science, and the Malta Human Genome Project falls under citizen science because people can volunteer to contribute their genome to the project.

For example, there is a particular type of thalassaemia (a blood disorder) which is found in Malta, and it causes low levels of haemoglobin in the blood which greatly affects the person’s quality of life, because the current treatments can have serious side-effects. The MHGP researchers were able to obtain blood samples from members of Maltese families with a genetic mutation that causes high levels of haemoglobin, and they hope that this will lead to a potential treatment for thalassaemia.

Another focus of the MHGP is on heart disease, which is one of the top health issues in Malta.

At the moment it costs about €1000 to sequence a human genome, and the project has around 50 in its records – the plans are to eventually sequence up to 4,000 Maltese genomes, which is around 1% of our population.

The Maltese exhibition features a video showing one of the researchers using an app to compare a Maltese genome to the reference genome and look for differences. The video isn’t very easy to understand, and a crucial part of the recording is missing from the bottom (showing the reference genome) but it’s still very interesting and worth watching a couple of times.

The display case includes some information about the Malta Human Genome Project, and examples of materials and tools used in a genetics lab.

Blue loading dye used for electrophoresis.

There’s also a table where you can use origami to create a fragment of DNA, which twists around itself in a shape called the double helix. If you missed it and you’d like to try it out, the template and instructions are available online.

If you’re interested in DNA, don’t miss out on the Chemistry section in the top floor at Esplora, where you can join base pairs together and magnetically form your own DNA double helix! There’s instructions on the wall and don’t forget to look up at the ceiling to see a special pool noodle model.

July 14, 2017July 14, 2017

Sparks – Citizen Science – I Like Clean Air

Hi and welcome to this post which is part of my series on the Sparks exhibition currently hosted at Esplora in Malta until the end of August 2017. You can read the rest of the series by viewing the Sparks category.

In my previous post I wrote about Doreen Walther’s Mosquito Atlas in Germany, and how she’s using citizen scientists to perform data collection all over the country.

This story is also within the “Citizen Science” theme, only here we see Shazia Ali-Webber take it in a different direction, using citizen science as a tool for social and environmental activism.

Shazia is a solicitor who lives in London, and she became concerned about the levels of air pollution in her neighbourhood, especially since she has three young children, and young children are worse affected by pollution than adults.

Shazia and three kids waiting to cross a busy road. — Credit: Martin Godwin for The Guardian.

Everyone should have access to clean air. -Shazia Ali-Webber

She formed a group called “I Like Clean Air” – it’s made up of concerned parents (and their children) who live nearby, and they campaign for better air quality in London (which has very high, illegal levels of pollution) through measures such as reducing the number of diesel vehicles on the streets.

Unlike other groups featured in the Sparks exhibition, this group is not a citizen science group per se – however it uses citizen science as a tool, and that is how the group members became involved in air quality monitoring.

By plotting the results of their samples on a map, campaigners can gain valuable information. On a practical level, they can find out which are the most polluted areas and streets, and avoid them when travelling through the neighbourhood, such as when walking to school. The second important use for this data, is that is serves as proof to back up their complaints, so that they can’t be easily dismissed. It’s not enough to just gather data, you also need to turn it into information, and then use it to further your cause. This same approach can work well for other community issues too.

The members of Shazia’s air pollution campaign group also claim that they noticed that their children’s wheezing and coughing corresponded with spikes of air pollution and episodes of smog, and this has made them even more determined to campaign for better air quality.

Shazia uses different types of air monitoring devices to measure pollution. Here she is attaching one of them to a traffic light pole in the street. Many of the tools her group uses are provided (along with training) by professional scientists, which helps to ensure that the data is accurate (and can therefore be taken seriously).

Shazia on a stepladder attaching a monitor to a pole. — Credit: Angela Moore

Shazia’s group was helped by Mapping for Change, which helps community groups like this one to collect data and then map and analyse it. I Like Clean Air was responsible for organising the installation of diffusion tubes in many locations across their neighbourhood, and then sent the used tubes to Mapping for Change for analysis. Besides an air quality map, Mapping for Change also has a map for monitoring high noise levels, and another for street accessibility issues for people with impaired mobility.

Another monitoring device, which Shazia helped to develop, is called the BuggyAir, and it’s designed to hang from the handles of a buggy while a parent pushes their child around the neighbourhood.

A view of the electronics inside the BuggyAir. — Credit: Science Museum

The Sparks exhibition includes material used in Shazia’s campaigning for better air quality, examples of the monitoring tools which she uses to track air quality in her neighbourhood, and an interesting short film.

An exhibition display of Shazia's campaign materials.

Citizen science is not the main focus of Shazia’s I Like Clean Air group – instead their main push is a petition. However citizen science has an important supporting role, and this story shows how science and technology can be used both to have a terrible effect on our environment and quality of life, but also to help us reclaim what we’ve lost.

Are you passionate about improving the effect of human impact on the Maltese environment? Could a citizen science group help further your cause?

July 14, 2017July 14, 2017

Sparks – Citizen Science – Mosquito Atlas

The exhibition has three themes, one of which is Citizen Science. Well really that’s also the theme of the whole exhibition!

A sign saying "Citizen Science"

The idea behind citizen science is that anyone can ‘do science’, you don’t need to be a scientist. There’s a whole spectrum of citizen scientists – some are running huge science projects of their own, while others are much less involved but contribute in small but meaningful ways to science projects being run by others (who may or may not be professional scientists).

The first story in this theme is about Doreen Walther and the Mosquito Atlas. Doreen is a biologist and the head of a lab in a German agricultural research centre, and she set up the Mosquito Atlas project in 2012. There are two main parts to the mosquito project. The first part is to track what mosquito species are found in Germany, where and how many, and also see if they are carrying diseases. The second part takes place in the lab, and involves breeding different kinds of mosquitoes and studying how they can transmit diseases.

A mosquito researcher at work. — Credit: Angela Moore

In my previous post about Pieter van Boheeven, we saw how he is trying to crowdsource the discovery of a new antibiotic – he’s hoping that by having a bunch of citizen scientists looking in unusual places, they might find something new and useful.

Doreen is also tapping into the power of crowdsourcing, but instead of asking participants to look for solutions, she’s asking them to perform data collection for research. In this case, involving the actual collection of mosquitoes!

I work with the public to monitor dangerous mosquitoes. -Doreen Walther

Research scientists working on a project are often working with or for an institution (like a University) and are physically in one place, together. If the project calls for collecting data from various locations, then the researchers have to travel to those locations to do field work, and if long distances are involved, then that quickly gets expensive and uses up precious funding.

The Mosquito Atlas project gets around this by asking citizen scientists who are already in those locations to do the data collection instead. This is a lot cheaper than sending researchers on field trips all over Germany, and it also gives better coverage.

There are of course some downsides to this approach. One of them is that you’re asking people who are not researchers, or even scientists, to do something scientific, and they might get it wrong. One safeguard against this in Mosquito Atlas, is that all the identification and processing of the mosquitoes is done by actual scientists back in the lab – the citizen scientists just have to capture the mosquitoes and send them in by post.

What about the capturing though? Again, the Mosquito Atlas project addresses this by providing very clear instructions for mosquito hunters on how to capture mosquitoes without damaging them, and how to kill and ship them. Shipping costs must be paid by the citizen scientist, but in return, the project will reply back to the person via email, with information about the captured specimens.

A pile of envelopes and parcels of captured mosquitoes. — Credit: Mosquito Atlas

I like how the mosquito hunting guide also explains the scope of the project, and encourages participants to avoid “the senseless killing of insects” – instead, it explains, only capture mosquitoes, and that this is for the greater good (aiming to prevent the transmission of diseases by mosquitoes).

The Sparks exhibition includes a map showing some of the mosquitoes that were sent in to the Mosquito Atlas.

A map indicating mosquito captures. — Some of the Mosquito Atlas data.

I love the mini stories, such as how the date of a capture led to insight about a particular species being frost resistant, or how a family sent in no less than 20 mosquitoes caught while on holiday.

Mosquitoes preserved in plastic.

You can also view the actual Mosquito Atlas map online!

The children’s letters look adorable – citizen science projects like this one are a great way to introduce children to the concept of scientific research (and hopefully sow the seeds of life-long scientific interest).

Letters about mosquitoes sent by children.

The exhibition also features the Spanish smartphone app called Mosquito Alert, which people can use to report mosquitoes and send in photos of them.

Photos sent in using mobile phones.

We have similar reporting projects available in Malta – here’s your chance to jump in as a citizen scientist (and get the rest of your family to join in too!) Maybe you could even start your own…

Spot the Alien Fish

Spot the Jellyfish

Malta Biodiversity Monitoring Network

July 13, 2017July 14, 2017

Sparks – DIY Biology – Bento Lab

The first of the three themes in the Sparks exhibition is DIY Biology. In my previous post I talked about the ‘story’ of Pieter van Boheemen, who is leading a citizen science project to try to discover new antibiotics.

This story is about biochemist Bethan Wolfenden and designer Philipp Boeing, and their product the Bento Lab, which is an “all-in-one DNA analysis lab” containing the basic equipment you need for molecular biology projects.

Creating a DNA Laboratory

When it comes to doing your own home biology experiments, the main barrier isn’t education or having enough space – it’s access to affordable tools.

For DNA projects, there are three main processes you need to be able to do: extract the DNA from the cells, amplify (multiply) it, and then visualise it so you can analyse it.

To extract DNA from a sample, you need a centrifuge. To amplify your tiny sample into enough DNA to be usable, you need a PCR (polymerase chain reactions) machine. And finally, an illuminated gel unit will let you visualise your DNA. Find out more by watching this short video course on DNA Analysis at Khan Academy!

Buying the necessary machines commercially would cost thousands and thousands of euro to set up a lab, which is out of reach for most hobbyists and even most community labs.

In the previous Sparks story, we saw how Pieter van Boheeven dealt with this by creating home-made lab equipment (which is relatively cheap, but ‘costs’ a lot more in time and effort to learn, to find all the parts, and to actually build the equipment).

In this story we see a different approach, the creation of a budget version of very expensive machines, which has a small capacity (not great for a commercial lab) but a wonderful size (and price) for schools, community labs and dedicated hobbyists.

This idea of creating smaller, budget-friendly molecular biology lab equipment is not a new one – the OpenPCR has been around for years, for example (and the Bento Lab creators credit it as part of their foundation!). It currently goes for $500, and you build it yourself (takes a few hours). However the idea of combining PCR, a centrifuge and gel electrophoresis into one portable box takes things a step further.

Open Source – the way forward!

The reason why OpenPCR is called “open” is that it is open source, which means that the creators make the plans (and lots of info about it) available to the public, at no charge. Instead of keeping secrets, the results of their hard work is available so that other people can benefit too and go on to build something further, such as, yes, the Bento Lab.

The creators of Bento Lab acknowledge that they have benefited greatly from the knowledge that other people have shared with them, either directly or via open source projects, and they’ve said that they are also going to make some of their project available to the public, such as the software which runs Bento Lab, and the plans for making the parts (so that other people can make their own Bento Lab parts).

Idea to prototype to product to production

Bethan and Philipp started with an idea, talked to a lot of people, came up with a model, and then sought University grants and competition prize money to use to continue developing the project, starting off with just a few hundred pounds. The more they developed the project, the more investment they were able to get.

This is an early version of the Bento Lab – back then in 2013, it was called the “Darwin Toolbox”. Presentation is important – this prototype helped other people visualise what it would look like and how it could work.

A prototype Darwin Toolbox — Credit: Bethan Wolfenden

Fast forward two years to 2015, and the renamed Bento Lab is looking a lot more polished!

A photo of the Bento Lab. — Credit: Bethan Wolfenden

Bethan and Philipp used the kickstarter platform to raise money to fund their first production run. The idea behind kickstarter is that instead of having one or a few main investors who each contribute a large amount of money for you to get your company going, instead you invite the general public to crowdfund you, so you have many investors contributing small amounts. As an incentive, you offer rewards such as gifts or discounts. There are pros and cons to both approaches, for both the entrepreneurs and the investors.

Here’s the Bento Lab kickstarter video.

I also enjoyed watching this presentation by Bethan from last year, because she also shares how the idea came about, and how, through talking to lots of people while it was still only an idea, she and Philipp realised that their product would actually interest a lot more people in a lot more fields than they originally thought.

Their kickstarter updates make for a fascinating behind-the-scenes look at the process of moving from a prototype product to full blown production, which includes problems such as dealing with suppliers dragging their feet, and materials that don’t look like the sample did.

The version of the Bento Lab that you can see in the Sparks exhibit is a beta model, and since then they have continued to develop the product until now, in July 2017, they’re getting ready to assemble the first batch of finalised Bento Labs, and then start the main production run. Exciting times!

Sparks exhibition of Bento Lab

Are you interested in starting your own technology company in Malta or creating a new product? Have a word with the nice people at Takeoff, who can guide you regarding many aspects of this challenging (but rewarding!) process.

Here’s the rest of my series about the interesting stories in the Sparks exhibition.

July 13, 2017July 14, 2017

Sparks – DIY Biology – Crowdsourcing antibiotics

The first of the three themes in the Sparks exhibition is DIY Biology.

A metal sign saying "DIY Biology"

When I first heard the term “DIY Biology” I was surprised, partly because DIY is something I associate with physics, and partly because I tend to think of biology as something that just happens, not something a ‘normal’ person can change. So I’ve quite enjoyed exploring this new field.

There are two “stories” in this theme – one is about searching for new antibiotics, and the other is about creating an affordable DNA lab for schools, hobbyists and citizen scientists.

DIY Biology includes working with genetics and molecular biology, and it’s true that this usually involves specialised (very expensive) equipment. Through the two stories, we see two very different approaches – in the first story, Pieter gets around the problem by starting a community lab and building home-made equipment using cheap or salvaged parts, with cheap custom-made laser cut wooden housings. In the second story, we see Bethan and Philip set out to condense the basic equipment of a professional DNA lab into one portable unit, and embark on a quest to manufacture and market it commercially as entrepreneurs.

Like all the “stories” in the exhibition, each of these heavily features people, to emphasise that citizen science, well, starts with a citizen.

Pieter Van Boheemen

Pieter is very active in promoting free and open source technology for citizen scientists to use. He not only runs projects like a community biotechnology lab in Amsterdam, but he also runs lots of activities, events and courses to equip both ‘normal’ people and teachers to design, build and use biotechnology equipment.

This story in the Sparks exhibition talks about one of Pieter’s projects, which is trying to solve the problem of antimicrobial resistance.

Some bacteria are beneficial and even vital to humans (like the ones in our intestines), but some can make us very sick and even kill us. Antibiotics have been vital in fighting bacteria, but the bacteria are evolving and becoming resistant…

Pieter is leading citizen scientists in looking for new antibiotics in plants, using home-made (and therefore cheaper) microscopes, spectrometers and incubators.

I believe we can crowdsource a new antibiotic – Pieter van Boheemen

A hand-made microscope. — A DIY microscope made with laser-cut wooden parts.

Home-made lab instruments — Left to right: Microscope, spectrometer, centrifuge, incubator.

A guide to looking for antibiotics. — A DIY protocol for finding antibiotics.

The second story of the DIY Biology theme is covered in the next post in this series.

July 12, 2017July 12, 2017

SPARKS at Esplora

Welcome to the first post in my blog series about the Sparks project! You can see all the posts by viewing the Sparks category.

Sparks is a 3-year project about RRI (Responsible Research and Innovation). The idea behind RRI is that scientific researchers have a responsibility towards society, and that society (and ‘ordinary’ people) also have a responsibility to get involved in deciding the directions that research should take, as well as providing their own resources such as knowledge, effort and information.

So the main aim of Sparks is to raise awareness among European citizens that they can get involved with scientific research too, they don’t need to be scientists to do it!

The tagline for Sparks is “Beyond the Lab: the DIY Science Revolution”, because it’s mostly about ‘ordinary’ people doing science outside the traditional setting of an industrial laboratory.

There are two facets to the project. The first is a touring exhibition, or rather 4 identical exhibitions, which are travelling around Europe, visiting 28 host countries and spending two months at a time in each location. The second facet is the activities that are organised in that location during the exhibition visit, to have more engagement by members of the public.

At the moment, one of the exhibitions is installed in Esplora and will be there until the end of August, and there are indeed some activities such as these Science Espresso events where you have the opportunity to engage with scientists and give them your input.

I spent some time browsing the exhibition and I very much enjoyed learning about the featured projects.

The exhibition is divided into 4 sections; three themes plus an art installation. The themes are “DIY Biologists”, “Health Hackers”, and “Citizen Scientists”, and guess what, you could be a biologist/hacker/scientist too!

I left the exhibition feeling encouraged and inspired to be a citizen scientist.

Here’s a list of citizen science projects in Malta that you can join in with (or, hey, start your own!).

Spot the Alien Fish

Spot the Jellyfish

Malta Biodiversity Monitoring Network