Building Atoms with Arduino and Processing

BannerThis post is coming to you live from the Elephant & Castle Mini Maker Faire being held today at the London College of Communication.

The Atomic Arcade—an atom building game

The Atomic Arcade—an atom building game

The atomic arcade is an atom building game from Springtale funded as a science communications tool by the Institute of Physics. Whilst the game is still in early beta, it’s already made an appearance at the Dundee Science Festival.

I talked to Sonya Hallett—one of the people behind the intriguing game of proton smashing—about the game and why they brought it here to Maker Faire.

If you can’t make it here to the faire, you can also play the Atomic Arcade online.

The Elephant & Castle Mini Maker Faire is being held at the London College of Communication from 10am till 6pm. Entry is free to children (under 16) and students, tickets are £5 otherwise and available on the door.


Einstein's Workshop Showing Off Educational CAD Program

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Einstein’s Workshop, based in Massachusetts, has had enormous success teaching 3D design to children as young as 8 while getting them excited about math and programming.

Their secret?

They’ve developed an educational CAD program called BlocksCAD. The interface is easy for developing minds to grasp, with interlocking blocks and sliders, simple shapes, and quick visual 3D feedback to help kids learn the math concepts behind 3D geometry.

So they brought it to Maker Faire this weekend.

It’s also up on Kickstarter. Check it out, and give them some support.

But short term, head over to where the makerspaces hang out, just past the 3D Printer Village, and give BlocksCAD a try.

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A BlocksCAD screen, below.

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Popular at Public Lab

Out in Zone 5, Liz Barry of Public Lab is sensing strong interest in spectrometry.

The reason: “It’s like a Tricorder for $10!”

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Liz Barry of Public Lab

The Public Lab is a community where you can learn how to investigate environmental concerns.

Using inexpensive DIY techniques, Public Labs seeks to change how people see the world in environmental, social, and political terms.

And a good place to start: spectrometry.

“Because you can use it to tell what things are made of,” Liz says.

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The desktop spectrometer from Public Lab

Get out to Zone 5 and check it out!


Maker, Teacher, Blogger, Mom: Amy Oyler

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Amy Oyler has made homeschooling into a project, and homeschooling has made Amy Oyler into a maker. Her blog, The Scientific Mom, tracks Oyler’s hands-on projects as she teaches science to 8-year-old Kat. Amy started writing it to explain this whole homeschooling idea to friends and family, but it has grown in popularity as she has shared increasingly complex experiments and how-tos.

Amy always makes sure to share the science behind their projects, explaining that she’s careful to create a culture of research and correct information.

“I’ve raised my daughter with the idea that any question could lead us on an epic journey of exploration and discovery,” she says. “We’ve essentially decided that nothing is out of reach for us, if we have a question or a desire to learn something, there is bound to be a way to cultivate that somewhere.”

" After learning about pinball machines in Las Vegas, we came home and built our very own cardboard pinball machine," says Amy.

” After learning about pinball machines in Las Vegas, we came home and built our very own cardboard pinball machine,” says Amy.

As Kat has grown, Amy’s method has become one of collaborative discovery more than one-sided teaching. They reach out to scientists, professors, museums, and even hackers to learn about biology, chemistry, engineering, and physics. They built a biology lab in their home, and have a chemistry lab in progress. Kat visits museums, zoos, universities, science festivals, auto shops, makerspaces, and more, learning skills like bacteria culturing, soldering, 3D printing, and plasma cutting.

“Learning like this is fun because you get to do cool things like dissections, DNA extractions, and learn how everything works,” says Kat. “People in different generations talk to each other and share what they like to do, and can teach you all sorts of things.”

Kat may not be homeschooled forever, but Amy’s hooked on making, and has no plans to give it up.

“Making and tinkering gives us the ability to free ourselves from the binds of ‘I don’t know how to do this,’ and begin thinking more along the lines of ‘What do I have that I can use to make this?'” says Amy.


Launching $125,000 into space

The ISEE-3 spacecraft.

The ISEE-3 spacecraft.

With three days still left to go on their crowdfunding campaign, the hackers behind the Lunar Orbiter Image Recovery Project who wanted to recover the ISEE-3 spacecraft and return it to service, have passed their funding goal.

The project team is still looking for further funding however — another $25,000 — so they can use NASA’s Deep Space Network to range the spacecraft, and their crowdfunding campaign has been extended for another week to help reach that “stretch goal.”

Right now the team is waiting for the Space Act Agreement with NASA to be forwarded to the lawyers for final review — it should be signed in the next day or two — before proceeding. But at least at the moment they’re on track to make first contact with the spacecraft as early as the start of next week.

While the Morehead State University 21-meter dish will act as the primary ground station during the mission to reboot communications, until mid-July — when the spacecraft is within 2 to 3 million km of the Earth — it doesn’t have the power to establish a two-way communications link. The first attempt to contact the spacecraft will therefore be from the Arecibo Observatory in Puerto Rico.

Contacting the spacecraft as early as possible is crucial as every day that passes the ISEE-3 moves a quarter million miles (roughly the distance between the Earth and the Moon) closer to Earth, and each day that passes increases the the length of the burn — and hence the fuel — needed to make the necessary trajectory correction to position the probe into an orbit where it can produce some interesting science.


The Darwin Toolbox at the Edinburgh mini Maker Faire

Edinburgh Mini Maker Faire BannerThis post is coming to you live from the Edinburgh Mini Maker Faire—returning to Edinburgh for the second time—being held at the Summerhall here this weekend as part of the Edinburgh International Science Festival.

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There’s a huge range of makers here at the Edinburgh mini Maker Faire, from amateurs through to pro-makers, and even some professional scientists, and I talked to Philip Boeing from UCL about the Darwin Toolbox.

The Darwin Toolbox from Alasdair Allan on Vimeo.

The toolbox is an affordable biotechnology laboratory in a compact toolbox-size container that includes a centrifuge, a PCR machine and a gel electrophoresis unit with transilluminator, all of which should mean that you can be get started doing real DIY genetics at home.

The Darwin Toolbox should be coming to Kickstarter later in the year, so look out for that if you’re thinking you might want to get started with genetics at home, or if you’re a scientist that’s looking out for a cool toolbox to be used in the field.


Make: Books Author Takes Honorable Mention in SPARK Competition

EK01 Earth & Space Science Kit Prototype

Congratulation to Robert Bruce Thompson, author or co-author of many Make: Books, including Illustrated Guide to Astronomical Wonders, Illustrated Guide to Home Forensic Science Experiments, and Building the Perfect PC:

Robert Bruce Thompson (The Home Scientist, LLC; Winston-Salem, NC) has won an honorable mention in the prototype category of the Science, Play and Research Kit (SPARK) Competition, for his “EK01 Earth and Space Science Kit.” The competition, sponsored by the Gordon and Betty Moore Foundation and Society for Science & the Public, challenged entrants to create the equivalent of a new chemistry set for the 21st century. Winners were selected in two categories: prototypes – projects that are operational and demonstrable – and ideations – fleshed out project ideas that have not yet been developed into prototypes, but have a strong potential for development.

EK01 will provide the equipment, chemicals, specimens, and instructions for performing experiments in geology, hydrology, atmospheric science, astronomy, as well as environmental and plant science. The kit will require you to bring a few things of your own, such as a binocular or small telescope, pocket scale, and some common household items.

Thompson’s The Home Scientist already offers many great science kits to go along with Thompson’s books (including Illustrated Guide to Home Biology Experiments and Illustrated Guide to Home Chemistry Experiments). The photo above shows the tentative components of the new kit, but it’s subject to change. Keep an eye on the Home Scientist store for this upcoming offering.


Makerspace in the Classroom

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During my eight-plus years of teaching students in a makerspace-style environment, I have witnessed first-hand a surge of interest in problem-based curriculum from both our youth and their parents due to its ability to engage students and to help them retain the knowledge.

This is why the marriage between the classroom and the makerspace is so potent. It fills the gap between classroom theory and the physical world. Historically, sparse classroom budgets have been the root cause for a lack of modern equipment in the classroom. This made sense, of course, when an entry-level 3D printer could cost more then $20,000. Now, a derivative of the technology can be purchased with the proceeds of a single bake sale, or even through parent donation.

The beauty of the makerspace is its ability to not only inspire students, but to accelerate their knowledge intake through exciting and imaginative curricular application. In order to facilitate this, schools need to consider the design constraints imposed by makerspace equipment and how it might affect classroom layout.

(more…)


Blog from the Sea of Cortez: Useful Science?

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In earlier posts, we talked about our hypothesis: falling costs and accessibility of the tools needed for science and exploration are opening up a new opportunity for amateur explorers. Well, science and exploration are much bigger ideas than just the tools.   And it’s important we be honest about the entire process as we prepare for our trip to Cortez. For us, it didn’t start with a scientific hypothesis. It started with a curiosity, with the structure, explanation, and process modeled from there.

Mac Cowell, co-founder of DIYBio.org and Genefoo, has been spearheading the scientific portion of our trip. Here he gives an explanation of how we’re thinking about it, and how it’s coming together.

Enter Mac…

As David announced, we’re heading down to the Sea of Cortez in the 59-year wake of John Steinbeck and Doc Ricketts, who sailed the Sea of Cortez in a leisurely expedition of scientific discovery the 40’s: cruising around, philosophizing, and surveying the marine life of the gulf.

Like them, we’re going to sail Baja California in the same spirit of leisure and science. Only, we’re bringing robots, modern biotechnology, and the DIY spirit. Instead of collecting and cataloging marine macrofauna, we’re going to survey some of the genomes of the microbes that live in the gulf using DNA sequencing and metagenomics. Or at least we’re going to try. We want to put our tools to the test, and find out just how much is possible.

We’re not pioneering new scientific methods or trying to run a significant scientific study (Steinbeck and Ricketts were). When we started, we didn’t even have a hypothesis to test. As hobbyists and dilettantes, we just wanted to explore the sea of genomes surrounding us using some of the fascinating – and increasingly affordable – technologies pioneered by genomics researchers, and now makers.

Side note: We’re very aware of the legal and ethical issues surrounding this trip. That’s one of the main reasons we’re going: to find the boundaries and how they will affect citizen exploration. We care a lot about doing the right thing. The next post will explore some of those regulations and challenges. That said, please do let us know in the comments if you have comments, concerns, or research ideas.

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Metagenomic opportunities

There’s a lot of DNA floating around in the microbes in the ocean, and the vast majority of it has never been sequenced. A single droplet of sea water is estimated to contain perhaps 1-2 trillion bases of DNA spread amongst millions of microbes. There is much, much more when considering the rest of the marine ecosystem, magnitudes more when including viruses. Scientists estimate that perhaps only 1-10% of all microbes survive for study outside of their environment and can be grown under laboratory conditions, so being able to directly sequence DNA from an environmental sample can provide a more complete, while still biased, picture of the microbial members of a particular ecosystem (Gilbert 2011).

Some scientists are starting to rethink the very boundaries that delineate an organism – instead of treating each microbe as a complete individual, perhaps it makes more sense to consider spatially distinct but functionally connected communities of microbes as a single entity – a “meta-organism” (Zarraonaindia 2013).

Thinking about this notion of meta-organisms and using DNA sequencing to directly investigate the genes and genomes of communities of microbes are core aspects of a relatively new area of study called metagenomics. According to a recent review, metagenomics can formally be described as the field of research concerned with investigating the consortia of genes and genomes from a particular niche and asking “Who’s there? What are they doing? Who is doing what? And how is evolution driving this?” (Kennedy 2010).

Falling costs of DNA sequencing have resulted in explosive growth in metagenomics studies over the last decade. Perhaps one of the most famous was the Global Ocean Sampling (GOS) Expedition, led by showman-scientist Craig Venter, which collected samples of marine microbes via sailboat from 2004 to 2006 as it was sailed around the globe. In a pilot study conducted in 2003 with samples from the Sargasso Sea, the GOS team sequenced about 1 gigabase (GB) of unique DNA with shotgun Sanger sequencing and discovered more than a million new genes. Many more were discovered and annotated during and after the main GOS expedition.

Other studies have used metagenomics techniques to investigate the complex microbial communities of the human small intestine (to better understand human health), of the riverbed of an acid-mine drainage system (investigating new approaches to environmental remediation), and of a variety of marine sponges (searching for potential new drugs). A review of the field in 2011 by Gilbert & Dupont estimated that there had been about 45 major marine metagenomic studies since the mid-nineties.

Despite the advances in sequencing, it’s still only possible to sequence a small fraction of the DNA that can be isolated from a given community, so metagenomics studies are typically designed to selectively sequence the most informative fraction of DNA from the sample. The two designs are called Environmental single-gene surveys and random shotgun studies. To quote from that recent review on marine metagenomics,

“[Environmental single-gene surveys] can be seen as a directed, focused metagenomic study. Single targets are amplified using PCR and then the products are sequenced, providing an anlaysis of the range of different orthologs… for that gene within a given community.”

Random shotgun metagenomics is a study in which total DNA has been isolated from a sample then sequenced, resulting in a profile of all genes within the community. The community coverage of both approaches is entirely dependent on the depth of sequencing, that is, how many gene fragments are obtained during sequencing.”

So what approach are we going to take? We’re not sure yet. We’re still researching the typical protocols and costs (as well as legality) of both types of studies. You can check out our collection of literature on mendeley and suggest articles we should read. (For open-access introductions to metagenomics, check out this paper, this paper, and this review).

Some ideas: Could we design a single-gene survey to look for novel fluorescent proteins? I have no idea if there are conserved sequences amongst known fluorescent protein families that could be targeted by degenerate primers, but if that’s possible, then this could be a pretty cool little study – perhaps we’d find a new fluorescent protein!

At the least, we can do “classic metagenomics” and estimate the microbial diversity and population composition of several samples with DNA barcoding approaches. This would be another single-gene survey looking at 16s ribosomal DNA sequences and perhaps one or two well-known metabolic genes.

In addition, we could look at is how microbial diversity changes along with a particular environmental parameter, such as pH, temperature, depth, dissolved iron, nitrates, oxygen, or proximity to other organisms. We’re going to measure and record each of those with each sample we collect, along with GPS coordinates and photographs.

In any case, we’re going to try to do some basic metagnomics. I’ll be back after nailing down the specific methods we’re going to use – but essentially, we’re going to collect several samples of marine microbial communities, save their DNA for metagenomic analysis, take some microscopic images of the samples, and attempt to measure some of the environmental conditions of each sampling location.

I’m off to hit the books, and the hardware store.

Lab 1

References

Gilbert, J. a., & Dupont, C. L. (2011). Microbial Metagenomics: Beyond the Genome. Annual Review of Marine Science, 3(1), 347–371. doi:10.1146/annurev-marine-120709-142811

Kennedy, J., Flemer, B., Jackson, S. a, Lejon, D. P. H., Morrissey, J. P., O’Gara, F., & Dobson, A. D. W. (2010). Marine metagenomics: new tools for the study and exploitation of marine microbial metabolism. Marine drugs, 8(3), 608–28. doi:10.3390/md8030608

Men, A., Forrest, S., & Siemering, K. (2011). Metagenomics and beyond: new toolboxes for microbial systematics. Microbiology Australia, 32, 86–89. Retrieved from http://microbiology.publish.csiro.au/view/journals/dsp_journal_file.cfm?file_id=MA11086.pdf

Zarraonaindia, I., Smith, D. P., & Gilbert, J. a. (2013). Beyond the genome: community-level analysis of the microbial world. Biology & philosophy, 28(2), 261–282. doi:10.1007/s10539-012-9357-8


Building a Low-Cost Nanoscope with Lego and Makeblock

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Students at a workshop built a sub-$500 atomic force microcope out of Lego, 3D-printed parts, and Arduinos. Students from several schools participated in a five-day LEGO2NANO workshop [warning: link 502ing at the moment] where they built the microscope, which builds 3D images of nanoscale structures.

Using Lego allowed them to work on the working elements of the microscope without wasting time designing support structures. However, don’t discount the metal plates and beams visible in the photo. These are Makeblock, a relatively new (2011) aluminum building set with a lot to like about it.

Makeblock was a sponsor at World Maker Faire last weekend and exhibited some cool projects including an automated xylophone. The beams are very carefully designed and have the added bonus of having connector holes that align with Lego Technic beams, allowing projects like this which use aluminum for the support framework and plastic for holding components.

[via Wired.co.uk, photo credit: Alice Pyne]