The Light Bulb PCR Machine

This clever device shatters the cost of current thermal cyclers and increases the accessibility of this integral piece of bioware. For less than $50, it could be yours.

Citizen Scientists have already begun to empower themselves and others by making biology more accessible. The first wave of change, it seems, is coming in the form of cleverly-built hardware – PCR machines, incubators and centrifuges made from materials one normally wouldn’t  think to employ.

A few weeks ago I struck on a 2002 publication by Brian Blais describing a working PCR machine he built using a light bulb as its heating element.

Ingenius.

Since then, it seems there has been no further development in this potentially revolutionary type of machine – so I decided to build one myself. I had almost no prior electrical experience, but I was willing to learn. If I was able to build this machine in less than a week, then you can too (and it will probably blow this one out of the water).

Using only Home Depot and Radio Shack products accessible to anyone, I built this PCR machine for less than $20. This prototype requires a $30 Arduino Uno to operate (which was already available), but the control system in future models can be scaled down to a much simpler circuit, an LCD screen and a few buttons.

I decided to use 4’’ PVC pipe and couplings for the enclosure because of the range of attachments available. The machine consists of three layers: the top is a 3’’ to 4’’ adapter with holes to house the PCR tubes, the middle is a coupling that holds the fan and light bulb in place and the bottom is a coupling that shelters the arduino and a safety switch. The 110V AC is wired with a simple two-wire connector.

The arduino monitors the temperature  by using a thermistor, basically a resistor that lowers the resistance the hotter it gets. The thermistor is wired in-line with a 5V potential and an analog input pin of the Arduino. The hotter the thermistor gets, the higher the potential flows to the input pin.

During a run, the thermistor is placed inside one of the tube holes. For more accurate readings in the future, the thermistor can be submerged in water and mineral oil inside a PCR tube.

The thermistor can be substituted for a more consistent IC temperature sensor, such as the LM335, in future models.

The schematic for the machine is extremely simple – due to the Arduino’s simple interface requirements, many hardware components can easily be subbed for software programming.

5V relays are used to control the fan and light bulb. These relays  can be switched on and off using the native output of the Arduino – no amplification required.

 

The entire control module could fit onto the arduino using a prototyping shield called the makershield. I programmed the arduino to control the relays and sense the temperature through the thermistor, then wrote some code to allow the machine to cycle through the three designated temperatures for the PCR reaction.

The machine cycles quickly – a standard 1KB run takes less than 2 1/2 hours to complete. I am in the process of testing the machine using PCR reagents, but given Mr. Blais’s success in the 2002 model I am confident it will work.

Instead of buying a thermal cycler for your lab, I encourage you to go out and build your own machine! This entire system took about $50 (+ a computer to program it) and less than 5 manhours to construct.

My arduino code and more details about the machine to help get you started are available RusselDurret.com.

Russell Durrett is a Research Specialist in Bioinformatics and Genetic Engineering in the Mason lab at Weill-Cornell Medical College and is a cofounder of GenSpace NYC, the world’s first community biology lab.

You can find this article and many more in Issue 01 of Citizen Science Quarterly

Open Wide – a case for open source medicine (pt1)

All that may come to my knowledge in the exercise of my profession or in daily commerce with men, which ought not to be spread abroad, I will keep secret and will never reveal. – Hippocratic Oath

Medicine is full of secrets. I should know, since I’m a doctor.

While some philosophers will argue that there is no such thing as ‘good’ and ‘bad,’ our own personal system of values usually classifies everything relative to those two concepts.

Even secrets.

It sounds fairly simple, right? Good and bad are complete opposites, so the thing under consideration is either one or the other.

Medicine deals with human beings and their humanity; with all its complex systematic social interactions. Anyone would agree that keeping a patient’s medical history secret is a good thing.

What happens if a married patient contracts a sexually transmitted disease because he has been sleeping around? Telling his wife about it could potentially destroy his marriage. Suddenly the simple secret becomes a complicated burden. Ethics committees would like you to think that there is only one correct answer, and lawyers know that there is only one answer that will keep you out of court. To actually be thrust into the middle of such a situation is not a pleasant task at all.

You learn that something can be both good and bad at the same time.

Then there are other secrets in medicine… secrets that leak out from time to time… and suddenly aren’t so secret anymore. For example, modern medicine for all its remarkable achievements at prolonging life (or at least quality of life), is still plagued with false assumptions, charlatans and snake-oil salesmen. Sometimes your doctor is doing what he was trained to do, but this method, drug or procedure was the fashion at the time of training — more simply, “because it’s what everybody else is doing.”

There have been many interesting revelations lately in popular press,  about back surgeries that offer results that are no better than physiotherapy, about drugs that don’t do nearly as well as the pharmaceutical companies claim they should, about stents and bypass surgery being no better than treatment with pills — and yet nothing is new.

As far back as the 1970′s Archie Cochrane started taking a long, hard look at the practice of medicine and basically asked, “Is what we are doing as effective as we think it is?”

This is a vital question in a science such as medicine.

The scientific method is not only about answering the question and designing experiments — but sometimes data has actually to support the claims. The status of science is the only reason we doctors are allowed to literally take people’s lives into our hands and do things to people that no homeopath or chiropractor is allowed to do.

When we speak we are supposed to be supported and guided by absolute, verifiable and reproducible facts.

But then someone like Cochrane comes along and begins to turn medicine on its head, by showing that some of the things we have been doing as ‘standard procedure’ has no additional benefit, compared to not doing them at all.

Which brings us to the next step – if it has no benefit, then why bother doing it? After all, patients aren’t coming to visit us as a social call. They realize that medicine has limitations — but they want a combination of the most effective treatments at the cheapest cost and the minimum intervention.

So why do these bad little secrets creep into what is apparently a solid, peer-reviewed and highly regulated profession?

The answer is simple.

Medicine is a vast field that embraces many disciplines — from physics and biochemistry to statistics and sociology — passing briefly through traditional medical fields like anatomy, physiology and pathology.

That trend is growing at a geometric — if not exponential rate. Several  I learned at medical school are now obsolete. Non-physicians are aware of this change. Especially those who follow the constant, “aspirin is good/aspirin is evil,” 20-year-old debate. Even basic CPR has been changed again. Imagine what is happening to immunology or oncology.

There is no way someone can keep up.

We are human, so we try to hang on to a rock when we are in danger of being swept away by change. This rock is often stubbornness or our own judgment and critical thinking. We read about new things, and then we choose to believe them or not. If a new study, “sounds good and logical,” we accept it, and if it, “sounds badly designed or illogical,” we reject it.

Suddenly medicine has stopped being a science, and turned into a belief.

Compound this with two facts:

  1. All medical research is profit driven (either by a university, a corporation or an individual)
  2. Some studies are completely false — even peer-reviewed ones.

Now you have a recipe for disaster.

Suddenly, someone is out to convince the doctor that this new machine or this new medication works. All they have to do is convince him and present an idea that, “sounds right and makes sense.” Sound familiar?  Sounds like a snake-oil salesman.

In the second part of this series, we’ll look at the current state of medical equipment and how the ‘open source’ concept could benefit everyone — even the manufacturers and vendors of snake oils.

Steven Miron, MD is a licensed practitioner with many years experience operating a private practice. However, nothing he says in this magazine should be construed as medical advice and you should always talk to your personal doctor before making medical decisions.

You can find this article and many more in Issue 01 of Citizen Science Quarterly


It’s a Fab, Fab World!

At Singularity University, on the NASA Ames research campus in California, we have an innovation lab that is sponsored by Autodesk, a design and visualization software company.

Makerbot (cc) Bre Petis

People use the lab’s computers and software to design new objects very precisely, and to render them with photo-realistic quality.  The resulting digital files can then be sent to a 3D printer.  We have several of these, including a professional Stratasys unit and some DIY-cool MakerBots.  In a few hours, they have something they can hold in their hands.

With these tools, any idea can be made into reality in just a few hours.

While it’s nice to have these tools at our fingertips, this technology, called digital fabrication, is available to almost anyone through companies like Shapeways and Ponoko, which offer access to these printers and other tools online.  These services are leading a revolution in personal-scale manufacturing by allowing designers, materials suppliers, printer manufacturers and customers to work together and make a growing array of products.

Most machines can print only one type of material at a time, usually plastic or metal.  They’re complicated and expensive devices, ranging in size from a microwave to a fridge, and they’re packed with electronics and wiring.

Bespoke Innovations Prosthetic

Bespoke Innovations Prosthetic

Yet they are unbelievably cool machines, and addictive.  They’re radically changing the way things are being design, developed, and manufactured.  Prototypes can be made and tested rapidly.  Customization is easy, too, because each unit starts as a digital file and is made on demand.For example, Scott Summit, of Bespoke Innovations in San Francisco, is using these tools to reimagine the world of prosthetics.

He uses digital fabrication to make unique replacements that are not only perfect copies of the remaining limb, but incorporate  exquisite personal artistic expressions as well.

“Fab” technology is still pretty new, but it is improving exponentially, as is often the case for digital technologies.  Everything related to the field is growing – from the diversity of the outputs, to the industries starting to use them, to the sophistication of the printers.  One company, Organovo, has already replaced plastic with living cells, and is using the machines to print blood vessels, and perhaps soon, complete organs, like lungs or kidneys.

Extrapolating this curve, it is clear that digital manufacturing will bring changes in manufacturing and distribution of many goods.  And while it’s not yet possible to fab something as common as a cell phone with a single device, chances are good we will eventually get there.

Looking further out, some foresee the day we have machines so sophisticated that they are able to make more fully functional fab machines, creating limitless manufacturing ability, leading to an age of abundance.  All that would be needed is raw materials (possibly any matter, since all things are made of the same atomic stuff), some energy, and the digital instructions to make the good.  Ask them when these universal fab machines will be reality, though, and the estimates range widely, typically between twenty and forty years.

I’m a biologist, though, and I have a slightly different perspective on fab technology.  What I perceive is that universal fabricators already exist, and indeed have existed for some time.  They’re not just under our noses, they make our noses.  They’re called cells.

Living cells make a vast array of compounds, and can also make all the structural components required to make more cells.  They do this biochemistry with common compounds found in nature, like carbon and nitrogen, and with a wide range of energy sources, the most basic being sunlight.  The digital instructions that control cells are all written in genetic code, usually but not always DNA.

Nature has been making and tinkering with bio-fabs for over 4 billion years.  Some are simple, stand-alone machines, like bacteria.  Others are fantastically complicated networks consisting of trillions of interconnected fabricators.  Our planet is literally teeming with them, in all shapes and sizes.  They are so prolific that they compete with each other for material resources and energy, even going so far as to feed on each other or their remains.  Their genetic programs produce many different shapes and sizes and behaviors.  Look deeper, at the kernel of their genetic programs, though, and we find just three core functions:

  1. Find energy and raw materials
  2. Avoid predation and death
  3. Reproduce

We humans are, not surprisingly, a special case.  We are the first of nature’s bio-fabs that are able to make non-biological tools and to write our own design programs.  This is the essence of technology.  It’s hard work but it’s made us the most effective builders on the planet.  With our technology, we have dominion over every other organism, and even other people if they aren’t as adept at technology as we are.

In May of 2010, we reached a significant milestone, with Craig Venter and his research team using technology to make the first human-programmed cell, a bacterium.  Biology begets technology which begets biology.  We’ve come full circle.

What this practically means is that limitless manufacturing ability is already at hand.  And it can be harnessed to address human needs simply by becoming more adept at writing and executing DNA code and/or organizing cells into structures that are useful.  Systems and synthetic biology empowers us in the first task, and a detailed knowledge of developmental pathways, or how to 3D print cells, the second.  Combined, these allow us take control over life’s core functions and add a fourth attribute: usefulness to humanity.

The manufacturing processes we use today are undeniably useful.  We’ve literally transformed our societies and our planet with them.  The downsides are that they require a substantial amount of human effort to build and maintain, they consume large amounts of energy, and they produce waste products that can be quite toxic to living creatures, including us, and the environments that they live in.  In the long-term, they’re not sustainable.

In the city, where living things are marginalized, it’s easy to forget about life.  But hike into the countryside, dive in the ocean, or browse the growing number of DNA and biological databases, and one is quickly reminded that this a living world, and that life is not just abundant, but also amazingly robust and diverse.  If we can become adept at making synthetic genomes and synthetic organisms, there’s a good chance we can increasingly use them to manufacture the things we need for our modern, technological lifestyles, and to integrate living things back into the urban environment.

Bio-fabrication offers tantalizing improvements, a path to making products and structures and other useful things using natural compounds and the cheap and plentiful energy of sunlight or sugar.  Waste products would be biocompatible, and obsolete or broken devices easily recycled through composting or digestion.  And important from an economic and cultural perspective, direct human effort would be minimal because the cellular bio-fabs would do most of the work.  Effectively, our role would be to design and build useful cellular systems, and to be good caretakers of the living things we create, not so different from farmers or ranchers.

When I look to the future, I see things like bio-designed shoes made of cells and other natural compounds, as durable and comfortable as one you might be wearing, only not manufactured in a faraway factory, but grown in all shapes and sizes in a nearby field.  I see homes that are 3D printed from cellular materials that, after deposition, knit together to form bone or bamboo-like composites.  Or better yet, grown from special seeds.  And as our 3D printers become capable of working with living and non-living materials at the same time, things like submarines that are part dolphin, and airplanes that are part bird.  Such hybrid manufacturing would combine the best man-made technology with the elegance of what nature has created seamlessly.

There’s a lot that has to happen before we can realize even these simple examples.  For one thing, we have to train a new generation of makers that see biology as part of the engineering repertoire.  This is already happening with the international Genetically Engineered Machines program created by MIT, and the mushrooming DIYbio and citizen science movement.

For another, we need better tools, including design software that facilitates the making of living things, complete with metabolic and developmental libraries, plus any safety or regulatory parameters.  Autodesk is already exploring how their software could enable this.

But the key thing may be a global understanding that biology is a technology, and perhaps the most important technology at hand for sustaining our species and our planet, and shed our fears of using it more broadly to serve our needs.

After all, using technology is what we humans do best.

Andrew Hessel is the Co-Chair of Bioinformatics and Biotechnology at Singularity University as well as the founder of an innovative research cooperative called PinkArmy.

You can find this article and many more in Issue 01 of Citizen Science Quarterly


The first issue of Citizen Science Quarterly is done!


I am without words to express how unbelievably ecstatic I am to finally get to announce that sentence above. These past few months have been both an amazing and challenging experience. The closer we got to this day the more and more I realized, I entirely underestimated how much goes into starting and running a magazine. Especially when everyone working on it is in a different time zone.

Yet, thanks to everyones kind support and the hardwork of everyone who contributed, we made it! And for that I can’t thank you enough.

Now to the part that yall probably want to hear. The print is done, along with all of the shirts and merit badges.  If you’ve already ordered a copy it will ship monday or tuesday at the latest. And if you haven’t had the opportunity to order a copy, they are now in stock in the shop.

The End?

Nope.

Just the beginning.

Vol 02.

We are now accepting article submissions for the second issue of CSQ. Whose theme is that of “New Frontiers”, (interpret it how ever you’d like).  The deadline to submit is May 5th, which may seem far away but trust me, deadlines have a way of sneeking up on you, so please submit ASAP. We want to hear what you have to say.

New Website Design

If you’ve been on CitizenScienceQuarterly.com lately (which you have because thats where you currently are) you’ve probably noticed it’s no longer the old black and white design. We’ve changed it to not only make it easier on the eyes but to allow for the publishing of online articles not suitable for a quarterly print but still important for citizen science. As well we’ve been working out some upgrades to the CSQ shop…but thats for a later announcement ;)

On behalf of the entire CSQ staff and citizen scientists everywhere,

You are AWESOME!

Cheers,

Jacob Shiach (the Editor)