Join Eri Gentry, founder of BioCurious, the world’s first “hackerspace for biology” on a journey from garage biology to community lab.

For the first time, serious biological research can be done at home. With the decreasing costs of biotech equipment came a growing community of amateur biologists. The most common name for this group is “DIYbio” (Do-It-Yourself biology), a 2,000 plus group of scientists, students, engineers, artists and entpreneurs, whose interests range from wanting to learn how genetic testing works to wanting to completely overhaul the ivory tower that is scientific research.

Full description at OSCON.com

Also, Paul + friends at the Melbourne Hackerspace in Australia are assembling 1 or 2 OpenPCR kits as you read this. Paul mentioned a UStream/Google+ discussion, so stay tuned! Check out Twitter (http://twitter.com/#!/search/openpcr) and discuss on the OpenPCR Google Group.

Hi all, It’s a delight to see OpenPCR on so many desktops! Josh and I spent the past year staring at mostly-disassembled prototypes with wires all over the place. It makes it all worth it to see everyone assembling their kits, posting pictures, and having a blast doing it. At the end of the post there’s several pictures that I thought you would enjoy of OpenPCR around the world!

Here’s a couple examples of what’s going on with OpenPCR 2 weeks after shipping:

• A high school in Hawaii is testing for genetically modified foods, with plans to upgrade to identifying and tracking non-native species.
• A college professor in Missouri is booting up her biotech class + gel electrophoresis and has successfully amplified DNA
• A biotech company in Utah has amplified DNA to successfully test OpenPCR
• OpenPCR assembled by Singularity University students in Mountainview, California

How you can help

Over the past year we’ve designed, engineered, and shipped our first product. We are now seeking seed funding to take our company to the next level (and build some new awesome stuff). If you know someone who would be interested in investing in OpenPCR, we would love an introduction! Email me (tito@openpcr.org) or send your friends to AngelList (http://angel.co/openpcr).

Also, we’ve raised the price of OpenPCR from $512 to $599. This allows us to get OpenPCR out to distributors around the world — if you’ve got a shop, give us a holler (contact@openpcr.org).

Join the OpenPCR Google group to chat about OpenPCR! We’ve got some great conversations brewing and it would be great to hear from you! http://groups.google.com/group/openpcr

Tito

Hi everyone,

The eagerly awaited OpenPCR kit is now shipping! UPS picked up the first batch of kits and OpenPCRs are on their way to users in 5 continents and 13 countries around the world. For $512, every OpenPCR kit includes all the parts, tools, and beautiful printed instructions – you ONLY need a set of screwdrivers.

A PCR machine is basically a copy machine for DNA. It is essential for most work with DNA, things like exposing fraud at a sushi restaurant, diagnosing diseases including HIV and H1N1, or exploring your own genome. The guy who discovered the PCR process earned a Nobel Prize in 1993, and OpenPCR is now the first open source PCR machine.

The price of a traditional PCR machine is around $3,000. So, do people in garages have great PCR machines? Not really. Howabout high school or middle school teachers? Nope. Howabout smaller medical testing labs or labs in India or China? Nope. Even some big bio labs try their luck on eBay. We set out to change that.

Josh and I prototyped OpenPCR over about 4 months — it was a lot of fun. Last May we unveiled the first OpenPCR prototype to all a bunch of crazy people on Kickstarter, 158 people gave us a total of $12,121. With that we designed and manufactured a repeatable, works-all-the-time device — it took a lot of hard work. Now we’re done and ready to share!

OpenPCR Firsts:

1. First commercially available PCR machine for $512

We get a lot of people who come up to us and say “jumping jillikers, batman! we paid $10,000 for ours and it’s this big (make refrigerator-sized hand motion)!”. While modern PCR machines aren’t fridge sized anymore, we’re proud to say that OpenPCR is the most affordable and most compact PCR machine out there.

2. First Arduino USB storage device:

This is a big deal for you Arduino hackers out there. A normal Arduino can only talk back and forth over a serial port. This is a pain to set up, and we wanted OpenPCR to just plug-in and go. How does it work? When OpenPCR is plugged in, the Arduino mounts itself as a USB drive called “OpenPCR”. The computer passes love notes to OpenPCR by writing to that file, and Arduino sends love notes back by writing to another file. The implementation was tough, and there are size restrictions due to the size of the chips used by Arduino, but it’s pretty simple to make use of. We also built a cross-platform app for your Mac or PC in Adobe Air so that the we could have a simple computer control interface. Simply plug in your OpenPCR to your computer with USB. No setup besides downloading the OpenPCR app! (Josh and Xia totally pulled off a miracle on this!) If you’ve got questions on this specifically, be sure to post below!

No cutting corners

The clear vision of OpenPCR that made it great was driven by 2 things. First off, Josh is an incredible engineer and we both enjoyed learning a lot of new things over the past year — everything from how to make circuit boards, machine metal parts, laser cutting, Arduino hacking, USB hacking.  I’d say 90% of the success of OpenPCR was lots of hard work. Hard work is great but there are lots of projects where hard work is put in but never “pays off”. How did we stay on course? I think the prototype + showing it off on Kickstarter/Maker Faire had a lot to do with it. We of course had lots of exciting ideas about new functionality and extra things over the past year. The beauty of having built our prototype was we knew if we could just get to that point we would have a hit.

For example, we designed OpenPCR to be assembled by hand. The printed Build Instructions are a big part of OpenPCR and we did a lot of work to get them right. As we finalized the OpenPCR design a few steps stood out as “hard”. We switched from thermal paste to thermal pads (not messy, no need for gloves), assembled circuit boards (no need for a pro soldering setup), and pre-epoxied the thermistor. The OpenPCR kit is easy to build because of those decisions. We’ve still got to publish the gel pictures showing how great OpenPCR works, but that’s been well tested ourselves. If you’ve got an OpenPCR kit coming your way and would like to post pictures of a gel run afterwards, we would love to see your results too!

The intent of the prototype was simple – we wanted a PCR machine for people like us. That meant a 16 well PCR machine controlled by computer, with a built in screen, good for the lab bench or a workshop/garage. And that’s exactly what OpenPCR is.

Where did the time go?

After Kickstarter started in May, we worked for going on 14 months now. Between Josh and I, I estimate we put about 3,000 hours into OpenPCR, not counting the time leading up to the prototype. We’ve got 57 posts and 600+ comments on the OpenPCR blog, covering a lot of aspects of OpenPCR development. In the past few months we’ve kept our heads down getting everything out the door and we’ve got some stories to share. Short answer is, there’s a lot of blogging to catch up on.

Special thanks to Xia Hong, Eri Gentry, and Will Reinhardt who volunteered lots of their time to help OpenPCR.

Just the beginning

OpenPCR is designed for labs, classrooms, and garages. Tell your science-y friends about OpenPCR, “Like” us on Facebook, or write us and tell us that you stopped by! You can also get your own OpenPCR kit!

Do you want to see us develop more breakthrough biotechnology? Along this journey we uncovered a lot of opportunities for PCR and other biological devices. We’re a new company and would love to meet other passionate people. Our hurdles right now are manufacturing (mechanical engineers!), distribution (sales + marketers!), and new hardware (hackers!)/software (hackers!)/bioware (biologists!) + industrial design. If you’re in the Bay Area and want to get in on making all this crazy DNA stuff useful to regular people, send us an email: contact@openpcr.org.

For more information, we’ve gotten a lot of media attention over the past year  including NYTimes, GQ France, Biotechniques, and USA Today.

Ordered a kit and wondering where it is? We have shipped a first batch of kits and emailed out tracking numbers to the recipients. If your kit hasn’t shipped yet, we’re working on shipping a second batch and will keep you updated.

Hi OpenPCR fans!

OpenPCR first came to life last February, and we showed off our first prototype at Maker Faire last May. Those of you following the blog know we designed, refined, and engineered our hearts out. Today, Josh and I are pleased to make the first version of the OpenPCR design docs public. Whether you’re a hardware junkie, circuit board lover, or code addict, we’ve got you covered!

Code, CAD, and Circuits

http://openpcr.org/downloads

• OpenPCR CAD (SolidWorks 2011) for all 100+ components of OpenPCR
• Eagle files for the OpenPCR Brains circuit board
• Arduino control software (still being revised)
• Adobe Air software interface (still being revised)

Instructions

We also invite you to check out the OpenPCR assembly instructions which come bound and printed with every kit we ship. The cover features beautiful glasswork by Dale Chihuly, and you can read the rest of the story here: http://openpcr.org/instructions/

A question for you — What OpenPCR stories would you like to hear? Any components or topics you would like us to write up in detail? Feel free to reply to this post or email us at contact@openpcr.org

Tito and Josh

“All I’m sayin is,if they took DNA samples for bin Laden,who did they match it against,& that was one ruddy fast PCR,can I have your machine?” – upulie

“Did they bring PCR machine on the site to confirm Bin Laden’s death?” – seanjeon

The US military used DNA to identify Osama Bin Laden very quickly after he was killed. How? Although we don’t have intimate knowledge of Osama’s DNA identification, here’s one way that OpenPCR could potentially be used in a similar situation.

What’s DNA Fingerprinting?

DNA fingerprinting compares a sample of DNA to a previously verified sample. In Osama Bin Laden’s case, there were samples of his relative’s DNA available so a rough DNA fingerprint was on hand. The job of the scientists was to quickly analyze the new DNA sample and see if it matched what was on file.

Fingerprinting begins with a DNA sample. A quick and easy source of DNA is spit. Spit has cheek cells in it and every cheek cell has a copy of the entire human genome. The human genome is 3 billion pieces of information. As comparison, a Tweet contains up to 140 letters, so 21 million tweets to send out your genome (or Osama’s genome for that matter)! Even with recent leaps in biotechnology, reading all that DNA today costs a lot of money (thousands of dollars) and time (about a month).

We’re all a little bit different…

Luckily there’s a shortcut for quick DNA identification instead of sequencing the entire genome. Some bits of DNA are very important (like one letter that determines your ability to taste bitterness), while others vary a lot between people without a clear function. It’s these highly variable sections that are used for DNA fingerprinting because they differ greatly between individuals, but are similar between relatives. In the case of Osama Bin Laden, however a reference sample of his DNA was not available. Instead, samples from family members were used to compile his fingerprint.

The internationally accepted standard for DNA fingerprinting uses 13 STRs (short tandem repeats) to create a unique fingerprint. A short tandem repeat is 1 to 4 letters of DNA that is found repeating over and over in the human genome. For instance, one gene used for DNA fingerprinting contains a repeated pattern of “CTTT”, i.e. “CTTTCTTTCTTTCTTT”. This is from the FGA gene in humans, and it has been seen repeating from 12 to 50 times. By looking at the number of repeats in all 13 STRs, a unique fingerprint is created for each person.

Do it yourself

The tools for doing this type of analysis are accessible to hobbyists with a budget.

First, extract the DNA from your spit sample.

You can practice with stuff in your kitchen after watching this video on extracting DNA from a banana:

Next, you’ll need a PCR machine such as OpenPCR, which is like a xerox machine for DNA. Starting with a small DNA sample such as a spit sample, a PCR machine will selectively copy just the 13 STR sequences. You’ll also need short pieces of DNA primers to copy each STR. The DNA sequences for all 13 STR primers are available here.

Finally, use gel electrophoresis to visualize the DNA after PCR. Gel electrophoresis is a tool for measuring DNA. With the earlier example of FGA for instance, gel electrophoresis can tell you how many copies of the “CTTT” pattern are in the sample genome. By looking at the length of all the STR primers you’ll have a fingerprint unique to yourself.

If you’re fingerprinting a friend, you will need to take extra precautions to make sure your own DNA does not contaminate the experiment. For instance, just coughing on the DNA sample could ruin your experiment, since you’ll end up fingerprinting yourself. DNA fingerprinting is a bit more complicated than can be explained in this quick article, but post in the comments if you’re interested. And that’s how DNA fingerprinting works!

The OpenPCR PCB

That's one large Arduino shield

As much fun as that was, I’ll let a pick and place robot do it next time. I’ve been looking at Screaming Circuits for PCB assembly in the ~100 unit range, though please feel free to suggest any other companies in the comments.

The boxes you see in the background are OpenPCR components for the first kits. We’re just awaiting one more shipment from China (expected next week), and making some final software changes, and then these boxes are out the door.

GQ_scribd

IN THE ANTRUM OF THE BIOHACKERS

Do you know about the hackers who roam the internet and [pirate] information networks? You will love biohackers, their cousins who play with life and biology. Followers of Do It Yourself, these wild scientists [mount / rig up] their own amateur laboratories in garages, manipulating cells and DNA. (Unlike the) fantasy of Dr. Frankenstein, they aspire to free science from the yoke of the multinationals. And they promise to (revolutionize) our lives. (The Natural and Life) sciences have never been so fun.

(Text: Valentine Faure, Photos: Peter Van Agtmael / Magnum for GQ)

Mountain view, [???] of San Francisco, at the heart of Silicon Valley. At the Hackers Dojo, a vast [hangar, shed?] populated by geeks working in silence at their computers on mysterious projects, there are [a hundred] who have made the trip here this Sunday at the [call?] of the group BioCurious. There are sudents, traders, computer scientists, chemists, and one [tramp?] wearing sunglasses, united by their common passion, “Biohacking.” In their makeshift laboratories in their garages, closets, and kitchens, they manipulate living organisms as other might garden or trick out their car. To what purpose? Having fun extracting DNA from a banana, or attempting to invent the biofuel of the future. Producing a bacteria capable of making a green fluorescent yogurt, or analyzing their own genome. Creating a living organism able to absorb an oil spill, or working toward furthering cancer research. [This is?] “Do It Yourself” genetic biology, which [passes up] official laboratories to realize these feats at home.

MANIPULATING [ LIFE / THE LIVING ] AT HOME
In 2005, Robert Carlson, scientist and apostle of biohacking, predicted the emergence of amateur biology. “The [advent / coming] of garage biology is near,” he wrote. “[As] the skills and technologies develop, the synthesis and manipulation of genomes will no longer be confined to ivory towers.” ___________________

Since then, biotechnological enterprises have been heavily affected by [the crisis???], and costs have continued to drop. For a few hundred dollars, one can rig up a lab at home, finding bargain materials on eBay, tinkering with a webcam to make a microscope or using ones armpits as an incubator. And, in the current of the “Open Science” movement, which encourages applying the philosophy of free information to  science, “DNA Tinkerers” have [swarmed/spread/propagated???].

In Paris, Boston, and even in Bosnia, handfuls of wizard apprentices share protocol, ideas, and results of their experiments on online forums. Joseph Jackson recently [moved?] to Silicon Valley “because that’s where all the [weird guys/freaks] are going.” He studied political science at Harvard “thinking that politics was the best tool at our disposition for resolving problems.” After discovering the narrowness of spirit and eagerness of the people at Harvard, he instead became a kind of entrepreneur-activist-transhumanist. With Eri Gentry, the smiling queen of the biohackers and Tito Jankowski, a towering blond 24 year old originally from Hawaii, two other amateur biologists at the heart of the movement, he founded the group Bio Curious. In their newly acquired space, all three teach aspiring hackers how to construct their own labs on the cheap, or conduct their experiments at home, teaching them safety rules, in short, working to spread the [domestic practice of the "manipulation of life." Not just to train [ Sunday biologists / Weekend Warriors].

LIBERATING SCIENCE FROM THE INFLUENCE OF COMPANIES
DIY Biology, for Joseph, is the breakdown of industrial and institutional barriers. Then end of the seizure of knowledge by multinationals motivated only by profit. “It is vital that [citizens/people] are able to use biotechnology. It’s a return to the [normal / way things used to be???]. Biology was always domesticated. During the Age of Enlightenment, research was conducted by rich erudite aristocrats, who could afford to purchase the necessary materials.” Thomas Edison, or Benjamin Franklin – who placed all of their inventions in the public domain– [ figure prominently] in the pantheon of biohackers as the best examples of [a Science] that is creative, participative, and humanistic. “And then the industrial revolution upset everything, in [re?]orienting the research of science toward the search for profit,” continues Joseph. “And big multinationals like Monsanto dictated the trajectories, and imposed their agenda in matters of technology and health. [Although we should be] in an era of exponential progress, we are blocked by the mechanism of monopolies, with patents of a duration of twenty years.” Today, biohackers belong to a generation [to whom nothing is forbidden by patents or copyrights????].

Pullquote: “Creating genomes will become a personal activity like painting or sculpture” – The physicist Freeman Dyson

Page 161 Caption: Tito Jankowski, one of the three creators of the group BioCurious, practices high level biology in a small apartment in San Francisco.

Page 162 Caption: At 23 years old, Russel Durrett created Genspace, his own lab, where he tries to fabricate [new/novel] antibodies. With his project of creating a new strain of yeast, he hopes to revolutionize medical research bypassing an official lab.

“Napster, Ebay, Amazon, Blogs, all of these (challenged) the concepts of creation, professionalism, and commerce that we thought were written in stone. Imagine the impact of an analogous change in science.” Yes, let us imagine it. In 2007, the [great?] physicist Freeman Dyson exposed (shared?) his views on the future of biotechnology. “Genetic engineering will remain unpopular and controversial as long as it remains an activity concentrated in the hands of big corporations. I see a radiant future for biotechnology when (if?) it follows the path of the information industry: in becoming small and domesticated, instead of large and centralized… Creating genomes will become a personal activity, a new form of art as creative as painting or sculpture.” So, we can possible sell (buy?) DIY kits for creating new species of roses, of parrots, of snakes and of dogs. And in schools, children will be able to make baby dinosaurs rather than observing them in books.

The myth of the Garage Revolution
This vision could seem chimerical in 2011 but Dyson [predicts] “the domestication of biotechnology will dominate our lives over the next fifty years, [just as] computer have dominated our lives for the last fifty.” In Wwaiting to become the Steve Jobs of tomorrow, Joe brought his LAVA-AMP with him, a “low cost DNA amplifier”, which at first glance looks like a toy. More rapid, less expensive, consuming less energy, his machine makes DNA tests possible anywhere, and could be used to improve the screening of illnesses (H1N1, bird flu). For today, the object can certainly make part of the perfect panoply of [a biohacker]. “This could become an emblematic object, in the manner of the iPod, and in fifteen years we’ll say “Oh yeah, I remember that thing!”

The emergence of these new tools will sooner or later pose the crucial question of their commercialization. In 2011, we can still ask whether a mass market exists for these personal DNA amplifiers, but biohackers already have the response. An analogy with the [personal computer] revolution feeds their dreams of grandeur: after all, they ague, in the 1970s, when computers were the size of a (????), we asked with skepticism who could ever need a computer at home. Secondly, it is [now well established] that many great inventors started out as hackers, and that the greatest technological enterprises were born in garages– Apple, Hewlett-Packard, Google, (?????) Netscape Navigator. In reality, the vast majority of “garage entrepreneurs” benefited from their experiences in conventional enterprises, but the myth of the “enterprise born in a garage is part of the American dream: the triumph of talent and effort, of [sole genius against all?]. The garage or the lab improvised in a bathroom, it’s there where a bold future is invented, away from conventions and institutions.

THE BIOBRICK: THE ELEMENTARY UNIT
Last February, Wired Magazine [published an article titled?] “The New Industrial Revolution”. Its founder Chris Anderson announced the the [expansion?] of manufacturing production done at home – of cars, bikes, t-shirts, mugs, or jewelry, [making a contribution of know-how????] across the planet. “Upheavals happen when industries democratize, when they are torn from the monopoly of enterprises, of government, or other institutions, and they are transferred to all the world. The internet democratized publishing, multimedia, communications, provoking an enormous enlargment in [both the public and players in this digital world?].” DIY biology sits at the crossroads of all these forces in action: crowdsourcing, domestication, the end of professionalism, participative production. And the development of synthetic biology. If the computer revolution [was built using?] elementary particocles called “bits”, the next has already begun using what amateur biologists call “biobricks,” portions of DNA of standardized behavior, that allow us to [think of] new creatures that are purely abstract, in the same way an engineer imagines a machine composed of different pieces. By combining genetic circuits, like Legos, synthetic biology can create forms of life that are new, genetic machines with a determined function.

“THE COOLEST [CONTEST] IN THE WORLD”
Organized each year by the prestigious Massachusetts Institute of Technology, the iGEM contest (for “International genetically engineered machines competition”) gathers projects from students around the world using biobricks. This competition has become the institutional rendez-vous of biohackers. On this cold Saturday in November, many have had to travel to Boston: one hundred and forty teams this year, versus five the first year in 2004. There is an [academic?] atmosphere in the lobby: grouped before the posters summarizing their projects, these young scientists revise their presentation, [encouraged?] and trying to indentify their most dangerous adversaries. Among them, Russell Durret, who was 19 when he first [heard about?] iGEM: “the coolest thing in the world.” The next day he was on a bus to Boston to attend the event. The day after that, he decided to devote his life to synthetic biology. This year, he is participating for the first time in the contest, under the banner of New York University. Very confident in his chances, here he is at age 23 become a “molecular biologist”. “Most people think that in order to practice science, you need a degree, a masters, a doctorate, and a post-doctorate… I took a shortcut: I got my degree, and I created my own lab.” In the seventh story of a building in Brooklyn, you have to step over buckets collecting rain water leaking from the ceiling to access Genspace, his “lab.” The materials were recovered from a laboratory that went bankrupt. On a shelf, the book “Biology for Dummies.” On his computer screens, multicolored forms [of madness] incomprehensible to a philistine. At the moment, Russell is working on a project that he said could “revolutionize research in antibodies.”  He makes a strain of yeast that imitates the human immune system, and can enable a discovery of a [new antibody?]. Right now, performing the operation takes a month, and costs about $700. “With this system, it takes less than a week, and costs virtually nothing,” ensures Russell.

THE [CAUTIOUS] SCIENTISTS
The scientific community is rather [cautious about?] the emergence of biohackers. A researcher at Boston University summarizes the general opinion in these terms: “I’m not afraid of these people, but they will mess up.”  “Scientists aren’t afraid because they think that DIY biology is just a jellyfish in tupperware,” responds Russell. “They don’t realize that people are [already gathering], professionalizing…” It’s hard to say exactly how many there are today. “Some want us to talk about them, ” explains Robert Carlson, “but others don’t want [advertising?]. For some years, our government has been completely paranoid and has been [shown agression?] toward the people who practice biology from home, even in a legal manner. It’s what I expected: in cases of severe repression, people will not stop, they will hide away. And that’s exactly what has happened.

MY NEIGHBOR FRANKENSTEIN?
[The biohacker figure in?] Dr Frankenstein, isolated creator of living organisms he has no control over, [he is real?], [enough to feed the fantasies?]. My neighbor [creating] an ebola virus in his kitchen? “It’s not very probably, because it’s very complicated to do. It’s very difficult to do something harmful. But it’s also difficult to do something helpful.” says agent Ed You, FBI, charged with monitoring the development of the practicing of synthetic biology. He works hand in hand with little groups of DIY biologists. “We realize it’s an extremely promising field,” he explains, “but there is a large spectrum of risks. We just want to make sure that people understand the laws, and that they themselves are being safe. If something happens, the legal response could inhibit the development of medicine, of biodefense countermeasures, this is not desirable.” At the Mountain View Hackers Dojo, when [discussing/addressing?] issues? related to the safety of the excercise of amateur manipulation of life, one man intervenes: “That’s exactly as if we had told the first man that invented fire: [No, are you crazy? Are you going to teach that to your children, to the whole world around you?].” Nodding heads of approval around the room. [In other words], while we’re with the biohackers, we have the feeling of being a the dawn of a very, very big revolution.

[INFOGRAPHIC] THE PANOPLY OF A BIOHACKER

FORMATION
Harvard University, MIT, and the book Biology for Dummies

MODELS
Apple, Facebook, Napster, and all enterprises founded in a garage by a [smart guy?] become millionaire

INFLUENCES
Punk culture and its emulators, Do It Yourself, hackers and the “Open Science” movement

MENTORS
Chris Anderson, founder of Wired, Robert Carlson, scientist and apostle of biohacking, the physicist Freeman Dyson, and Benjamin Franklin, writer, physicist and american diplomat of the 18th century

ANNUAL RENDEZ-VOUS
The iGEM contest in Boston, international competition of synthetic biology that was held in November 2010.

TOOLS
The biobrick, basic element for constructing new biological systems, and materials acquired on eBay and customized.

COLLABORATORS
The biotech and pharmacological industries, academic research institutions.

(The missing steps are the drugs given to livestock wiped out native vultures, leading to a rise in the wild dog population, leaving an estimated 48,000 people dead from dog attacks + rabies over the ensuing 14 year period.)

As I highlighted in my last article, species identification is important and a PCR machine is a key tool of DNA identification. Imagine if species identification were so easy that the monitoring of hundreds of species was commonplace. Might we be able to notice and understand trends more quickly? Here are a few of my favorite excerpts from Conniff’s “What are Species Worth? Putting a Price on Biodiversity“. (See the primary research on the cost of species decline)

For instance, Prochlorococcus is an ocean-dwelling genus of cyanobacteria and among the most abundant life forms on Earth. Why should we care? Because it produces about 20 percent of the oxygen we breathe — and yet until an MIT microbiologist named Sally Chisholm discovered it in 1986, Prochlorococcus was unknown. We need to understand in short that our lives depend on species most of us have never heard of — species we otherwise tend to shrug off as obscure, trivial, even undesirable.

Vultures, for instance. When we cause a species to go into decline, we almost never know — and hardly even stop to think about — what we might be losing in the process. In truth, it may be hard to think about, because the cascading effects of our actions are sometimes freakishly distant from the original cause. So in India in the early 1990s, farmers began using the anti-inflammatory drug diclofenac for the apparently worthy purpose of relieving pain and fever in their livestock. Unfortunately, vultures scavenging on livestock carcasses accumulated large quantities of the drug and promptly died of renal failure. Over a 14-year period, populations of three vulture species plummeted by between 96.8 and 99.9 percent.

Losing these efficient scavengers meant livestock carcasses often got left in the open to rot. It was one of those “ecosystem services” — manufacturing oxygen, soaking up carbon dioxide, preventing floods, taking out the garbage — that species generally provide unnoticed, until they stop. But the A diversity of species can help prevent the emergence of new diseases. impacts went well beyond the stench, according to a 2008 article in Ecological Economics. Moving into the niche vacated by the vultures, feral dog populations boomed by up to 9 million animals over the same period. Dog bites and the incidence of rabies in humans also increased, and the authors conservatively estimated that an additional 48,000 people died during the 14-year period as a result. Calculating the bottom-line worth of what we get from the natural world is notoriously difficult. But even pricing lives at a fraction of developed world values, the near-total loss of three insignificant vulture species has so far cost India an estimated $24 billion.

Read the full article: “What are Species Worth? Putting a Price on Biodiversity” by Richard Conniff
Supporting research, primary source: Counting the cost of vulture decline – An appraisal of human health and other benefits of vultures in India

• asprin
• most antibiotics
• treatments for lymphoma and leukemia (Madagascar rosy periwinkle, pictured)
• lung, breast, and uterine cancer (Pacific yew tree, Arthur Barclay, a $1,700,000,000 a year product today)
• rapamycin fungus found on Easter Island, a coating for stents (medical device for arteries) which potentially has a positive effect on the lifespan of the patient.
• Something you discover!

What do you think? Was the source of these discoveries a surprise to you? Do you have an interest in tackling this new frontier?

==========
When adding up the benefits from three centuries of species discoveries, I’m tempted to start, and also stop, with Sir Hans Sloane.  A London physician and naturalist in the 18th century, he collected everything from insects to elephant tusks.  And like a lot of naturalists, he was ridiculed for it, notably by his friend Horace Walpole, who scoffed at Sloane’s fondness for “sharks with one ear, and spiders as big as geese!”   Sloane’s collections would in time give rise to the British Museum, the British Library, and the Natural History Museum, London.  Not a bad legacy for one lifetime.  But it pales beside the result of a collecting trip to Jamaica, on which Sloane also invented milk chocolate.

We still scoff at naturalists today.  We also tend to forget how much we benefit from their work.  Since this is the final column in this series about how the discovery of species has changed our lives, let me put it as plainly as possible:  Were it not for the work of naturalists, you and I would probably be dead.  Or if alive, we would be far likelier to be crippled, in pain, or otherwise incapacitated.

Large swaths of what we now regard as basic medical knowledge came originally from naturalists.  John Hunter, for instance, was a colorful London physician, a generation or two after Sloane, and his passion for animals made him a model for Dr. Dolittle.  (He may also have been the original Dr. Jekyll and Mr. Hyde for his nighttime work sneaking cadavers in by the back door.) While others were only dimly beginning to contemplate the connection between humans and other animals, he made detailed flesh-and-blood comparisons, discovering, among other things, how bones grow and what course the olfactory nerves travel.

Hunter, now regarded as the father of modern surgery, came out of a Scottish tradition that treated the study of nature as essential for developing a doctor’s observational skills, and he drilled this attitude into his students.  Among them was Edward Jenner, a country doctor who spent 15 years studying cuckoos (perhaps one reason he later got labeled a quack).  But this research, combined “with Hunter’s insistence on finely honed observation and cogent presentation, helped prepare Jenner’s mind for his great work,” according to science historian Lloyd Allan Wells.  That work was the development of the world’s first vaccine, for smallpox.  Establishment physicians balked.  But Jenner’s bold idea would lead in time to vaccines against countless other deadly diseases, from yellow fever to polio.   He thus gets credit (with a faint nod to the cuckoo) for saving more lives than anyone in the history of medicine.

You may perhaps be thinking that chocolate milk, Dr. Dolittle, and cuckoos make a very curious case for the importance of species.  But our debt to the naturalists also takes more conventional form: Roughly half our medicines come directly from the natural world, or get manufactured synthetically based on discoveries from nature.  The list includes aspirin (originally from the willow tree), almost all our antibiotics (from fungi that evolved in nature, not a Petri dish), and many of our most effective cancer treatments.  I can remember a pale girl in second grade going off to die of lymphoma or leukemia; children with those diseases almost always died then.  Now they routinely live, because of drugs developed from the Madagascar rosy periwinkle, a flowering plant.  Many patients with lung, breast, uterine, and other cancers also now recover because in 1962 a botanist named Arthur S. Barclay collected samples of the Pacific yew tree, leading to the development of the anticancer drug Taxol.   For those who think natural resources should stand or fall based on their current cash value, yew trees would have been basically worthless in 1961.  But today, according to industry analysts IMS Health, Taxol is a $1.7 billion-a-year product.

Beyond giving us powerful new drugs, discoveries from the natural world also frequently open our eyes to the unsuspected workings of our own bodies. One of the more obvious effects of being bitten by the South American pit viper, Bothrops jacara, says the Harvard pediatrician Aaron Bernstein, is that “your blood pressure drops to the floor, and then you drop to the floor.” So kill all the vipers, right?  On the contrary, says Bernstein, a co-author of the 2008 book “Sustaining Life:  How Human Health Depends on Biodiversity.”  The study of a key enzyme from this snake’s venom revealed a new mechanism for controlling human blood pressure.  ACE inhibitors, the direct result, are now our most effective remedy for hypertension and congestive heart failure, and certainly save more lives than these snakes ever killed.

Likewise, rapamycin, also known as Sirolimus, developed from a soil fungus on Easter Island, suppresses immune response through a pathway previously unknown to medicine.  It’s now widely used for organ transplants and as a coating on heart stents.  By itself, that might not make anyone run around with an “I <3 Fungi” bumper sticker.  But consider this:  A 2009 paper in Nature reported that mice dosed with rapamycin experienced a 28 to 38 percent increase in subsequent lifespan—and these mice were 60 years old (or the mouse equivalent) to start with.  So Baby Boomers, are we starting to feel the fungal love?

Given the untapped potential of the natural world, you might think governments and drug companies would be racing to save species and screen them for other such extraordinary powers.  In fact, says James S. Miller, vice president for science at the New York Botanical Garden, “only a tiny percentage of the world’s plants have been screened,” and even those “have only been screened against a small fraction of the diseases for which they could be effective.”  Instead, pharmacologically-active compounds developed over millions of years and found effective in the world’s harshest laboratory—nature—routinely vanish, as the species in which they evolved go extinct.

There’s one final way we owe our lives to naturalists.  The absence of epidemic disease is now so completely taken for granted that it’s hard to imagine we ever lived otherwise.  But malaria once routinely killed people from the Gulf of Mexico to the Great Lakes.  Yellow fever epidemics swept down like the wrath of God on cities as far north as Boston.  In the nation’s worst outbreak, in 1878, one in eight residents of New Orleans died, and everything south of Louisville, Ky., was “desolation and woe.”  All that changed in the miraculous 1890s, when researchers suddenly identified the causes of yellow fever, typhus, plague, dysentery and, above all, malaria.   In each case, the solution depended on having precise knowledge—both taxonomic and behavioral — of the species involved, from microbial organisms to mosquitoes.  As Patrick Manson, the father of tropical medicine (and a great Scottish naturalist), once put it, the study of the origins and causes of disease “is but a branch of natural history.”

It’s worth remembering all this now because some scientists say we are on the brink of a new era of epidemic diseases, with H.I.V., SARS, H1N1, and Ebola merely the ominous harbingers.  New diseases are emerging because logging roads are reaching into the remotest habitats.  Some scientists also think that deforestation is stripping away our biological buffer — the natural community of animals and plants that would normally dilute the effect of a disease organism and prevent it from spilling over to humans.

It’s hard to accept that you and I may be vulnerable.  Our brief century of freedom from disease has given us the delusion that we are separate from nature, somehow hovering above the world in which we live.  So we no longer think it worthwhile to spend our money studying the species around us (better to search for life in outer space).  And we accept the loss of forests and wetlands, not thinking that it may translate in time to the loss of our own families and friends.   When the new wave of emerging diseases comes washing up on our doorsteps, we may find ourselves asking two questions:  Where are the naturalists to help us sort out the causes and cures?  And where are the species that might once have saved us?

But why wait?  Why not ask those questions now?

POSTSCRIPT: The natural world ought to be a source of pleasure and consolation. So I’ve avoided pushing the conservation message too hard in this series. But I also hope readers are wondering what they can do in their own lives to slow the loss of species. Fortunately, a lot of the changes we can make to help the environment also help with our own economic struggles. Here’s a baker’s dozen of ideas. I invite readers to add their suggestions:

1. Reduce meat in your diet and stick to sustainable fisheries. (Find a pocket guide for your region.)

2. Buy less stuff, or buy it used.

3. Favor companies and countries that value the environment. (But beware of greenwashing. BP used to tout itself as environmentally aware.) Check the green rankings of top companies.

4. Add up your annual energy consumption (including air travel, gasoline, electricity, and heating fuel) and set a program to cut back by five percent a year. Be clever and you may hardly notice. Start by making a one degree change in the thermostat, and replacing incandescent light bulbs with compact fluorescent lights. (Some energy audit programs will do it for you and you will spend less for the service than you will save in utility costs in the first year alone.)

5. Walk, bike, or take public transportation. The exercise will do you good (and you might see an interesting bird or bug on route).

6. Get acquainted with some of our weird, delightful fellow species. Any book by Gerald Durrell, for instance, “My Family and Other Animals,” is a fine place to start,

7. Learn to identify 10 species of plants and animals in your own neighborhood, then 20, and onward.

8. Stop using lawn pesticides and fertilizers. They contaminate nearby waterways. For the same reason, don’t dump old prescriptions down the toilet.

9. Reduce water use, particularly for lawns; it depletes a limited resource, sometimes directly damaging habitat.

10. Plant trees, and since maintaining them is the hard part, stick around to be a tree steward.

11. Lobby public officials to do smart things like installing more sidewalks, limiting carbon emissions,
and investing in conservation of threatened species.

12. Adopt a species that needs help and actively support its conservation. Groups exist focused on tigers, rhinos, chimpanzees, gorillas, orangutans, frogs, and so on.

13. Encourage your local zoo to focus on species conservation.

Richard Conniff’s work has appeared in Smithsonian, National Geographic, Time, The Atlantic, The New York Times Magazine, and on National Public Radio. He is the author of several books, most recently, “The Species Seekers: Heroes, Fools, and the Mad Pursuit of Life on Earth.” He blogs at strangebehaviors.com. Twitter:@RichardConniff.

OpenPCR prototype PCR Machine v 0.000001, sitting atop a spool of solder to help with airflow.

What a successful year. Last February we assembled our first OpenPCR prototype. Right after that, we made a mad rush for Maker Faire in San Mateo, California. By that time we had a beautiful laser cut case (sponsored by Ponoko) and a machine that worked. Hundreds of people support OpenPCR on Kickstarter, doubling our $6,000 goal for the first crowd-funded biotech project in history. OpenPCR featured in Nature Magazine (excellent photo taken by Josh) (link) and the New York Times (link), among others.

Congratulations to all! Josh and I have learned an incredible amount in the past year. Everything from h-bridges, power supply design, and PCB fabrication, to peltiers, thermistors, CNC machining, and USB control. It is great to be working together!

Yesterday we celebrated while out sailing in the San Francisco Bay! Also thanks to Eri for writing us up on the BioCurious blog (link).

Josh and I aboard an Olson 25', on a 5 hour sail around Angel Island in the San Francisco Bay. Thanks to Eri Gentry for the picture!

The below is a gel showing PCR reactions from the final OpenPCR prototype that will be used for our kit production. This experiment was done to validate various polymerases rather than test OpenPCR, but thought you may want to see it. Lane 1 at the right is a control with no polymerase. Lanes 2 – 4 show amplification of a ~1kb amplicon with different polymerases/salt concentrations. Lanes 3-4 have a different loading dye, but pay attention to the fluorescent DNA band (imaged with GelGreen / Invitrogen Safe Imager).

This is just an early glimpse – when we release the final machine kit, we’ll include a gel image with well-by-well results for an identical reaction. That release is thankfully getting closer – over the weekend Tito and I tested a prototype with full mechanical assembly and got excellent results, so we’re just getting the final pieces into production. Stay tuned for the official release date!

Not everyone is content to fill their labs with centuries-old technology. Samara Rubenstein, the manager of the Sackler Educational Laboratory for Comparative Genomics and Human Origins at the American Museum of Natural History, said home scientists could extract their DNA by rinsing their mouth with salt water, breaking apart the sloughed-off cheek cells with dish detergent, and then rinsing out the DNA with rubbing alcohol. “It’s really cool,” she said.

Other experiments for home labs can be found at Ology, a corner of the museum’s Web site.

After the DNA is extracted, more options are becoming available for identifying the organism using a technique known as PCR, or polymerase chain reaction. A new project, OpenPCR, is designing new home tools for DNA analysis. Tito Jankowski, who founded the project with Josh Perfetto, said the kit would give anyone the chance to analyze DNA.

Mr. Jankowski said one possible experiment for home scientists would be to test for their reactions to certain food. Only some people, for instance, taste the bitterness in brussels sprouts, a trait that has been linked to a part of our genome that the kit can identify.

Eri Gentry, an entrepreneur in San Francisco, said she had already tested herself for this gene, using a $200 kit from Carolina Biological Supply, which sells to school science labs.

“Some of these things you do not because it’s the quickest way to do it, but because you learn a lot,” she said.

We’ve moved to using a silicone/kapton (pending testing) heater with an integrated thermistor for the heated lid so as to increase the ease of assembly & reliability. We’ve selected a copper heat block for the wells which has excellent thermal properties (high thermal conductivity and low specific heat), and is plated in chrome to protect the copper. We’ve placed the thermistor which measures heat block temperature inside the block to more accurately measure the block temperature, which has improved the thermal control dramatically. We’ve also optimized the air flow through the case/power supply to cool the heat sink more rapidly, thus improving cooling performance.

We’ve made a few changes to aid ease of assembly of our kits. We’ll be including an ATX power supply which has all cables other than the 24 pin motherboard connector removed to save room in the case. Due to the amount of surface mount components on our board which can be tricky to solder, we’ll be including pre-assembled circuit boards as part of our kit. We’ve also moved to the newer Arduino Uno, and are currently researching how we might leverage the new USB capabilities that it provides.

Tito and I are hard at work sourcing all the materials for our kit, which we plan on shipping mid-December. We have large lead times on some of the more custom or hard-to-find components, so our priority right now is getting our orders in. As such, some tasks such as documenting the design & assembly instructions have taken a back seat for the moment, but rest assured that when we begin shipping kits, there will be complete open source designs/bill of materials on our website for those of you that want to hack on your own. We’ve also started accepting pre-orders for our kits if you want to be assured of getting one of the first batch of units. Kits will include all the parts you need to build your own OpenPCR – you’ll just need some basic tools like screwdrivers.

We have plans for some great new things once we finally get past our OpenPCR ship date — stay tuned!

Reversing a longstanding policy, the federal government said on Friday

that human and other genes should not be eligible for patents because

they are part of nature. The new position could have a huge impact on

medicine and on the biotechnology industry.

The new position was declared in a friend-of-the-court brief filed by

the Department of Justice late Friday in a case involving two human

genes linked to breast and ovarian cancer.

“We acknowledge that this conclusion is contrary to the longstanding

practice of the Patent and Trademark Office, as well as the practice of

the National Institutes of Health and other government agencies that

have in the past sought and obtained patents for isolated genomic DNA,”

the brief said.

It is not clear if the position in the legal brief, which appears to

have been the result of discussions among various government agencies,

will be put into effect by the Patent Office.

If it were, it is likely to draw protests from some biotechnology

companies that say such patents are vital to the development of

diagnostic tests, drugs and the emerging field of personalized medicine,

in which drugs are tailored for individual patients based on their

genes.

“It’s major when the United States, in a filing, reverses decades of

policies on an issue that everyone has been focused on for so long,”

said Edward Reines, a patent attorney who represents biotechnology

companies.

The issue of gene patents has long been a controversial and emotional

one. Opponents say that genes are products of nature, not inventions,

and should be the common heritage of mankind. They say that locking up

basic genetic information in patents actually impedes medical progress.

Proponents say genes isolated from the body are chemicals that are

different from those found in the body and therefore are eligible for

patents.

The Patent and Trademark Office has sided with the proponents and has

issued thousands of patents on genes of various organisms, including on

an estimated 20 percent of human genes.

But in its brief, the government said it now believed that the mere

isolation of a gene, without further alteration or manipulation, does

not change its nature.

“The chemical structure of native human genes is a product of nature,

and it is no less a product of nature when that structure is ‘isolated’

from its natural environment than are cotton fibers that have been

separated from cotton seeds or coal that has been extracted from the

earth,” the brief said.

However, the government suggested such a change would have limited

impact on the biotechnology industry because man-made manipulations of

DNA, like methods to create genetically modified crops or gene

therapies, could still be patented. Dr. James P. Evans, a professor of

genetics and medicine at the University of North Carolina, who headed a

government advisory task force on gene patents, called the government’s

brief “a bit of a landmark, kind of a line in the sand.”

He said that although gene patents had been issued for decades, the

patentability of genes had never been examined in court.

That changed when the American Civil Liberties Union and the Public

Patent Foundation organized various individuals, medical researchers and

societies to file a lawsuit challenging patents held by Myriad Genetics

and the University of Utah Research Foundation. The patents cover two

genes, BRCA1 and BRCA2, and the over $3,000 analysis Myriad performs on

the genes to see if women carry mutations that predispose them to breast

and ovarian cancers.

In a surprise ruling in March, Judge Robert W. Sweet of the United

States District Court in Manhattan ruled the patents invalid. He said

that genes were important for the information they convey, and in that

sense, an isolated gene was not really different from a gene in the

body. The government said that that ruling prompted it to re-evaluate

its policy.

Myriad and the University of Utah have appealed.

Saying that the questions in the case were “of great importance to the

national economy, to medical science and to the public health,” the

Justice Department filed an amicus brief that sided with neither party.

While the government took the plaintiffs’ side on the issue of isolated

DNA, it sided with Myriad on patentability of manipulated DNA.

Myriad and the plaintiffs did not comment on the government’s brief by

deadline for this article.

Mr. Reines, the attorney, who is with the firm of Weil Gotshal & Manges

and is not involved in the main part of the Myriad case, said he thought

the Patent Office opposed the new position but was overruled by other

agencies. A hint is that no lawyer from the Patent Office was listed on

the brief.

Reversing a longstanding policy, the federal government said on Fridaythat human and other genes should not be eligible for patents becausethey are part of nature. The new position could have a huge impact onmedicine and on the biotechnology industry.
The new position was declared in a friend-of-the-court brief filed bythe Department of Justice late Friday in a case involving two humangenes linked to breast and ovarian cancer.
“We acknowledge that this conclusion is contrary to the longstandingpractice of the Patent and Trademark Office, as well as the practice ofthe National Institutes of Health and other government agencies thathave in the past sought and obtained patents for isolated genomic DNA,”the brief said.
It is not clear if the position in the legal brief, which appears tohave been the result of discussions among various government agencies,will be put into effect by the Patent Office.
If it were, it is likely to draw protests from some biotechnologycompanies that say such patents are vital to the development ofdiagnostic tests, drugs and the emerging field of personalized medicine,in which drugs are tailored for individual patients based on theirgenes.
“It’s major when the United States, in a filing, reverses decades ofpolicies on an issue that everyone has been focused on for so long,”said Edward Reines, a patent attorney who represents biotechnologycompanies.
The issue of gene patents has long been a controversial and emotionalone. Opponents say that genes are products of nature, not inventions,and should be the common heritage of mankind. They say that locking upbasic genetic information in patents actually impedes medical progress.Proponents say genes isolated from the body are chemicals that aredifferent from those found in the body and therefore are eligible forpatents.
The Patent and Trademark Office has sided with the proponents and hasissued thousands of patents on genes of various organisms, including onan estimated 20 percent of human genes.
But in its brief, the government said it now believed that the mereisolation of a gene, without further alteration or manipulation, doesnot change its nature.
“The chemical structure of native human genes is a product of nature,and it is no less a product of nature when that structure is ‘isolated’from its natural environment than are cotton fibers that have beenseparated from cotton seeds or coal that has been extracted from theearth,” the brief said.
However, the government suggested such a change would have limitedimpact on the biotechnology industry because man-made manipulations ofDNA, like methods to create genetically modified crops or genetherapies, could still be patented. Dr. James P. Evans, a professor ofgenetics and medicine at the University of North Carolina, who headed agovernment advisory task force on gene patents, called the government’sbrief “a bit of a landmark, kind of a line in the sand.”
He said that although gene patents had been issued for decades, thepatentability of genes had never been examined in court.
That changed when the American Civil Liberties Union and the PublicPatent Foundation organized various individuals, medical researchers andsocieties to file a lawsuit challenging patents held by Myriad Geneticsand the University of Utah Research Foundation. The patents cover twogenes, BRCA1 and BRCA2, and the over $3,000 analysis Myriad performs onthe genes to see if women carry mutations that predispose them to breastand ovarian cancers.
In a surprise ruling in March, Judge Robert W. Sweet of the UnitedStates District Court in Manhattan ruled the patents invalid. He saidthat genes were important for the information they convey, and in thatsense, an isolated gene was not really different from a gene in thebody. The government said that that ruling prompted it to re-evaluateits policy.
Myriad and the University of Utah have appealed.
Saying that the questions in the case were “of great importance to thenational economy, to medical science and to the public health,” theJustice Department filed an amicus brief that sided with neither party.While the government took the plaintiffs’ side on the issue of isolatedDNA, it sided with Myriad on patentability of manipulated DNA.
Myriad and the plaintiffs did not comment on the government’s brief bydeadline for this article.
Mr. Reines, the attorney, who is with the firm of Weil Gotshal & Mangesand is not involved in the main part of the Myriad case, said he thoughtthe Patent Office opposed the new position but was overruled by otheragencies. A hint is that no lawyer from the Patent Office was listed onthe brief.

Via the New York Times

Read the brief here: Department of Justice Brief on Genes

Disclosure: I am not a good lawyer. Full Disclosure: I am not a lawyer at all. Are you? Chime in!

We get a lot of wonderful comments from all of you on the OpenPCR blog. I wanted to highlight one recent post that I really liked. Tom Benedict posted the following rules of thumb on our Dieter Rams 10 Principles for Good Design post:

- Good design uses as much commercial off-the-shelf as possible. (e.g.
don’t re-invent the screw standard if you can use screws from the
hardware store or McMaster Carr.)

- Good design provides for “getatability” of the parts. This term was lifted from an article in American Machinist from the early 1900′s. (Corollary – If you design one part to be almost impossible to get to, chances are it’s the part that will break first.)

- Good design assumes the thing will have to be taken apart. (e.g. If
the faceplate of an electronics enclosure has all the lights, switches,
buttons, and knobs, and the electronics themselves are bolted to another
part of the enclosure, provide connectors so the two parts can be
separated when the enclosure is taken apart.)

- Good design follows function. (e.g. If the thing being designed needs
to be able to be stacked, don’t make it shaped like an Airstream
trailer.)

- Good design maximizes bulk purchasing and minimizes spares. (e.g. If
it requires twenty push button switches, use the same push button switch
in every case. You reduce costs through bulk purchasing, and only need
one or two spare switches to cover every switch on the device.)

- Good design is easy to make. (e.g. It is POSSIBLE to machine a
90-90-90 sharp inside corner in a block of metal, but it’s a real pain
and will cost a fortune. If a rounded corner will work just as well, use
the rounded corner: it’s easier to make.) Talk to your manufacturer.
They’ll know the tricks for making a design cheap and easy to build.

Thanks, Tom!
Tito