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November 22 2013

Koalition plant DNA-Rasterfahndung

§ 81 h StPO sieht sog. Massengentests vor. Allerdings sind diese grundsätzlich freiwillig und bedürfen der schriftlichen Einwilligung der Betroffenen. Bei der Fahndung in Mordfällen wird freilich ein erheblicher Druck erzeugt, weil sich der Testverweigerer zwangsläufig verdächtigt macht. Diese Regelung will die große Koalition nach einem Bericht von ZEIT-Online jetzt dahingehend ausweiten, dass künftig zur Aufklärung von Sexual- und Gewaltverbrechen bei Massengentests auch sogenannte Beinahetreffer verwertet werden können, wenn die Teilnehmer vorab über die Verwertbarkeit zulasten von Verwandten belehrt worden sind. Dieses “Family-Searching” wäre bereits deshalb problematisch, weil damit das Erfordernis der Einwilligung des Betroffenen umgangen würde.

Derzeit dürfen festgestellte DNA-Identifizierungsmuster mit den DNA-Identifizierungsmustern von Spurenmaterial automatisiert abgeglichen werden, um feszustellen, ob das Spurenmaterial von diesen Personen stammt. Künftig könnte man dann auch feststellen, ob das Spurenmaterial zu einem Verwandten einer Person passt, deren DNA man schon erfasst hat. Dieser Verwandte hat natürlich nie in den Gentest eingewilligt. Das ist nicht nur verfassungsrechtlich fragwürdig, sondern erhöht auch die Gefahr der Verdächtigung oder gar Verurteilung Unschuldiger. Denn es gibt auch uneindeutiges Spurenmaterial, das nicht wissenschaftlich exakt einer Person zuzuordnen ist.

In allen möglichen Bereichen erliegt die Politik immer wieder der Verlockung, alles das was technisch möglich ist bzw. möglich erscheint, auch umzusetzen. Das läuft auf eine rechtsstaatswidrige Ermittlung um jeden Preis hinaus, die die Grenze zum Unrechtsstaat langsam verwischt.

(via lawblog)

October 03 2012

Biohacking: The next great wave of innovation

Genspace and Biocurious logosGenspace and Biocurious logosI’ve been following synthetic biology for the past year or so, and we’re about to see some big changes. Synthetic bio seems to be now where the computer industry was in the late 1970s: still nascent, but about to explode. The hacker culture that drove the development of the personal computer, and that continues to drive technical progress, is forming anew among biohackers.

Computers certainly existed in the ’60s and ’70s, but they were rare, and operated by “professionals” rather than enthusiasts. But an important change took place in the mid-’70s: computing became the domain of amateurs and hobbyists. I read recently that the personal computer revolution started when Steve Wozniak built his own computer in 1975. That’s not quite true, though. Woz was certainly a key player, but he was also part of a club. More important, Silicon Valley’s Homebrew Computer Club wasn’t the only one. At roughly the same time, a friend of mine was building his own computer in a dorm room. And hundreds of people, scattered throughout the U.S. and the rest of the world, were doing the same thing. The revolution wasn’t the result of one person: it was the result of many, all moving in the same direction.

Biohacking has the same kind of momentum. It is breaking out of the confines of academia and research laboratories. There are two significant biohacking hackerspaces in the U.S., GenSpace in New York and BioCurious in California, and more are getting started. Making glowing bacteria (the biological equivalent of “Hello, World!”) is on the curriculum in high school AP bio classes. iGem is an annual competition to build “biological robots.” A grassroots biohacking community is developing, much as it did in computing. That community is transforming biology from a purely professional activity, requiring lab coats, expensive equipment, and other accoutrements, to something that hobbyists and artists can do.

As part of this transformation, the community is navigating the transition from extremely low-level tools to higher-level constructs that are easier to work with. When I first leaned to program on a PDP-8, you had to start the computer by loading a sequence of 13 binary numbers through switches on the front panel. Early microcomputers weren’t much better, but by the time of the first Apples, things had changed. DNA is similar to machine language (except it’s in base four, rather than binary), and in principle hacking DNA isn’t much different from hacking machine code. But synthetic biologists are currently working on the notion of “standard biological parts,” or genetic sequences that enable a cell to perform certain standardized tasks. Standardized parts will give practitioners the ability to work in a “higher level language.” In short, synthetic biology is going through the same transition in usability that computing saw in the ’70s and ’80s.

Alongside this increase in usability, we’re seeing a drop in price, just as in the computer market. Computers cost serious money in the early ’70s, but the price plummeted, in part because of hobbyists: seminal machines like the Apple II, the TRS-80, and the early Macintosh would never have existed if not to serve the needs of hobbyists. Right now, setting up a biology lab is expensive; but we’re seeing the price drop quickly, as biohackers figure out clever ways to make inexpensive tools, such as the DremelFuge, and learn how to scrounge for used equipment.

And we’re also seeing an explosion in entrepreneurial activity. Just as the Homebrew Computer Club and other garage hackers led to Apple and Microsoft, the biohacker culture is full of similarly ambitious startups, working out of hackerspaces. It’s entirely possible that the next great wave of entrepreneurs will be biologists, not programmers.

What are the goals of synthetic biology? There are plenty of problems, from the industrial to the medical, that need to be solved. Drew Endy told me how one of the first results from synthetic biology, the creation of soap that would be effective in cold water, reduced the energy requirements of the U.S. by 10%. The holy grail in biofuels is bacteria that can digest cellulose (essentially, the leaves and stems of any plant) and produce biodiesel. That seems achievable. Can we create bacteria that would live in a diabetic’s intestines and produce insulin? Certainly.

But industrial applications aren’t the most interesting problems waiting to be solved. Endy is concerned that, if synthetic bio is dominated by a corporate agenda, it will cease to be “weird,” and won’t ask the more interesting questions. One Synthetic Aesthetics project made cheeses from microbes that were cultured from the bodies of people in the synthetic biology community. Christian Bok has inserted poetry into a microbe’s DNA. These are the projects we’ll miss if the agenda of synthetic biology is defined by business interests. And these are, in many ways, the most important projects, the ones that will teach us more about how biology works, and the ones that will teach us more about our own creativity.

The last 40 years of computing have proven what a hacker culture can accomplish. We’re about to see that again, this time in biology. And, while we have no idea what the results will be, it’s safe to predict that the coming revolution in biology will radically change the way we live — at least as radically as the computer revolution. It’s going to be an interesting and exciting ride.


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August 20 2012

DNA: The perfect backup medium

It wasn’t enough for Dr. George Church to help Gilbert “discover” DNA sequencing 30 years ago, create the foundations for genomics, create the Personal Genome Project, drive down the cost of sequencing,  and start humanity down the road of synthetic biology. No, that wasn’t enough.

He and his team decided to publish an easily understood scientific paper (““Next-generation Information Storage in DNA“) that promises to change the way we store and archive information. While this technology may take years to perfect, it provides a roadmap toward an energy efficient, archival storage medium with a host of built-in advantages.

The paper demonstrates the feasibility of using DNA as a storage medium with a theoretical capacity of 455 exabytes per gram. (An exabyte is 1 million terabytes.) Now before you throw away your massive RAID 5 cluster and purchase a series of sequencing machines, know that DNA storage appears to be very high latency. Also know that Church, Yuan Gao, and Sriram Kosuri are not yet writing 455 exabytes of data, they’ve started with a more modest goal of writing Church’s recent book on genomics to a 5.29 MB “bitstream,” here’s an excerpt from the paper:

We converted an html-coded draft of a book that included 53,426 words, 11 JPG images and 1 JavaScript program into a 5.27 megabit bitstream. We then encoded these bits onto 54,898 159nt oligonucleotides (oligos) each encoding a 96-bit data block (96nt), a 19-bit address specifying the location of the data block in the bit stream (19nt), and flanking 22nt common sequences for amplification and sequencing. The oligo library was synthesized by ink-jet printed, high-fidelity DNA microchips. To read the encoded book, we amplified the library by limited-cycle PCR and then sequenced on a single lane of an Illumina HiSeq.

If you know anything about filesystems, this is an amazing paragraph. They’ve essentially defined a new standard for filesystem inodes on DNA. Each 96-bit block has a 19-bit descriptor. They then read this DNA bitstream by using something called Polymerase Chain Reaction (PCR). This is important because it means that reading this information involves generating millions of copies of the data in a format that has been proven to be durable. This biological “backup system” has replication capabilities “built-in.” Not just that, but this replication process has had billions of years of reliability data available.

While this technology may only be practical for long-term storage and high-latency archival purposes, you can already see that this paper makes a strong case for the viability of this approach. Of all biological storage media, this work has demonstrated the longest bit stream and is built atop a set of technologies (DNA sequencing) that have been focused on repeatability and error correction for decades.

In addition to these advantages, DNA storage has other advantages over tape or hard drive — it has a steady-state storage cost of zero, a lifetime that far exceeds that of magnetic storage, and very small space requirements.

If you have a huge amount of data that needs to be archived, the advantages of DNA as a storage medium (once the technology matures) could quickly translate to significant cost savings. Think about the energy requirements of a data center that needs to store and archive an exabyte of data. Compare that to the cost of maintaining a sequencing lab and a few Petri dishes.

For most of us, this reality is still science fiction, but Church’s work makes it less so every day. Google is uniquely positioned to realize this technology. It has already been established that Google’s founders pay close attention to genomics. They invested an unspecified amount in Church’s Personal Genome Project (PGP) in 2008, and they have invested a company much closer to home: 23andme. Google also has a large research arm focused on energy savings and efficiency with scientists like Urs Hozle looking for new ways to get more out of the energy that Google spends to run data centers.

If this technology points the way to the future of very high latency, archival storage, I predict that Google will lead the way in implementation. It is the perfect convergence of massive data and genomics, and just the kind of dent that company is trying to make in the universe.

May 31 2012

February 19 2012

May 24 2010

Four short links: 24 May 2010

  1. Google Documents API -- permissions, revisions, search, export, upload, and file. Somehow I had missed that this existed.
  2. Profile of Wikileaks Founder Julian Assange (Sydney Morning Herald) -- he draws no salary, is constantly on the move, lived for a while in a compound in Nairobi with other NGOs, and cowrote the rubberhose filesystem which offers deniable encryption.
  3. OpenPCR -- producing an open design for a PCR machine. PCR is how you take a single piece of DNA and make lots of copies of it. It's the first step in a lot of interesting bits of molecular biology. They're using Ponoko to print the cases. (via davetenhave on Twitter)
  4. Metric Mania (NY Times) -- The problem isn’t with statistical tests themselves but with what we do before and after we run them. First, we count if we can, but counting depends a great deal on previous assumptions about categorization. Consider, for example, the number of homeless people in Philadelphia, or the number of battered women in Atlanta, or the number of suicides in Denver. Is someone homeless if he’s unemployed and living with his brother’s family temporarily? Do we require that a women self-identify as battered to count her as such? If a person starts drinking day in and day out after a cancer diagnosis and dies from acute cirrhosis, did he kill himself? The answers to such questions significantly affect the count. We can never be reminded enough that the context for data must be made as open as the data. To do otherwise is to play Russian Roulette with the truth.

April 13 2010

Historiker Shlomo Sand: Es gibt kein jüdisches Volk | Frankfurter Rundschau - Top-News 20100413

[...] Jetzt aber erklärte man ihm [...], dass in der Fachwissenschaft kein Mensch mehr an die Vertreibung der Juden durch römische Truppen glaube [...] Es sei zunächst christliche Lehre gewesen, dass Gott die Juden bestraft habe - für den Gottesmord oder dafür, dass sie nicht Christen geworden seien oder für beides - und ihnen ihr Land nahm [...] [W]as ist dann Israel? [...] Ihr habt uns dorthin getrieben. Die Nazis. Aber nicht nur die. [...] Niemand wollte uns haben. [...] Niemand. Darum ließen sie uns Israel. Und wir nahmen das Land und vertrieben seine Bewohner. Die [...] machten wir zu Bürgern zweiter Klasse. Israel muss das begreifen. Sonst wird es nicht überleben.[...] Es muss der Staat seiner Bürger werden [...] [der] nicht die Burg ist, auf die sich in der Not alle in der ganzen Welt verstreuten Mitglieder eines imaginären jüdischen Volkes flüchten können. [...] Das Existenzrecht Israels können wir nicht aus der Geschichte ableiten. Kein Staat der Welt kann das.

April 11 2010

Stephen Hawking: Humans are "Entering a Stage of Self-Designed Evolution" - - 20100329

[...] In the last ten thousand years the human species has been in [...] "an external transmission phase," where the internal record of information, handed down to succeeding generations in DNA, has not changed significantly. "But the external record, in books, and other long lasting forms of storage [...] has grown enormously. [...] [they] would use the term, evolution, only for the internally transmitted genetic material, and would object to it being applied to information handed down externally. [...] our human brains "with which we process this information have evolved only on the Darwinian time scale, of hundreds of thousands of years. [...] But we are now entering a new phase [...] "self designed evolution," in which we will be able to change and improve our DNA. "At first [...] these changes will be confined to the repair of genetic defects [...] I am sure that during the next century, people will discover how to modify both intelligence, and instincts like aggression."
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