Entries Tagged "DNA"

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When Biology Becomes Software

All of life is based on the coordinated action of genetic parts (genes and their controlling sequences) found in the genomes (the complete DNA sequence) of organisms.

Genes and genomes are based on code — just like the digital language of computers. But instead of zeros and ones, four DNA letters — A, C, T, G — encode all of life. (Life is messy, and there are actually all sorts of edge cases, but ignore that for now.) If you have the sequence that encodes an organism, in theory, you could recreate it. If you can write new working code, you can alter an existing organism or create a novel one.

If this sounds to you a lot like software coding, you’re right. As synthetic biology looks more like computer technology, the risks of the latter become the risks of the former. Code is code, but because we’re dealing with molecules — and sometimes actual forms of life — the risks can be much greater.

Imagine a biological engineer trying to increase the expression of a gene that maintains normal gene function in blood cells. Even though it’s a relatively simple operation by today’s standards, it’ll almost certainly take multiple tries to get it right. Were this computer code, the only damage those failed tries would do is to crash the computer they’re running on. With a biological system, the code could instead increase the likelihood of multiple types of leukemias and wipe out cells important to the patient’s immune system.

We have known the mechanics of DNA for some 60-plus years. The field of modern biotechnology began in 1972 when Paul Berg joined one virus gene to another and produced the first “recombinant” virus. Synthetic biology arose in the early 2000s when biologists adopted the mindset of engineers; instead of moving single genes around, they designed complex genetic circuits.

In 2010, Craig Venter and his colleagues recreated the genome of a simple bacterium. More recently, researchers at the Medical Research Council Laboratory of Molecular Biology in Britain created a new, more streamlined version of E. coli. In both cases, the researchers created what could arguably be called new forms of life.

This is the new bioengineering, and it will only get more powerful. Today you can write DNA code in the same way a computer programmer writes computer code. Then you can use a DNA synthesizer or order DNA from a commercial vendor, and then use precision editing tools such as CRISPR to “run” it in an already existing organism, from a virus to a wheat plant to a person.

In the future, it may be possible to build an entire complex organism such as a dog or cat, or recreate an extinct mammoth (currently underway). Today, biotech companies are developing new gene therapies, and international consortia are addressing the feasibility and ethics of making changes to human genomes that could be passed down to succeeding generations.

Within the biological science community, urgent conversations are occurring about “cyberbiosecurity,” an admittedly contested term that exists between biological and information systems where vulnerabilities in one can affect the other. These can include the security of DNA databanks, the fidelity of transmission of those data, and information hazards associated with specific DNA sequences that could encode novel pathogens for which no cures exist.

These risks have occupied not only learned bodies — the National Academies of Sciences, Engineering, and Medicine published at least a half dozen reports on biosecurity risks and how to address them proactively — but have made it to mainstream media: genome editing was a major plot element in Netflix’s Season 3 of “Designated Survivor.”

Our worries are more prosaic. As synthetic biology “programming” reaches the complexity of traditional computer programming, the risks of computer systems will transfer to biological systems. The difference is that biological systems have the potential to cause much greater, and far more lasting, damage than computer systems.

Programmers write software through trial and error. Because computer systems are so complex and there is no real theory of software, programmers repeatedly test the code they write until it works properly. This makes sense, because both the cost of getting it wrong and the ease of trying again is so low. There are even jokes about this: a programmer would diagnose a car crash by putting another car in the same situation and seeing if it happened again.

Even finished code still has problems. Again due to the complexity of modern software systems, “works properly” doesn’t mean that it’s perfectly correct. Modern software is full of bugs — thousands of software flaws — that occasionally affect performance or security. That’s why any piece of software you use is regularly updated; the developers are still fixing bugs, even after the software is released.

Bioengineering will be largely the same: writing biological code will have these same reliability properties. Unfortunately, the software solution of making lots of mistakes and fixing them as you go doesn’t work in biology.

In nature, a similar type of trial and error is handled by “the survival of the fittest” and occurs slowly over many generations. But human-generated code from scratch doesn’t have that kind of correction mechanism. Inadvertent or intentional release of these newly coded “programs” may result in pathogens of expanded host range (just think swine flu) or organisms that wreck delicate ecological balances.

Unlike computer software, there’s no way so far to “patch” biological systems once released to the wild, although researchers are trying to develop one. Nor are there ways to “patch” the humans (or animals or crops) susceptible to such agents. Stringent biocontainment helps, but no containment system provides zero risk.

Opportunities for mischief and malfeasance often occur when expertise is siloed, fields intersect only at the margins, and when the gathered knowledge of small, expert groups doesn’t make its way into the larger body of practitioners who have important contributions to make.

Good starts have been made by biologists, security agencies, and governance experts. But these efforts have tended to be siloed, in either the biological and digital spheres of influence, classified and solely within the military, or exchanged only among a very small set of investigators.

What we need is more opportunities for integration between the two disciplines. We need to share information and experiences, classified and unclassified. We have tools among our digital and biological communities to identify and mitigate biological risks, and those to write and deploy secure computer systems.

Those opportunities will not occur without effort or financial support. Let’s find those resources, public, private, philanthropic, or any combination. And then let’s use those resources to set up some novel opportunities for digital geeks and bionerds — as well as ethicists and policy makers — to share experiences and concerns, and come up with creative, constructive solutions to these problems that are more than just patches.

These are overarching problems; let’s not let siloed thinking or funding get in the way of breaking down barriers between communities. And let’s not let technology of any kind get in the way of the public good.

This essay previously appeared on CNN.com.

EDITED TO ADD (9/23): Commentary.

Posted on September 13, 2019 at 11:40 AMView Comments

Mailing Tech Support a Bomb

I understand his frustration, but this is extreme:

When police asked Cryptopay what could have motivated Salonen to send the company a pipe bomb ­ or, rather, two pipe bombs, which is what investigators found when they picked apart the explosive package ­ the only thing the company could think of was that it had declined his request for a password change.

In August 2017, Salonen, a customer of Cryptopay, emailed their customer services team to ask for a new password. They refused, given that it was against the company’s privacy policy.

A fair point, as it’s never a good idea to send a new password in an email. A password-reset link is safer all round, although it’s not clear if Cryptopay offered this option to Salonen.

Posted on November 16, 2018 at 2:11 PMView Comments

How DNA Databases Violate Everyone's Privacy

If you’re an American of European descent, there’s a 60% chance you can be uniquely identified by public information in DNA databases. This is not information that you have made public; this is information your relatives have made public.

Research paper:

“Identity inference of genomic data using long-range familial searches.”

Abstract: Consumer genomics databases have reached the scale of millions of individuals. Recently, law enforcement authorities have exploited some of these databases to identify suspects via distant familial relatives. Using genomic data of 1.28 million individuals tested with consumer genomics, we investigated the power of this technique. We project that about 60% of the searches for individuals of European-descent will result in a third cousin or closer match, which can allow their identification using demographic identifiers. Moreover, the technique could implicate nearly any US-individual of European-descent in the near future. We demonstrate that the technique can also identify research participants of a public sequencing project. Based on these results, we propose a potential mitigation strategy and policy implications to human subject research.

A good news article.

Posted on October 15, 2018 at 9:34 AMView Comments

Oblivious DNS

Interesting idea:

…we present Oblivious DNS (ODNS), which is a new design of the DNS ecosystem that allows current DNS servers to remain unchanged and increases privacy for data in motion and at rest. In the ODNS system, both the client is modified with a local resolver, and there is a new authoritative name server for .odns. To prevent an eavesdropper from learning information, the DNS query must be encrypted; the client generates a request for www.foo.com, generates a session key k, encrypts the requested domain, and appends the TLD domain .odns, resulting in {www.foo.com}k.odns. The client forwards this, with the session key encrypted under the .odns authoritative server’s public key ({k}PK) in the “Additional Information” record of the DNS query to the recursive resolver, which then forwards it to the authoritative name server for .odns. The authoritative server decrypts the session key with his private key, and then subsequently decrypts the requested domain with the session key. The authoritative server then forwards the DNS request to the appropriate name server, acting as a recursive resolver. While the name servers see incoming DNS requests, they do not know which clients they are coming from; additionally, an eavesdropper cannot connect a client with her corresponding DNS queries.

News article.

Posted on April 18, 2018 at 6:29 AMView Comments

Hacking a Gene Sequencer by Encoding Malware in a DNA Strand

One of the common ways to hack a computer is to mess with its input data. That is, if you can feed the computer data that it interprets — or misinterprets — in a particular way, you can trick the computer into doing things that it wasn’t intended to do. This is basically what a buffer overflow attack is: the data input overflows a buffer and ends up being executed by the computer process.

Well, some researchers did this with a computer that processes DNA, and they encoded their malware in the DNA strands themselves:

To make the malware, the team translated a simple computer command into a short stretch of 176 DNA letters, denoted as A, G, C, and T. After ordering copies of the DNA from a vendor for $89, they fed the strands to a sequencing machine, which read off the gene letters, storing them as binary digits, 0s and 1s.

Erlich says the attack took advantage of a spill-over effect, when data that exceeds a storage buffer can be interpreted as a computer command. In this case, the command contacted a server controlled by Kohno’s team, from which they took control of a computer in their lab they were using to analyze the DNA file.

News articles. Research paper.

Posted on August 15, 2017 at 6:00 AMView Comments

The Fallibility of DNA Evidence

This is a good summary article on the fallibility of DNA evidence. Most interesting to me are the parts on the proprietary algorithms used in DNA matching:

William Thompson points out that Perlin has declined to make public the algorithm that drives the program. “You do have a black-box situation happening here,” Thompson told me. “The data go in, and out comes the solution, and we’re not fully informed of what happened in between.”

Last year, at a murder trial in Pennsylvania where TrueAllele evidence had been introduced, defense attorneys demanded that Perlin turn over the source code for his software, noting that “without it, [the defendant] will be unable to determine if TrueAllele does what Dr. Perlin claims it does.” The judge denied the request.

[…]

When I interviewed Perlin at Cybergenetics headquarters, I raised the matter of transparency. He was visibly annoyed. He noted that he’d published detailed papers on the theory behind TrueAllele, and filed patent applications, too: “We have disclosed not the trade secrets of the source code or the engineering details, but the basic math.”

It’s the same problem as any biometric: we need to know the rates of both false positives and false negatives. And if these algorithms are being used to determine guilt, we have a right to examine them.

EDITED TO ADD (6/13): Three more articles.

Posted on May 31, 2016 at 1:04 PMView Comments

Kuwaiti Government will DNA Test Everyone

There’s a new law that will enforce DNA testing for everyone: citizens, expatriates, and visitors. They promise that the program “does not include genealogical implications or affects personal freedoms and privacy.”

I assume that “visitors” includes tourists, so presumably the entry procedure at passport control will now include a cheek swab. And there is nothing preventing the Kuwaiti government from sharing that information with any other government.

Posted on April 18, 2016 at 12:46 PMView Comments

Police Want Genetic Data from Corporate Repositories

Both the FBI and local law enforcement are trying to get the genetic data stored at companies like 23andMe.

No surprise, really.

As NYU law professor Erin Murphy told the New Orleans Advocate regarding the Usry case, gathering DNA information is “a series of totally reasonable steps by law enforcement.” If you’re a cop trying to solve a crime, and you have DNA at your disposal, you’re going to want to use it to further your investigation. But the fact that your signing up for 23andMe or Ancestry.com means that you and all of your current and future family members could become genetic criminal suspects is not something most users probably have in mind when trying to find out where their ancestors came from.

Posted on October 22, 2015 at 6:40 AMView Comments

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Sidebar photo of Bruce Schneier by Joe MacInnis.