Summer school on synthetic biology

During the week of September 15-19, 2014 I participated in the summer school on societal implications of synthetic biology. Organized by Kristin Hagen and Margret Engelhard from the European Academy of Technology and Innovation Assessment and by Georg Toepfer from the Center for Literary and Cultural Research Berlin, it was held in Berlin, Germany, at the Center for Literary and Cultural Research.

Participants came from different countries - Austria, Italy, Germany, the Netherlands, Canada and the United States. Similarly, their backgrounds were quite diverse - biology, chemistry, philosophy, sociology, political science, and communications. The main goal of the school was to have an interdisciplinary discussion about synthetic biology as an emerging area of science and its implications for society. Participants wrote papers and presented them at the school. Additionally, several experts from various fields gave their talks. Below is a short summary of what we talked about:

The meanings and metaphors of life. Synthetic biology inevitably raises questions related to our understandings of life. On one hand, there is no universal definition of life and both philosophers and scientists continue to ponder over whether it is even possible to come up with such a definition. On the other hand, there may be no need for such definition, because a) we have an intuitive understanding of what life is and adapt as it changes, and b) having limited definitions works for specific purposes, such as understanding of how to create an artificial cell or argue against the scientific possibility of creating life from scratch. Metaphors that we use to answer the grand questions of life or to promote scientific advancements in synthetic biology bring together the domains of nature, artificiality, control, and aesthetics. Those metaphors are not “innocent” as they open some opportunities and close others.

Synthetic biology (SB) as a field. Synthetic biology is not a homogeneous discipline, it is a fuse of approaches that draw on synthetic chemistry, genetic engineering, and bioinformatics. The engineering of metabolic pathways, which allows to use bacteria and other microorganisms to produce chemicals, plays an important role in SB breakthroughs. Chemical synthesis of DNA, which allows a synthesized DNA to be inserted into an existing organism, is another important area of synthetic biology. The presentations that explained various types and flavors of synthetic biology talked about cells, pathways, chassis, microbes, reproduction, and evolution; they were colorful and full of exciting possibilities. We talked about promises of synthetic biology a lot, but I don’t think that science necessarily needs promises to justify its existence. As someone pointed out, science is a quest for knowledge, it should be interesting and exciting as such. I’m not sure science is a pure quest for knowledge, considering the convergences between science, technology, and industry. Nevertheless, I completely agree that it is exciting to learn about the world even if it's not clear whether this knowledge has applications.

Forms of communication and public dialog. Previous debates, such as the mad cow disease or GMO debate, and the resulting negative reactions demonstrate the importance of transparency in public communication of science. Early public engagement is seen as a way to improve understanding and acceptance of technology. On the other hand, the goal is not simply to promote public understanding and acceptance of technoscience, but rather to let voices of the public contribute to decision-making and regulatory frameworks. Many forms of public engagement, including polls, surveys, citizen panels, public discussions, and so on, have been promoted in the EU, and the results seem to indicate that even though not many people have heard about synthetic biology, many see continuities with previous scientific advancements and technologies and are willing to consider both positive and negative aspects of it.

Even from the short overview above it is obvious that there is a great diversity in the issues surrounding synthetic biology and approaches to their evaluation. Can they be integrated or synthesized? My own suggestion is to take a problem- rather than a debate-oriented approach and look for solutions to specific problems, while avoiding taking things for granted. Everyone has their interests and values and even the best intentions may result in bad outcomes. To use M. Foucault’s approach, we need to examine the order of things and the complex arrangements of what’s visible and hidden and what or who is included and excluded.

It was a week of stimulating discussions. The atmosphere was very friendly and collegial, and the disagreements were often phrased as humorous, slightly sarcastic remarks over dinner or drinks. My take-away from this summer school is that interdisciplinary dialog is possible, necessary, and fruitful. It works provided that we have ample time to interact and go beyond formalities (i.e., beyond formal presentations and opinion polls). The school has ended, but the work continues. We will revise our papers based on collective feedback, and they will become chapters in a forthcoming book.

See also:

• a school press-release with pictures
• a great website by Britt Wray, one of the school's participants, who writes about synthetic biology, among other things, in a much more exciting way

Big data report from the White House

Another big data review, this time from the White House - "Big Data: Seizing Opportunities, Preserving Values" (pdf). The report explains what big data is (large, diverse, complex, longitudinal, distributed, making possible unexpected discoveries and creating an asymmetry of power between those who hold the data and those who intentionally or inadvertently supply it) and describes implications of big data for public and private sectors. In addition to many known and less known examples of how big data can be good or bad, the report provides initial thoughts on recommendations for big data governance. It divided its approach to policy framework into four overlapping core areas:

1. Big data and citizens - improve public services while preventing the government from accruing unlimited power by using increased surveillance, algorithmic profiling, and metadata tracking.

2. Big data and consumers - reduce cost of commercial services and personalize them while mitigating security breaches and risks of discrimination based on consumer profiles and lack of consumer awareness and data transparency.

3. Big data and discrimination - do less harm and prevent discriminatory uses of identification and re-identification techniques.

4. Big data and privacy - get used to less privacy while reconsidering the notice and consent framework.

In the concluding section the report had the following recommendations:

• Advance the Consumer Privacy Bill of Rights.
• Pass National Data Breach Legislation.
• Extend Privacy Protections to non-U.S. Persons.
• Ensure Data Collected on Students in School is Used for Educational Purposes.
• Expand Technical Expertise to Stop Discrimination.
• Amend the Electronic Communications Privacy Act.

It's a thorough report and is definitely worth a read, but similarly to my and my colleagues big data review (pre-print), it's just the beginning of studying implications and governance of big data.

NIH report: Big data recommendations based on small data?

I've been browsing slides from the last BRDI Symposium, "Finding the Needle in the Haystack: A Symposium on Strategies for Discovering Research Data Online", and found a report for the National Institutes of Health about the management and analysis of large biomedical research data (pdf available here).

It is an interesting report that provides a lot of details about data and technologies in biomedical research as well as about existing efforts in data sharing. The recommendations make sense, since they follow most of the recommendations with regard to research data - more money, more policy, more training:

• Promote data sharing by establishing a minimal metadata framework for data sharing, creating catalogs and tools and enhancing data sharing policy for NIH-funded research.
• Support the development and dissemination of informatics methods and applications by funding software development.
• Train the workforce in quantitative sciences by funding quantitative training initiatives and enhancing review expertise in quantitative methods of bioinformatics and biostatistics.

Even more interesting is what evidence is provided to support these recommendations. The report is based on a relatively small literature corpus (~25 citations plus footnotes) and on the analysis of comments that were solicited via an NIH request for information on management, integration, and analysis of large biomedical datasets. Overall, 50 respondents replied and made 244 suggestions. Is it enough data to make recommendations for NIH? If we begin with the assumption that more support for large datasets and biomedical computations is needed (which seems to be the case with this report), then there is almost no need to analyze costs and benefits of data sharing, the role of large datasets in providing solutions for biomedical problems, and so on.

HathiTrust vs The Authors Guild: It's fair use

Image from "That public domain diva" blog

The court ruled that the HathiTrust project is fair use and that they can continue with the orphan works project. Below are some details from the court's opinion, which is an interesting but sometimes hard-to-process read.

Background

Several universities partnered with Google to digitize their collections (the Mass Digitization Project). The HathiTrust partnership is creating a shared digital repository, with approximately 73% of it protected by copyright. After digitization, Google retains a copy of the book and the universities get of each scanned work, which includes images of the pages and text. After that the universities "contribute" their digital copies to the HathiTrust Digital Library ("HDL"). The works are used within the HDL in three ways: full-text search; preservation; and access for people with certified print disabilities.

In addition to this, four of the HathiTrust Universities (all except Indiana University), participate in the Orphan Works Project (OWP), an initiative that provides full copies of works that are protected by copyright but whose rights holders cannot be located.

Problem / Motions

According to The Authors Guild (plaintiffs), the digitization creates two reproductions of the original (images and text? I didn't understand this). And in total, 12 unauthorized digital copies are created. Plaintiffs sought to prohibit the universities from a) provision of works to Google, b) the reproduction, distribution and display of copyrighted works, c) proceeding with the orphan works, and to impound all unauthorized digital copies within their possession.

Decisions

There are many arguments in the opinion, but the most important were that associations cannot enforce the rights of their members with regard to copyright, that the orphan works project is not ripe for adjudication, so the universities can continue working on it, and that the way HathiTrust library uses the digitized material can be accepted as fair use.

The totality of the fair-use factors suggest that copyright law’s "goal of promoting the Progress of Science . . . would be better served by allowing the use than by preventing it. ... The enhanced search capabilities that reveal no in-copyright material, the protection of Defendants’ fragile books, and, perhaps most importantly, the unprecedented ability of print-disabled individuals to have an equal opportunity to compete with their sighted peers in the ways imagined by the ADA protect the copies made by Defendants as fairuse.

While I think that the arguments for further digitization and more access to copyrighted material could've been stronger, it's a good start. I hope sooner or later more authors see the benefit of providing access to digital copies of their materials through the libraries and we'll develop better business models to satisfy the goals of providing access, promoting creativity, and making sure authors get paid for their work.

Cloud computing

From an article in First Monday [Jaeger, P., Lin, J., Grimes, J., & Simmons, S. (2009). Where is the cloud? Geography, economics, environment, and jurisdiction in cloud computing. First Monday, 14 (5)]:

Cloud computing refers to an emerging model of computing where computing services are provided by specialized data centers. The origin of the metaphor of cloud computing is in computer diagrams.

A cloud consists of large data centers operated by technology companies, which provide technology development, physical infrastructure, process management, etc. and deliver a variety of computing services to the users. The cloud can host users' applications, facilitate batch processing (e.g., processing an archive of newspaper articles), or provide other services in conjunction with existing IT infrastructures (cloud bursting or handling peaks in traffic).

Where is the cloud? The question is important because "cloud computing represents centralization of information and computing resources, which can be easily controlled by corporations and governments". The following considerations are important for the construction of data centers:

• Physical space (geography, weather, safety)
  
• Proximity to high–capacity Internet connections
• Affordable electricity and other energy resources
• The laws, policies, and regulations of the jurisdiction

The latter includes the issues of access, reliability, security, confidentiality and privacy, liability, intellectual property, ownership of data, portability of data, and auditability.

Lack of international standards and policies slows down the development and use of cloud computing. Also, education of users is important. Currently, most information is provided in terms of services (ToS) and similar documents, which have poor readability.

Stock issues

Working on my paper to be presented at the ICA annual conference, I stumbled upon a very interesting point (the PDF was password-protected, so I had to manually type the whole quote - very annoying):

In argumentation and debate theory, stock issues are the general issues that a policy advocate must successfully address in order to persuade targets in favor of a proposed action (Ehninger & Brockeriede, 1978; Inch & Warnick, 2002; Lee & Lee, 1989). Most theorists agree that successful policy persuasion depends on addressing two major aspects of the problem - ill and blame - and two critical aspects of its solution: cure and cost-benefit (e.g., Inch & Warnick, 2002). That is, policy advocates must establish that there is a significant wrong or harm to be resolved (ill), that particular causes are to blame (blame), that the advocated plan of action can work to resolve ill (cure), and that the plan has both strong benefits and few manageable limitations (cost-benefit)

Framing in policy terms can be viewed as a rhetorical strategy in debates that touch upon issues that go beyond policy issues.

Further reading:

• Ehninger, D., & Brockeriede, W. (1978). Decision by debate (2nd ed.) New York: Harper and Row.
• Inch, E.S., & Warnick, B. (2002). Critical thinking and communication: The use of reason in argument. Boston: Allyn & Bacon.