March 11, 2014
Synthetic biologists shine light on genetic circuit analysis
(R & D) – In a significant advance for the growing field of synthetic biology, Rice Univ. bioengineers have created a toolkit of genes and hardware that uses colored lights and engineered bacteria to bring both mathematical predictability and cut-and-paste simplicity to the world of genetic circuit design.
March 6, 2014
“Biological time travel”
(Harvard Magazine) – From glowing fish to bacteria that can count, synthetic biologists are now able to create life forms never before seen on earth. “Historians and Ecclesiastes be damned,” says Sophia Roosth, assistant professor in the history of science. “In the first decades of the twenty-first century, a number of things are new under the sun.” In a lecture last Wednesday drawn from her forthcoming book, Synthetic: How Life Got Made, Roosth, a Joy Foundation Fellow this year at the Radcliffe Institute for Advanced Study, described her analysis of recent attempts at “de-extinction,” the effort to recreate extinct or endangered species using modern technologies.
March 5, 2014
Synthetic Biology and Venter’s Life at the Speed of Light
Craig Venter’s book Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life describes the completion of the first functioning organism with a completely synthetic genome and places this accomplishment within the context of the history of genetics. While several reviews can be found online, this article will look at the specific bioethics issues that arise in discussing Venter’s process of making a synthetic organism as well as his vision for a future where digital technology and biological information merge to potentially solve many of the world’s problems.
Venter’s goals are to determine a minimal genome necessary for life, create this genome in the lab, and create the necessary cellular machinery to operate the genome. In the book, he explores the definition of life, and feels that his research helps answer the question “What is life?”
Summary of the Process
Venter’s group began by synthesizing the genome of Phi X 174. Phi X 174 was the first virus genetically sequenced, so it was used as a test subject for the Venter group’s process for synthesizing long pieces of DNA in the laboratory. They wanted to use this well-studied genome to double check that their process was working. At that time, scientists had not successfully made long sequences of DNA in the lab without the DNA breaking or introducing errors. By 1999 the Venter group was able to successfully re-create the DNA sequence for Phi X 174 using their method.
While the media may have touted the construction of the Phi X 174 genome as “creating life in the lab” the Venter group did not consider it so because Phi X 174 is a virus, not a cellular organism. Venter considered this accomplishment merely one step toward the end goal of making an actual synthetic organism.
In 2007 the Venter group was able to reconstruct the genome of M. genitalium, a well-studied bacterial organism. This established a method by which they would then construct a genome that had never been constructed in the laboratory before. Additionally, they demonstrated that the genome of one bacterial organism can be placed into the cell of a different species of bacteria, which had its DNA removed, and the cell will behave according to the identity of new DNA. In the end, they synthesized a M. mycoides genome and placed it within a M. capricolum cell. Final tests showed that the organism behaved like a M. mycoides cell (Venter, 123).
Ref: “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome” Science
After the preliminary studies with Phi X 174, Venter funded a private review board to investigate the ethics and implications of making life in the lab. This group was headed by Arthur Caplan, at the time working at the University of Pennsylvania. The review was published in Science as “Ethical Considerations in Synthesizing a Minimal Genome.”
Additionally, because the Venter group had constructed a virus, and there were political issues associated with the potential for other countries making synthetic viruses, completion of the Phi X 174 also sparked an ethics review by the government’s National Science Advisory Board for Biosecurity on dual-use research.
Then, in 2010, when the J. Craig Venter Institute announced that they had created “the world’s first self-replicating synthetic (human-made from chemical parts) genome in a bacterial cell of a different species, President Obama had the Presidential Commission for the Study of Bioethical Issues evaluate the research and its implications. The Commission published a document entitled “New Directions: The Ethics of Synthetic Biology and Emerging Technologies” evaluating the ethical issues surrounding Venter’s work.
Both the independent review board and the Presidential Commission for the Study of Bioethical Issues brought up several key points, one of the more important of them is whether Venter actually created life in the lab. Both they and Venter point out that synthetic biology is really a form of genetic engineering (Venter, 83), so many of the same ethical concerns that were considered when the human genome project was happening apply to synthetic biology as well.
There are, however, a few additional bioethics issues that are specific to this technology:
- The Venter group did develop a robust approach to making large sequences of DNA in the lab by inputting the desired code into the computer. While some question whether this technology can really be used to make a functioning bacterial cell, it does have implications for creating a synthetic virus. Viruses are rather simple organisms that consist of a container for holding DNA, the actual viral DNA (or RNA) that invades a cell, and sometimes, a virus will have some mechanism for inserting itself into a cell. The concern is that this technology may be used for bioterrorism. This is why the government board on dual-use technologies evaluated the research. While Venter sees his work as solving more problems than it creates, he considers this one of the key areas of concern (Venter, 155).
- Because the bacterial cells with the synthetic DNA are capable of replication, there is potential to introduce synthetic organisms, ones without precursor parents, into the environment. Unlike naturally-occurring organisms, these do not have an ancestral history. Venter lauds this as an accomplishment because, as he stated in the beginning of the book, he sees the scientific endeavor as understanding and controlling life (Venter, 8), and introducing new organisms into the environment is a type of control. However, the President’s Commission says that this can also be cause for concern. Indeed, they question whether synthetic organisms, once released into the wild, will be controllable “We are far from being proficient speakers of the language of life, and our capacity to control synthetic organisms that we design and release into the world is promising but unproven” (Commission, 22).
- Synthetic biology is a changing field, and while ethical recommendations and considerations have been made, the President’s Commission believes that dialog, critique, and public education are important for this changing field (Commission, 15-16). To that end, the Commission developed some guiding principles that Venter mentions but does not discuss in detail in his book: 1) public beneficence, 2) responsible stewardship, 3) intellectual freedom and responsibility, 4) democratic deliberation, and 5) justice and fairness. (See The Commission’s report for details on each of these.)
- Finally, there is a question of how to deal with patents. While the process to make a synthetic organism may be patentable, are synthetic genomes able to be patented? They do not fall under the category of “natural phenomena” because they were technically engineered. However, as we saw with the Myriad Genetics’ case, one cannot patent human genes.Additionally, there may be a question of how similar is too similar. In the case of Venter’s research, the synthetic genes are modeled on naturally occurring genes, but may have slight differences. This also brings up the question of whether living things can be patented at all, assuming Venter’s group did make a novel living organism in the lab.
While the goal of this article is to address bioethics issues, there are several philosophical issues that play an important role in Life at the Speed of Light that ought to be mentioned. The book begins by contemplating what the definition of life is. According to Venter, his experiment answers this question by showing that life is information, namely DNA.
A key theme throughout Life at the Speed of Light is Venter’s exasperation with vitalism. In this case, he is referring to the scientific use of the term “vitalism,” a term that was originally used to describe the belief that cells have a vital force that cannot be measured empirically. Venter, however, expands the term to mean a belief that life is anything more than chemistry (Venter, 17 and 18). In other words, he uses an antiquated notion to encompass anything other than his definition of life. For Venter, the information and complexity seen in the cell emerges out of chemical properties, and his group’s ability to replace the genome of one organism with another serves, at least from his point of view, as definitive proof that vitalism is an antiquated notion based on poor science:
The other major impact of the first genome transplants was that they provided a new, deeper understanding of life. My thinking about life had crystallized as we conducted this research. DNA was the software of life, and if we changed that software, we changed the species, and thus the hardware of the cell. This is precisely the result that those yearning for evidence of some vitalistic force feared would come out of good reductionist science, of trying to break down life, and what is meant to be alive, into basic functions and simple components. Our experiments did not leave much room to support the views of the vitalists or of those who want to believe that life depends on something more than a complex composite of chemical reactions. (Venter, 109)
Venter is uninterested in the implications of a purely reductionistic view of life and expressed surprise that the ethics board that he funded spent time in their Science paper discussing the religious and philosophical implications (Venter, 81). For Venter, ethics appears to be about permissibility. Is he doing anything illegal or that will cause religious groups to protest? The ethics committee said that they “could not find references in the Bible or other religious writings that forbade the creation of new forms of life” (Venter, 79). For Venter, this signified that he did his due diligence to appease those who may have philosophical or religious concerns about his work.
Finally, Venter addresses his critics’ claims that he did not actually make life in the lab, because he used already existing templates and cellular machinery (See, for example, page 32 of the Commission’s report). Some contend that he did not make life “from scratch.” Venter appropriately points out the ambiguity of the phrase, “from scratch,” and questions what his detractors would consider a completely synthetic organism (132). However, he does not adequately address the fact that the two species of bacteria were specifically chosen because their genetics were similar and therefore, the cellular machinery (organelles and proteins) used to read the DNA should be compatible between one species and the other. Furthermore, his group specifically chose M. mycoides as the DNA donor and M. capricolum as the host cell because they knew from other studies that the experiment does not work if M. capricolum is the DNA donor and M. mycoides is the host (Venter, 102). He likens the feat to trying to run PC software on a Mac (Venter, 112), but really, it is more like trying to get a Word document on a PC to open in the Office Program for Mac. However, in responding to his critics, Venter downplays the role of cellular machinery in order to advance the narrative that DNA is the essence of life.
This article is meant to address the book by Venter, rather than the entire field of synthetic biology. It is difficult to write about the bioethics issues in Life at the Speed of Light because Venter’s goal is to discuss the process and laud the benefits. It downplays the concerns, but assures the reader that the concerns have been adequately addressed.
Most disconcerting about the book is Venter’s disregard for any views contrary to his own or that critique his work. Venter discusses his own position with an air of rational superiority while he, himself, makes un-objective philosophical claims. He believes in the moral and intellectual superiority of scientists, and presumes that if scientists are doing synthetic biology, it can only serve for the public good and for furthering progress. His goal is to convince the public of the benefits of synthetic biology. While the book seems educational in nature, it is not so much about empowering the public to decide whether synthetic biology is safe, but rather to show them that it really is all under control.
Venter, J. Craig. Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life. New York: Viking Penguin, 2013.
February 21, 2014
MIT’s Synthetic Biology Center collaborates with Pfizer to advance synthetic biology research in drug discovery and development
(MIT News) – Today, MIT’s Synthetic Biology Center (MIT SBC) announced a collaboration with Pfizer Inc. that is designed to translate leading discoveries in synthetic biology to advance drug discovery and development technologies. This three-year research collaboration spans multiple therapeutic areas at Pfizer and involves several core investigators within the MIT SBC. The MIT SBC is an interdisciplinary research and educational initiative of the Department of Biological Engineering, which integrates faculty from other MIT departments.
February 19, 2014
What technology is revolutionizing cancer treatment? The same one that is changing the world
(Medical Daily) – What are the most tomorrow technologies in the field of cancer medicine? The first thought that comes to mind for many people would be personalized medicine, while others would immediately champion nanotechnology. Yet underlying both these revolutionary fields is the new technology that has been made possible by the startling advances in genomic sequencing: synthetic biology. Scientists are beginning to design DNA molecules, proteins, and complex genetic circuits — biological organisms.
February 6, 2014
NASA: Engineered microbes could help support life in space
(Costa Rica Times) – Engineered microbes could aid in the settlement of life in space, NASA Ames Research Center’s director said at a Stanford conference on Tuesday. Altered bacteria could provide the necessary ingredients for life, such as breathable air, on places like Mars or the moon, S. Pete Worden told the annual symposium of the NASA Innovative Advanced Concepts Program. “We can edit the genome to help us live in space,” he said.
January 31, 2014
Synthetic-biology firms shift focus
(Nature) – The product marks a shift for the industry, which has typically focused on the synthesis of drugs and commodities such as biofuels and rubber. Now, synthetic-biology companies are turning to ‘fine chemicals’: food and fragrance ingredients that command high prices in small batches. “The products take less time to develop, they take less money to develop, and they’re much less risky,” says Goldsmith.
January 17, 2014
Scientists simulate life by creating first functional ‘plastic’ cell: How close are we to producing artificial life?
Scientists are hoping to understand the origin of life better by creating artificial cells in the lab. A group of scientists from Radboud University in Nijmegen, Netherlands, has for the first time created an artificial “plastic” cell, complete with working organelles that are able to carry out chemical reactions. The study was published in the journal Angewandte Chemie. (Medical Daily)
January 15, 2014
Fun with genetic engineering: Why letting students tinker with microorganisms is good for education and society
Elaborate competitions to build the best robot or design cages to protect falling eggs have been a rite of passage for generations of engineering students. Today, there’s a new contest with the same creativity and competitive spirit, but vastly more sophisticated projects–like mixing-and-matching bits of DNA to create new microorganisms that produce biofuels or costly medicines. (Huffington Post)
January 9, 2014
Synthetic gene helps HIV vaccine hit shape-shifting foe
An HIV vaccine that uses a synthetic gene to trigger an immune response might offer a way to protect against the virus where others have failed. Most vaccines work by training immune cells called B-cells to produce antibodies against a virus. Another approach is to stimulate T-cells, which kill cells infected with the virus. This is known as inducing cellular immunity. (New Scientist)
December 28, 2013
Interview with Dr. Eric Drexler
Interview with Dr. Eric Drexler during his recent book tour for Radical Abundance (PublicAffairs, 2013).
“To begin with, it’s important to understand that the prospects I describe involve something more than nanotechnology in the present sense — they involve developments that are outside the fields of material science and much simple nanoscale devices. The long-range revolutionary potential of developments at the nanoscale will come from atomically precise manufacturing, a technology analogous to digital information technologies or 3D printing: a general-purpose way to make intricate patterns of something, in this case, patterns of advanced materials that form advanced products of all kinds.” (Nanotechnology Now)
December 17, 2013
Booster of red blood cells synthesized for first time
In a tour de force of biological chemistry, scientists have pieced together an entire protein hormone from scratch, and demonstrated that it works just as well in mice as the natural version. If verified, the complete synthesis of erythropoietin, a hormone that stimulates the production of red blood cells, would mark a new stage in the production and study of biological therapeutics. (Scientific American)
December 13, 2013
Fun with genetic engineering: Why letting students tinker with microorganisms is good for education and society
As the New York Times observed, “iGEM has been grooming an entire generation of the world’s brightest scientific minds to embrace synthetic biology’s vision – without anyone really noticing, before the public debates and regulations that typically place checks on such risky and ethically controversial new technologies have even started.” (Forbes)
December 9, 2013
‘Life at the Speed of Light: From Double Helix to Dawn of Digital Life’ by J. Craig Venter
Now, in “Life at the Speed of Light,” Venter goes behind the breakthrough, exploring the biological advances that made his artificial critter possible and offering an insider’s view of one of science’s hottest new fields. (Washington Post)
November 19, 2013
Do-it-yourself biologists doing no harm, survey finds
There’s little to fear from the existing Do-It-Yourself Biology (DIYbio) movement, concludes a report released today by the Woodrow Wilson International Center for Scholars in Washington, D.C. “There’s been a lot of debate in the biosecurity community about what DIYers may or may not be doing, from making narcotics to pandemics to viruses that kill heads of state (I’m not joking),” writes Wilson fellow and report co-author Daniel Grushkin in an e-mail to ScienceInsider. He hopes the report will “dispel a lot of these myths, so that the discussion can move beyond suspicion and risks, and start focusing on opportunities.” (Science)
November 18, 2013
Genetic engineering enables human immunity to take on cancer, revolutionary therapy
Developments in genetic engineering make it possible to ‘re-programme’ the human immune system so that T cells – white blood cells that normally fight viruses – recognize and kill cancer cells. This approach, which directly harnesses the potency of the immune system, holds the prospect of a powerful new weapon in the fight against cancer. (Science World Report)
Design fiction: Grow your own, life after nature
“GROW YOUR OWN… is a new exhibition created by Science Gallery at Trinity College Dublin that invites you to consider some of the potentially ground-breaking applications and uncertain implications of synthetic life. Tackling the provocative questions that designing life raises, GROW YOUR OWN… gives you the opportunity to help shape future discussions around synthetic biology – an emerging approach to genetic engineering, bringing together engineers, scientists, designers, artists and biohackers to design ‘living machines’. (Wired)
November 12, 2013
Changing the communication: Polymers disrupt bacterial communication
Artificial materials based on simple synthetic polymers can disrupt the way in which bacteria communicate with each other, a study led by scientists at The University of Nottingham has shown. The findings, published in the journal Nature Chemistry, could further our knowledge on how better to control and exploit bacteria in the future and will have implications for work in the emerging field of synthetic biology. (Phys.org)
November 6, 2013
Will the Nagoya Protocol impact your synthetic biology research?
The United Nations (UN) is working to ensure that the benefits of genetic resources are shared in a fair and equitable way via the Nagoya Protocol to the Convention on Biological Diversity, though questions remain about how this treaty will impact research in synthetic biology. A new report from the Synthetic Biology Project at the Woodrow Wilson International Center for Scholars looks at how the protocol may affect U.S. researchers working in the field of synthetic biology. (Phys.org)
November 5, 2013
Designer piercings: New membrane pores with DNA nanotechnology
A new way to build membrane-crossing pores, using Lego-like DNA building blocks, has been developed by scientists at UCL, in collaboration with colleagues at the University of Cambridge and the University of Southampton. The approach provides a simple and low cost tool for synthetic biology and the technique has potential applications in diagnostic devices and drug discovery. (Phys.org)
October 30, 2013
Synthetic biology’s malaria promises could backfire
Claims about the benefits of a biotech project to make artemisinin are overblown, says Claire Marris. In April, a consortium led by the global health NGO PATH — and comprising the University of California, Berkeley, synthetic biology company Amyris and pharmaceutical firm Sanofi — announced the first industrial production of ‘semi-synthetic artemisinin’. (Sci Dev Net)