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Latest revision as of 15:31, 27 October 2010

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The Purpose of ZJU-IGEM Team

    The initiative that we participate in the iGem competition is simple. Because it was a great pleasure when everybody with their creative imagination, come up with the distinctive ideas in the Brain-storm session and then stands at a unique position to understand and accomplish the project. Such unique pleasure may not be easily discovered when we were sitting in classroom learning the specific subjects or doing research in the lab. Because iGEM competition encourages the multi-discipline cooperation, it impels our team to summon team members from different discipline like biology, chemistry, mathematics, software, automation with their different perspectives. As scientists and researchers these days tends to work in the more and more specialized field which leads to isolation and estrangement. We realize that iGem competition could be a precious opportunity to set-up the cooperative relationship between all the young iGEMers. Moreover, it encourage us to jump out off the intrinsic perception set by our major to listen to others opinion, similar as perspective taking in scientific research. And innovative idea may be come up with during this alternatively position changing process. More importantly, iGEM competition provides us a unique experience to play crucial roles in the booming synthetic biology realm. Since this filed is still new and booming, we could play roles as questioners, operators, biobrick producers, biobrick end-users, policy makers and even judgers. This particular character of IGEM competition leads us to pay more attention not only in terms of mere scientific research, but also we need to set up a big picture of synthetic biology in our minds, we must consider the social implication of synthetic biology and particularly our project, and to dig it even deeper, we need to enquire the philosophical significance of them.

The Aim of Human Practice Project

    Synthetic biology has become a popular concept in recent years, it appears on the newspaper, magazines and other medias frequently. The reason why synthetic biology catches so many attentions from the public is that few other scientific concepts could match the simplicity and scope of this concept. Synthetic biology poses a brilliant example of giving the public a big picture so that they can quickly understand. Then the communication between scientists and the public is possible. Yet the space between researchers and public is appropriately far enough, so the scientific research won't expose to the public opinion. However, only the comfortable public relationship is not enough, the development of synthetic biology still needs a solid foundation in a philosophical perspective to cope with the men intoxicated with the prospect of unlimited power and also with apathy with the powerless. That is what our human practice project aims to do at the beginning stage of synthetic biology.

The Implication of Our Project- Gene Composer, Bach

    Our project is named after a well-known Composer, Johann Sebastian Bach, whose bravura works brought Baroque period to its ultimate maturity. In the realm of music, composers can enrich the music styles by controlling of harmonics and adaptation of rhythms and forms. Likewise, in our project, our gene composer is able to recompose the input coding sequence by synonymous substitution, optimization and RIPS (ribosome initiation per sec) design so that the discordant tunes of codon bias in versatile biobricks could be synchronized. And by controlling the information flowing rate which represents as the RIPS, the recomposing process will significantly improve the compatibility of the biobricks and the stability of the biological machine. Additionally, our project of gene composer leaps forward to the goal of standardization. By synonymous substitution and RIPS design, researchers will be able to set up a universal language of coding sequences to characterize and standardize versatile biobricks. In might future, changing a biobrick in a biological machine will be as easy as changing a hard drives in a laptop. Plug a new one in, off you go. And that will be the plug-and-play mentality of synthetic biology world.

Philosophical Enquiry of Synthetic Biology

    Synthetic biology, combines the element of engineering, chemistry, computer science and molecular biology, seeks to assemble the biological tools necessary to redesign the living world. It is such similar as the physics applies in the electronic engineering and chemistry applies in the chemical engineering. But synthetic biology has a distinctive difference with the above two. It brings the engineering concept to the living organisms rather than to the lifeless substance. Moreover, in the might future, the distinctions between vivid biosphere and lifeless mechanical world are no longer such apparent, because synthetic biology may blurs the dividing line of these two. Considering the peculiar character of synthetic biology, we believe the philosophical enquiry of synthetic biology is both necessary and interesting.

    Generally, the theoretical science aims to understand the world, while the practical science aims to change the world. Up till now, most of researchers, policy makers and critics consider the synthetic biology as a practical science or refer to as the synthetic biology technique. Because it quite possibly brings a radical revolution to the pharmaceutical industry, to the energy industry or even to the whole manufacture industry. It is nothing wrong for the synthetic biology to be treated as practical science. As the cheap malaria medicine-artemisinin could save millions of lives in the world and the sustainable energy produced by the bacteria can solve the global warming problem. Synthetic biology, as we hope, will benefit the world a lot. But we, researchers need to be vigilant at one point, the power philosophy inspired by the scientific technique -- that as Bertrand Russell once put it -- tends to regard everything non-human as mere raw material. Ends are no longer considered, only the skillfulness of the process is valued. Synthetic biology won't be the exception. And as the synthetic biology brings the engineering concept to the living organisms, this unique character even aggravates people's worries that synthetic biology technique could be no longer the vulgarity and ugliness that industrialism producing in our environment, it will depreciate the prestige of life. Because creating life is no longer the mere privilege of nature, it could be the manufactured products on stream line. As a result, the mechanistic view of world is strengthened while as the natural beauty of life is lost. That is no doubt a mournful result.

    The prestige of biology was the main weapon to against a mechanistic view of world. Immanuel Kant once said, respect human dignity means regarding persons not just as means, but also as ends themselves. Here I would like to broaden the definition from merely human to all living organisms. To make sure the synthetic biology technique will be used for good purpose, for benefiting the whole world, and to avoid the cold-blooded mechanism dominated world, scientists need to regard living organisms not just as means, but also as ends themselves. Sometimes when scientists are facing the choice, it is not to choose the best means to a given end, it's to choose the end itself for its own sake.

Does Synthetic Biology Draw A line in Darwin's sand?

    There is a well-known argument about synthetic biology that the biotic artifacts created by the synthetic biology departs from a core principle of Darwinian natural selection, leaving those biotic artifacts with no causal connection to historical evolutionary process. To strengthen this argument, the opponents of synthetic biology emphasize that the 3.598 billion years of evolutionary history must play some role in supporting an ethic of nature. Therefore, synthetic biology, this dramatic technological development is ethically problematic.

    To discuss this argument, we need to recognize why the opponents of synthetic biology emphasize the moral significance of evolution history or the ethic of nature. The moral significance of historical evolutionary process is fundamentally important for its proponents to seize the moral high ground. And then they can distinguish the so called "natural" and "artificial" by a moral standard. However such opinion involves the mixture of teleology, as we will prove and explain later, is not absolutely objective in this argument. Now to contradict this argument, we need to answer two questions. First, does the 3.598 billion years of evolutionary history own the moral significance of itself? Second, do the biotic artifacts created by synthetic biology against the core principle of Darwinian evolution?

    For the first question, my answer is no. For the nearly four billion years, the life on the earth was entirely shaped by the nature. However, 3.598 billion years of evolutionary history is a mere empirical fact, it is ethically neutral. As Michael Sandel once put it, Morality is not empirical. Whatever you have seen in the world, whatever you discover in the science can't decide moral questions. Morality stands a certain distance from the world, from the empirical world. That's why no science could deliver moral truth. Moreover, fossils that were contained at different geological layers, presented at arranged forms have substantiated evolution as an empirical fact. In this way, we cannot claim that the 3.598 billion years of evolution could not spontaneously provide some sort of ethic of nature.

    The reason why so many people tend to believe that the history of evolution has some moral significance is associated with the belief. There seems to be an immanent goal or cosmic purpose that justified the evolution process. Living organism's behaviors seem to be controlled by a plan or guided towards a certain aim. Everything that happens right now possibly serves for a purpose in the future. The idea that final causes exist in the nature is defined as teleology. Teleology also means design and purpose analogous to that found in human actions are also inherent in the rest of nature. To the eye of an untrained observer, the evolutionary history does provide an image that living organisms follow apparent teleology. However, as Hans Reichenbach once put it, it was the greatest discovery of Charles Darwin that the apparent teleology of living organisms can be explained in a similar way by a combination of chance and selection...Darwin saw that the progress of evolution can be explained in terms of causality alone and does not require any teleological conceptions. Yes, the long, beautiful Darwinian process of creeping depends on the universal cause and effect relationship and a little bit chance. Hence, it doesn't speak for any moral significance in the remote past or in the might future.

    For the second question, we still need to focus on the core principles of Darwinian evolution. The fact that biotic artifacts created by the synthetic biology have no causal connection to historical evolutionary process is no doubt. By building a synthetic organism made solely from chemicals and blueprints of DNA, synthetic biology will be able to create biotic artifacts entirely different from the any living organism existed in the natural history. No descent relationship or even no relative relationship. So the synthetic organisms will not be the products of natural selection. However, these biotic artifacts don't against the core principle of Darwinian evolution-chance and selection. They will also undergo survival struggling, evolution and elimination, maybe in lab, in the factory or even in the natural environment. Thus, the definition of the selection needs to expand from mere natural selection to a more specific artificial selection. This scenario recalls me the study of Non-Euclidean geometry. The essential difference between Euclidean and non-Euclidean geometry is the fifth postulate-the nature of parallel lines. According to our empirical intuition, we comfortably believe that within a two-dimensional plane, for any given line l and a point A, there is exactly one line through A that does not intersect l. And that is also what Euclidean geometry states. However, as for the Non-Euclidean geometry, there are at least two lines through A that does not intersect l. Likewise, the natural selection is the fifth postulate, it is about to be endowed a broader idea because of the application of synthetic biology. Moreover, it brings us new perspectives about Darwinian evolution, the potential relationship between natural and artificial biosphere, whether they are safely isolated, orderly competitive or inherent hated. To sum up, synthetic biology won't overturn the Darwinian evolution, in the contrary, synthetic biology will apply the core spirit of Darwinian evolution to a brand new world. The development of Non-Euclidean geometry proved important to physics in 20th century, and it help physician to discover the nature of the world. Likewise, the development of synthetic biology may prove essential for the biological engineering. The industrial age is drawing to a close, the life programming epoch is coming.

References:

1. Bertrand Russell, "A History of Western Philosophy", 1946, George Allen & Unwin Ltd
2. Hans Reichenbach, "The rise of Scientific Philosophy", 1954, University of California Press
3. Michael Sandel, "Justice: What's the Right thing to do?" Harvard open course
4. Author unknown, "Culture Clash", Nature 457,129-130 (8 January 2009)
5. Michael specter, "A Life of Its Own", The New Yorker, published September 28, 2009
   http://www.newyorker.com/reporting/2009/09/28/090928fa_fact_specter?currentPage=all
6. Sara Aguiton, "SynthEthic", iGEM 2009 Team: Paris
   https://2009.igem.org/Team:Paris/Ethics_ethicalreport#top
7. iGEM 2009 Team: Imperial College London
   https://2009.igem.org/Team:Imperial_College_London/Ethics
8. Philippe Marliere, "A Manifesto for Securely Navigating Synthetic Species", Syst Synth Biol (2009) 3:77–84
9. Christophe Preston, "Synthetic Biology: Drawing a Line in Darwinʼs Sand", Environmental Values 17 (2008): 23–39.
10. Roberta Kwok, "Five Hard Truths for Synthetic Biology", Nature 463, 288-290

Redeem

    Kant separates the watching crowd, rapidly crossing the lobby of BioX research center. His assistant, John has already waited beside the guard line with a serious look.

    "John, what's up now?"

    "Paul Nivel, synthetic biology Ph.D., former senior researcher of BioX, broke into the research center this morning. The security called the police and now he has been besieged in his lab. He claimed to have carried powerful explosive so we just hold our position now. However, detector hasn't discovered any suspicious explosive chemicals, I strongly doubt that this guy is just bluffing. What do you think, Kant?"

    Kant doesn't reply immediately. He carefully observes the lab through the class wall.

    "Through a series of amplifier to induce the cascade reaction, and then the E.coli will instantly generate huge amounts of nitroglycerin. The only outsource tool that are needed is an igniter. Then the whole research center could be blown up. What a delicate bomb, isn't it?" Kant talks to the air.

    Then he turns back and says to John:" Retrieve your smug and evacuate all those people outside immediately."

    "Yes, Sir."

    "Aha, Here comes the celebrated detective Kant, what do you want?" Nivel sarcastically says. "Paul, my old friend. How is your going all these years?" Kant says while he walks slowly toward Nivel.

    "Freeze! This nothing with you! "Nivel shouts.

    "Fine. You know, I have left this field for many years, I don't want to touch those bio staff anymore." Kant jokes. "But Paul, I still remember those wonderful times when we were preparing the wGEM Competition. We were working together all day and night. I also remember Our wGEM topic derived from yours aspiration. You pledged to focus on the biosynthesis research and the development of biosynthesis techniques to produce cheap anti-ADIS drug. And in a might future, you will crash down the monopolization of some merchandize pharmaceutical company so that the poor will be able to afford to buy those drugs. It has been so many years, right?" Kant asked.

    It remains silence for several seconds.

    "That is just a college student's naïve idea." Nivel suddenly says. "Damn those companies. They cheated and betrayed me, they stole all my efforts to apply the patents while in turn, frame me as the commercial spy. Now I have been wanted by the police. Leave me away Kant, I will blow up this research center. "

    "Calm down please, I don't think we have anything that we can't talk." Kant replies.

    "It's too late. I have sold my updated version to an abroad company. It's time to say goodbye." Suddenly, the whole laboratory falls into the darkness.

    "It seems that my interferon inducer works. If they were clever enough, they should never choose the BBa_R3572 as the relay." A voice in the darkness says.

    Now only Kant and that started time bomb are left in the darkness. Kant Clearly knows that his primary target is to turn off the reversible toggle switch before the amplifier begins to work. He quickly turns on his adaptable luminescence torch, gets to the bioswitch part, and finds that the pBAD promoter has almost reached to the critical expression level. He quickly searches in his mind to recall the methods of declining the pBAD expression level and quenching this process. He suddenly remembers that when he was preparing the wGEM competition, he occasionally learned that phosphogluconate has the unique function to quench this process. Then Kant immediately turns off his torch, takes the battery out, removes the electrode and pours all the phosphogluconate electrolyte into the reversible toggle switch part.

    The timer still counts: Five, Four, Three, Two , One，Zero ...

    After a depressive silence, Kant slowly walks out the BioX research Center.

    "Where is that guy?" John asks.

    "Gone." Kant says absent-mindedly.

    "Gone? How can you let this risky guy escape?" John blamed. But Kant says nothing.

    After a short period of silence, John suggests:" Shall we make a proposal to suggest the government closing all synthetic biology labs and prohibiting all relevant research instantly."

    "No," Kant replies, "Prohibition won't eliminate the risk, since the risk doesn't stem from the synthetic biology technology itself, but rather stems from people's avariciousness and conceit. We are both victims and accomplices." Then Kant just gazes to the far distance in a poker-face.