| Journal of Cosmology, 2010, Vol 8 JournalofCosmology.com June, 2010 Or the End of Life as We Know It? Venter's achievement has drawn mostly enthusiastic praise, with some likening it to "splitting the atom" and deserving of the Nobel Prize. Yet others' warn of a "Frankenstein monster" and "genetic pollution"; fearing that artificial genes and artificial life may take over the world, and end life as we know it. Scientists and bioethicists from around the world have been asked to comment and to explain. What is the real significance of this achievement, and is there any reason to feel fear? |
1. Synthetic Biology, Synthetic Cells, and Synthetic Risk. Steven A. Benner, Ph.D., Foundation for Applied Molecular Evolution, Gainesville FL Synthesis is not a field. Rather, it is a research strategy that can be applied to any field where enabling technology allows scientists to create new subject matter by design. In these fields, synthesis can complement observation, controlled perturbation, and analysis, tools taught in middle school as central to "the" scientific method. Technology to enable synthesis has been available to chemists for more than a century, and has contributed to nearly every advance in chemical theory. Synthetic molecules helped connect chemistry to quantum mechanics. Nearly all of our understanding of the workings of enzymes, metabolisms, and even diseases, has come with the help of chemically synthesized molecules. Synthesis, in turn, allowed chemistry as a field to complete its central paradigms faster than fields lacking synthesis. These fields include, of course, astrophysics and cosmology. Imagine how much faster we might advance if we could synthesize new stars or new universes. Planetary science is similarly lacking. Sadly, the Magrathea fabled in Hitchhiker's Guide does not exist. And, of course, biology has historically also lacked synthetic technology. At least until the 1970's, when biotechnology began to recombine DNA and provide synthetic tools to biologists. At first, biologists used biotechnology to cut and paste single genes, rearranging what was found naturally to create unnatural living systems (Szybalski, 1974). In the 1980's, however, synthetic biologists moved away from Nature, synthesizing entire genes that encoded proteins (Edge et al., 1981; Nambiar et al., 1984), creating new artificial genetic systems with extra nucleotide letters (Switzer et al., 1989), and expressing proteins with more than 20 different kinds of amino acids (Wang et al., 2001). These have already had enormous impact in medicine and upon our understanding of processes basic to life (Benner, 2009). Thus, "synthetic biology" is hardly a "new field". Indeed, the term "synthetic biology" was coined in 1974 by Waclaw Syzbalski to herald this new ability of biologists to test hypotheses about the intimate connection between life and its molecular structure by synthesizing new kinds of life with altered molecular structures (Szybalski, 1974). But synthesis can do more than test hypotheses. Pursuit of a synthetic "grand challenge" forces scientists across uncharted terrain where they must encounter and solve unscripted problems. Should their design paradigms be flawed, the synthesis will fail. This failure cannot be ignored, which is something that often happens to observations that contradict a cherished paradigm. Therefore, synthesis drives discovery and paradigm change in ways that observation and analysis cannot. Problem selection is key for synthesis to have this power, however. A synthetic challenge must be beyond the frontier of what is doable, but not far beyond. Absent this ambition, synthesis does not force discovery. Too much ambition, and the synthesis fails early. Add to this the sociology of the modern academy, where the need to raise money and be promoted drives scientists towards projects that cannot possibly fail. It is hardly surprising that much of modern "synthetic biology" is better described as "tinkering" with natural biological parts, not likely to advance concepts or technology. This was certainly not the case for the recent construction of a cell at the J. Craig Venter Institute (Gibson et al., 2010), a cell that contains no DNA other than chemically synthesized DNA. This challenge was ambitious, for sure, but did not seem to go hopelessly beyond known design paradigms. After all, synthesizing and cloning 1000 genes with 1 million nucleotides might seem to be a routine repetition of the process that had been used to successfully synthesize and clone a single gene built with 350 nucleotides 25 years earlier (Nambiar et al., 1984). This turned out to not be the case, as the JCVI paper with 24 authors shows. Indeed, the paper shows exactly how "grand challenges", if properly selected, drive technological innovation. New yeast chromosomes were needed to assemble 1 million nucleotides of DNA sequence. New technologies were needed to proof the assembly. As Venter and his colleagues noted, misplacing a single DNA building block in the one million targeted for synthesis delayed their efforts for months. The advances were, in the end, more technological than scientific. But they identified gaps in our design paradigms, in ways that less ambitious synthetic biology could not have. And what about this being the foreshadowing of a "Frankenstein monster" or "genetic pollution"? Nonsense of the most ignorant type. As Jim Collins has pointed out (Collins, 2010), "media reports hyping this as a significant, alarming step forward in the creation of artificial forms of life can be discounted. The work reported by Venter and his colleagues is an important advance in our ability to re-engineer organisms; it does not represent the making of new life from scratch." Indeed, the JCVI cell contains no functional information not already found in Nature. Were it not for a few non-functional DNA sequences introduced as "watermarks", we could not easily tell that the JCVI cells were not contaminants from the natural world. Since synthetic biology as a field has been with us for three decades, we have had more than enough time to evaluate its hazards, and the effectiveness of the "Asilomar" rules designed in 1975 to mitigate these hazards (Berg et al., 1975). Concerns about "monsters" and "ecological catastrophe" were exaggerated then as well, with the city of Cambridge, Massachusetts, banning recombinant DNA technology within its borders for a year. Had that ban continued world-wide, the damage to medicine would have been catastrophic. In the 1980s, a syndrome characterized by "immune deficiency" arose. Without synthetic biology, we would not have been able to even identify HIV as the causative virus, let alone develop cocktails that today effectively manage AIDS. And curiously enough, artificial genetic alphabets (Switzer et al., 1989), another early advance in synthetic biology, are key to the management of AIDS as well (Benner, 2004). Benner, S. A. (2009). Life, the Universe, and the Scientific Method, Foundation Press (www.ffame.org), Gainesville, FL, US. Berg, P., Baltimore, D., Brenner, S., Roblin, R. O., Singer, M. F. (1975) Summary Statement of Asilomar Conference on Recombinant DNA Molecules. Proc. Natl. Acad. Sci. USA 72, 1981-1984. Edge, M. D., Greene, A. R., Heathcliffe, G. R., Meacock, P. A., Schuch, W., Scanlon, D. B., Atkinson, T. C., Newton, C. R., Markham, A. F. (1981). Total Synthesis of a Human-Leukocyte Interferon Gene. Nature 292, 756-762. Gibson, D. G. et al. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science, advance on line publication. Nambiar, K. P., Stackhouse, J., Stauffer, D. M., Kennedy, W. G., Eldredge, J. K., Benner, S. A. (1984). Total synthesis and cloning of a gene coding for the ribonuclease S protein. Science, 223, 1299-1301. Switzer, C. Y., Moroney, S. E., Benner, S. A. (1989). Enzymatic incorporation of a new base pair into DNA and RNA. J. Am. Chem. Soc., 111, 8322-8323. Szybalski, W. (1974). In Vivo and in Vitro Initiation of Transcription. In: A. Kohn and A. Shatkay (Eds.), Control of Gene Expression, Plenum, New York, pp. 23-24, 404-405, 411-412, 415 - 417. Wang, L., Brock, A., Herberich, B., Schultz, P. G. (2001). Expanding the genetic code of Escherichia coli. Science, 292, 498-500. 2. The Chemically Synthesized Genome and Artificial Fear. Harold J Morowitz, Ph.D., Robinson Professor of Biology and Biochemistry, George Mason University, Fairfax, VA The extraordinary achievement of Craig Venter and colleagues (Gibson et al., 2010) in the insertion of chemically synthesized Mycoplasma DNA into a cell that contains no DNA, and which then continues to replicate, takes us back to 1967 when H.R. Bode and H.J. Morowitz (1967) first determined the size of a Mycoplasma genome and 1969 when K.W. Jeon, I.J. Lorch, and J.F. Danielli (1969) first reassembled a living amoeba from the membrane, cytoplasm, and nucleus of three cells. These beginnings have led to the assembly of a living Mycoplasma from a synthesized genome and the cell of a different strain (Gibson et al., 2010). Although the authors refer to "creation of a bacterial cell," I would tend to stay away from such a politically loaded word. They have copied a genome with some editing and inserted it into a cellular milieu where it functioned as a usual bacterial controller. Another feature may be noted. Mycoplasma and amoeba are among that taxa that are surrounded by cell membranes as distinguished from cell walls characteristic of most bacteria and plant cells. This facilitates insertion of synthesized components. The usefulness of mycoplasma in these studies takes us back over a hundred years when Nocard and Roux, followers of Pasteur, first discovered pleuropneumonia like organisms, the early name of mycoplasma, as the causative agent of bovine pleuropneumonia. The discoveries of Nocard and Roux led to the eventual eradication of the disease. It is noteworthy that the "synthetic" Mycoplasma genome passes through an informatic stage designated by the authors as digital (Gibson et al., 2010). This is an enormous advance since the work of the 1960s and points to the copying of an entire cell: genome, membrane, cytoplasm, and all. Copying a cell is not creating a cell but synthesizing an entity that uses the same biochemical rules and entities that characterize all the biota of the global ecosystem. We are still left with the question of whether another biochemistry is possible. Current work on biogenesis is pointing to the uniqueness of anabolism, but the techniques explored in this work may lead to an experimental embodiment of that unsettled issue. Copying living cells, while of the utmost technical and engineering importance, should not raise philosophical and ethical issues. These quibbles about the semantics, and the generation of what could best be described as "artificial fear" of what the Venter Institute team has done, in no way detract from the achievement in validating the theory of molecular biology that is the current basis of our understanding of the functioning of bacteria. These achievements are to be applauded, not feared. Gibson, D. G. et al. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science, advance on line publication. Jeon, K.W., Lorch, I.J., and Danielli, J.F. (1970). Reassembly of Living Cells from Dissociated Components, Science, 167 , 1627-1628 3. One Small Step for Bacteria, or One Giant Leap for Mankind? David W. Ussery, Ph.D., Comparative Microbial Genomics Group Leader, Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark. The term 'synthetic biology' has become fashionable and trendy, although the phrase can have several different meanings. I can think of three broad categories: The third approach is just starting to emerge, and in my opinion this holds the most promise, in that it is an attempt to reconstruct synthetic ecosystems. This is in contrast to the first approach, which is to make a single reduced organism which can be gradually engineered one gene at a time to make a final product, like standardized parts manufacturing. Hence, the aim is to slowly build up an interacting set of synthetic organisms, to populate a living ecosystem, which can act as a system to make the final biochemical products needed. Yes, it is true that Venter and colleagues achievement, is the first record of a bacterial chromosome that has been synthesized in the lab and then put into an empty cell, which then has been induced to grow. It has even been given a name 'Mycoplasma mycoides JCVI-syn1.0' (Gibson et al. 2010). However, I am not quite so sure that I go along with Craig Venter's idea that he has now made one small step for man, one giant leap for mankind. Nor do I believe, to use his words, that he has created 'the first self-replicating species we’ve had on the planet whose parent is a computer'. From a larger perspective, he's using pretty much the same genome sequence from an existing bacterial genome. Therefore, I am skeptical of the argument that this genome's 'parent is a computer'. From my perspective, as far as nearly all of the synthetic M. mycoides chromosomal sequence goes, its 'parent' is the result of billions of years of evolution, not someone sitting at the computer and intelligently designing an entire organism, from scratch, so-to-speak. If we listen to the wisdom found in 'real biology' - that is, in the biodiversity around us resulting from billions of years of evolution, we can see that the reason many bacterial genomes have built in redundancy and live in cooperating communities is to make them robust, to be hearty survivors, that can withstand change and insults to the system. True, the Venter research group has added a few 'secret codes' with a hidden message and email addresses in the DNA, for those clever few who can decipher it. But apart from those small changes, what they have synthesized is extremely similar to the original M. mycoides sequence. No new genes. No new promoters. No new regulatory networks. Nothing 'redesigned' here, really, in my opinion! It is certainly impressive that it cost $40 million to make this genome. However, so far this is just a 'proof of concept' type of experiment, the applicability of which is suspect. In fact, it would have been considerably less expensive to just grow a batch of M. mycoides and isolate chromosomal DNA, and make the few small changes to its DNA the old fashioned way with conventional genetic engineering. The insulin gene was made synthetically, with similar type of fanfare, more than 30 years ago. Not only was the creation of an insulin gene less expensive, but that the researchers could claim to be the first to synthesize a gene in the laboratory and put it into an organism and harvest the product. Today, people routinely will design changes in a gene's sequence, and put it into an organism, using genetic engineering tools. The choice of a Mycoplasma genome by the Venter team is certainly not an accident, as this has historically been claimed to have the smallest genome of any free-living organism. The original goal of the Venter team was to make a reduced genome with only the 382 genes necessary for a 'minimal genome', and then transplant this into something like a Mycoplasma capricolum recipient. The hoped-for synthetic organism already has a name (and a Wikipedia page) - Mycoplasma laboratorium - although this organism hasn't even been created yet! In the Venter team experiment they inserted the synthetic genome of Mycoplasma mycoides into a microbe who is much larger and has a genome twice the size (~1000 in M. mycoides compared to ~500 in M. genitalium). The Venter team made this choice in order to allow faster growing times. However, once a reduced genome is in place, this can be used as a 'chassis' to add new genes for various metabolic processes - in particular for the organism to produce hydrogen gas - preferably from CO2, water, and sunlight. By extension, we would wish to engineer a set of interacting organisms, and build up a robust [synthetic] ecosystem which could provide revolutionary benefits. From a biochemical perspective, this is certainly possible, and obviously such an organism capable of doing this could provide an ecologically sound alternative to fossil fuels, perhaps including sugars or biodiesel in addition to hydrogen gas. Certainly Venter and his team have not ushered in a scientific revolution, nor have they made a giant leap for mankind, as they wish us to believe. Nevertheless, this small step may have paved the way and can be built upon by others in the field of synthetic biology. 4. Craig Venter’s Synthetic Bacteria: The Dawn of a New Era? Manuel Porcar, Ph.D.1, and Andrés Moya, Ph.D.2,. 1Institut Cavanilles de Biodiversitat i Biologia Evolutiva, València, and Fundació General de la Universitat de València, Spain. 2Institut Cavanilles de Biodiversitat i Biologia Evolutiva; Centro Superior de Investigación en Salud Pública, València; and CIBER en Epidemiología y Salud Pública (CIBEResp), Spain. Last May the 19th, a relatively small team of researchers announced the "creation of a bacterial cell controlled by a chemically synthesized genome" (Gibson et al. 2010). The report, published in Science the following day, describes the synthesis and assembly of the 1.08-Mbp Mycoplasma mycoides genome, chemically constructed from digitized genome-sequence information, and its subsequent transplantation into the recipient cell of a closely related species (Mycoplasma capricolum). The whole M. capricolum genome was replaced by the synthetic genome, thus ensuing cells were controlled by the new chromosome alone. New cells grew logarithmically until progeny no longer contained any of the protein molecules harboured in the original recipient cell, as occurred with the previously reported transplantation technique (Lartigue et al. 2007). The scientific community was awaiting this breakthrough. First, because Craig Venter had announced the imminent construction of a bacterium with a functional synthetic genome many months ago; and, second, because the team had managed to synthesize whole genomes (Gibson et al. 2008) and successfully used the transplantation technique to change one bacterial species into another (Lartigue et al. 2007). Therefore, the transplantation of a functional synthetic genome was simply a matter of time. The report has had a huge and justly deserved impact, both in the media and on the scientific community. It is a landmark heralding the dawn of a new era: depicted by Venter as the first time a living organism on Earth has a computer for a parent. The "creational" status attributed to the work, used in the very title of the article in Science, can be criticized, however, because natural cells were required as recipient envelopes for the synthetic genomes to "come to life". Notwithstanding, the importance of the achievement is unquestionable, both for its historic significance and as a first step in the creation or totally synthetic life forms, whose genomes will not be mere copies of existing ones, but the result of mindful design. Indeed, Venter’s work can be seen as both a perfect demonstration of the power of current DNA synthesis techniques (certain to be improved in the future) and as proof of today’s limitations to significantly modify genomes to shape life at our will. It is important to highlight that there is a huge difference between making DNA (in the sense of copying it) and writing DNA (in the sense of designing nonexistent genetic information). Protein-coding genes can indeed be tuned though serial mutations and trial assays in an approach known as directed evolution. But these approaches often rely on existing genetic information and are carried out at a gene-by-gene scale. The complexity of living beings is a result of the force that has shaped every single organism on Earth: natural selection. And the way natural selection works is very different to the paradigm of Synthetic Biology (standardization, decoupling, and abstraction). The adaptive nature of gene products is obviously subjected to natural selection and whole genomes are selected or discarded on the basis of their overall behaviour. Evolution works on the genome scale whereas genetic engineering works on the gene scale. This might be the reason underlying failures in strategies aimed at optimizing natural organisms by engineering them to make them behave more "logically" (Chan et al. 2005), or the fact that successful metabolic engineering, even if nominally in the framework of SB, is often not performed through the Synthetic Biology basic principles cited above (Ro et al. 2006). Some of the most promising biological sciences, including Genetics, Molecular Biology and Evolutionary Biology, focus on components (parts). And for all these three branches of science, genes are the basic focal point (Moya, 2010). But, is it possible to appraise an organism via the study of all its parts? In other words, would perfect knowledge of each one of the thousands of genes a common bacterium harbours lead to perfect knowledge of the system as a whole (i.e. the bacterium), and thus allow us to predict its behaviour, even under changing environmental conditions, and to rationally design functional variants? The answer is probably no, because of the emergent properties that seem inherent to life, which make living beings much more than the mere sum of their parts (Moya et al. 2009). It is interesting to apply the Gödel theorem of undecidability to a cell: "within a cell, properties exist that are neither provable nor disprovable on the basis of the rules that define the system" (Moya, 2010). Emergent properties, which are very common in any living system, might well fall within this definition. The complexity of living organisms and the existence of emergent properties do not necessarily mean that synthetic life is not possible. But they both suggest that a strict reductionist (i.e. gene-centred) approach for Synthetic Biology is doomed to failure. Holistic and selection-based approaches combining rational design and evolution will be key tools in achieving purely synthetic life forms. These artificial organisms will be modified in order to accomplish a range of useful activities, ranging from bioremediation to drug or biofuel production. Craig Venter’s work is still far from gaining real control over the design of synthetic life forms, but it is the first technical step in paving the way towards this exciting goal. It seems comprehensible that such a breakthrough should stir up concern regarding the ethical issues posed by artificial life, and possible misuse of the technology. The topic falls outside the scope of this commentary, but a public debate is certainly needed to address these questions. However, it must also be asked: Can we really afford not to make the most of the potential Synthetic Biology offers? Acknowledgements: This work has been funded by European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement number 212894 and Prometeo/2009/092 (Conselleria d'Educació, Generalitat Valenciana, Spain) to A. M. The authors are very grateful to Fabiola Barraclough for the correction of the English text. Gibson D.G. et al. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science, advance online publication. Lartigue, C., Glass, J.I., Alperovich, N., Pieper, R., Parmar, P.P., Hutchison, C.A. 3rd, Smith, H.O., Venter, J.C. (2007). Genome transplantation in bacteria: Changing one species to another. Science, 317, 632-638. Moya, A. (2010). Gödel, Biology and Emergent properties. Biological Theory, in press. Moya A., Krasnogor N., Peretó J., Latorre A. (2009). Goethe's dream. Challenges and opportunities for synthetic biology. EMBO Reports,10, S28-32. Ro D.K. et al. (2006). Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature, 440, 940-943. 5. What is life? Evolution and Self-Reproduction. Edward N. Trifonov, Ph.D., Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel. Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno CZ-62500, Czech Republic Newspapers around the world printed articles about "life in a test tube", a description which Spiegelman disavowed: "When you create a living object the presumption is that the object didn't exist before. This I did not do. Working with simple chemical compounds, I take a primer of a living object and I generate many living objects from it." Yet Spiegelman, definitely, "played God", as Craig Venter and his colleagues (Gibson et al., 2010) play God today with the million-base long handmade DNA. Once inserted into the cytoplasm of a cell (whose genome had been removed) this artificial life form was able to program self-replication of a whole newly designed Mycoplasma strain. Spiegelman's monster accomplished the same. One important difference between the work of Spiegelman and the Venter team is the lack of evolution component in the latter case even after a billion replications. Spiegelman's monster evolved and there was evidence of mutation which was to the advantage of the "monster." Darwin (1859), describing the essence of natural selection, wrote about individuals with useful variations producing "offspring similarly characterized". In the absence of evolution or variation in Venter et al's artificial genome, I would object to calling their creation "synthetic life" as it is described in the media (e. g., MacLeod, 2010). One may argue whether, indeed, these undeniable attributes of life (self-reproduction and variations) could be considered as the conclusive dividing line between non-life and life. The very definition of life is a matter of centuries-long debates (Barbieri, 2003; Popa, 2004). One could recognize, however, a leading motif in over 100 known definitions of life (ibid), which was best formulated by Oparin (1961): "Any system capable of replication and mutation is alive". That is, again, self-reproduction and variation. In both cases, of Spiegelman’s "Monster", and Venter’s "Creation", the accomplishments are breathtaking. Judging by an explosion of interest in the media and the scientific community, the feeling is in air that we are witnessing the very transition from non-living to living matter. Did Venter et al create life from non-life? The sober answer is "not yet, but very close". And why is that? Because the Venter team copied the genetic blue print of life and then inserted it into a cell which contained living products. It cannot be claimed that "artificial life" is life as its ability to engage in self-reproduction required living matter products as starters (cytoplasm in Mycoplasma, and replicase in the case of Spiegelman’s RNA "Monster"). The task of achieving self-reproduction would, probably, be simpler and less expensive if purely synthetic and initially abiotic systems are explored, such as autocatalytic RNA synthesis in water (Costanzo et al., 2009; Lincoln and Joyce, 2009). What if these synthetic life forms not only replicate, but mutate and evolve? Let us not forget that Mycoplasma is a parasite and a pathogen. If there was evidence of evolution or the generation of variations in the Venter creation, should we be alarmed? We can only hope they would not be a problem. On the other hand, the viability of the synthetic strain would depend on the number of variations, and the hope they would not be too detrimental. Spiegelman’s synthetic RNA also mutated. What is the possibility of similar changes in the synthetic Mycoplasma? Some undesirable mutations may appear in consecutive cycles of further propagation of the strain (not unlike "ionfirmed" and "tp produce" in the text of the "creation" paper). For example, since the "watermark" messages cut into the designed genome are not under natural selection, they would be probably the first to mutate or get deleted, unless artificially assisted. Whether life is self-reproduction only, or reproduction and evolution, may one day turn out to be obsolete questions. Given the monumental technical progress manifested in the work on Mycoplasma we may soon pass the tipping point between and finally witness the transition of non-life to life. Perhaps that will result in a matter-of-factual definition of what is life; or it may lead to new questions as to the nature of what is not life. Costanzo, G., Pino, S., Ciciriello, F., Di Mauro, E. (2009). Generation of long RNA chains in water. J. Biol. Chem 284, 33206–33216. Darwin, C. (1859). Origin of species, John Murray, London. [Chapter 4]. 6. Gene Transfer, Synthetic Organisms, and the Origins of Life. Hiromi Nishida, Ph.D., Agricultural Bioinformatics Research Unit, Graduate School of Agriculture and Life Sciences, University of Tokyo, Japan. Life on Earth appeared around 4 billion years ago, and for thousands of years there have been great debates on how life began. Many biologists believe life evolved from proto-life and the first life forms were similar to archae and bacteria (Joseph and Schild 2010; Nitschke and Russell 2010; Russell and Kanik 2010). Thus, perhaps it is no accident that gifted scientists, led by J. Craig Venter (Gibson et al. 2010), have used bacteria, Mycoplasma, in their work in synthetic biology and in their attempts to create synthetic life. The technologies of molecular biology have much advanced markedly in the last decade, evolving beyond the insertion of single genes to the development of massively parallel DNA sequencers, and nucleotide sequences tens of thousands of base pairs in length. Using these advanced technologies, molecular biologists can now perform complex genetic experiments using whole genomes, instead of single genes. However, even within the eukaryote genome there are genes which were not inserted by scientists, but by viruses and prokaryotes (Koonin 2009; Koonin and Wolf 2008) . It is believed that soon after life forms similar to archae and bacteria appeared on Earth, that they may have transferred or combined their genes to fashion the first multi-cellular eukaryotes (Joseph 2009). Therefore, the genome of eukaryotes, including humans, contain genes which are believed to have originated in prokayotes (Koonin 2009; Koonin and Wolf 2008). Likewise, many of the genes within the prokaryotic and eukaryotic genes have been expressed in the cells of evolutionarily distant organisms. Genes may be turned on or off over the course of evolutionary history. However, continuing into modern times, genes continue to be transferred between prokaryotes and from prokaryotes to eukaryotes. At present, molecular biologists understand that if the recipient cell system recognizes the transferred genes (for example, the transcription factor of the cell can bind the gene promoters correctly), the transferred genes could be expressed. The transfer of genes between organisms may play a major role in evolution (Joseph 2009). For example, an abundance of mobile genetic elements have been found in nature, which can be transferred between different organisms and different species and which may be expressed in the different cells (Koonin 2009; Koonin and Wolf 2008). Therefore, if the transferred genome DNA was recognized and the genes of the genome were orderly expressed in a recipient cell, the cell would be controlled under the transferred genome information; and Gibson et al. (2010) did it! The work of Gibson et al. in the journal Science is a milestone in the research field of synthesis of an artificial organism (cell) and has implications not only for the origin of life, but the evolution of life. Specifically, Gibson et al. (2010) synthesized the genome DNA on the basis of the Mycoplasma mycoides genome sequence. The other parts of the recipient cell (for example, proteins and membrane) were products of Mycoplasma capricolum, which were not artificially synthesized. Thus, in point of fact, Gibson et al did not create synthetic life. Nor did they provide evidence for the abiotic origins of life as they modeled their genetic blue print on a living genome and utilized biological materials to create their synthetic genome. The question of the origins of life have not been answered as no one understands how the first DNA molecules were fashioned abiotically, and no one has been able to explain how the first cellular membrane may have been created, or even which came first: DNA? RNA? Membrane? At present nobody knows how to design a recipient cell. No one knows how to create the composition of the membrane, or the essential proteins for recognition of the transferred genome DNA, etc. Thus, again, it is not accurate to say that Venter and colleagues created a synthetic cell. To truly create synthetic life, it is essential to first create a synthetic cell and to synthesize a recipient cell. Gibson et al. (2010) stated, "The donor genome was methylated in the native M. mycoides cells and was therefore protected against resistriction during the transplantation from a native donor cell." As far as I know, among the species of the genus Mycoplasma, phylogenetically Mycoplasma mycoides is the most closely related toMycoplasma capricolum. However, as noted, over the course of evolutionary history prokarotes have exchanged genes. The classification system of bacteria is based on the genome sequence (whole or part, for example, 16S rDNA). May of the genes in one species of Mycoplasma could well have been acquired from a closely related or even a distantly related species. Therefore, from the viewpoint of the evolution of microorganisms, it could be asked: "Which species of Mycoplasma might serve as the most genetically independent recipient cell to the synthesized genome DNA designed on the basis of Mycoplasma mycoides genome DNA sequence?" Because the present microorganism genome consists of phylogenetically different parts which have been transferred between species, is it really accurate to say that the genome of one species of Mycoplasma was really transferred to an independent host? The bacterial species classification system based on the DNA or protein sequence comparison should be reconsidered, I think. The synthesized genome DNA-transplanted cell began replicating and making a new set of proteins (Gibson et al. 2010). DNA cannot replicate DNA by itself, cannot transcribe RNA by itself, and cannot synthesize protein by itself. The interaction between DNA and proteins (DNA binding proteins recruiting RNA polymerase complex or DNA polymerase complex) is essential for RNA transcription and DNA replication. Therefore, the first step of replicating and making a new set of proteins is the interaction between the transferred genome DNA and proteins already present in the recipient cell of Mycoplasma capricolum. What proteins were performed as an inducer to control the cell under the transplanted genome DNA information? It is very important and interesting to elucidate which proteins contacted the synthesized Mycoplasma mycoides genome at the first stage. The reaction triggers sequential RNA transcriptions and protein syntheses. To conclude: The team led by Venter must be congratulated for their technological tour de force which has profound implications for the origin and evolution of life. However, it is not really accurate to say they have created synthetic life, or even a synthetic genome. In fact, they may have inserted copies of genes intoMycoplasma capricolum which long ago originated in Mycoplasma capricolum, as M. mycoides and M. capricolum may have swapped genes recently as well as millions of years ago. Joseph, R. and Schild, R. (2010). Origins, evolution, and distribution of life in the cosmos: Panspermia, genetics, microbes, and viral visitors from the stars. Journal of Cosmology, 7, 1616-1670. Koonin, E.V. (2009). Evolution of genome architecture. Int. J. Biochem. Cell Biol. 41:298–306. Koonin, E.V., and Wolf, Y. I. (2008). Genomics of bacteria and archaea: the emerging generalizations after 13 years. Nucleic Acids Res. 36:6688–6719 Nitschke, W., and Russell, M. J. (2010). Just like the universe the emergence of life had high enthalpy and low entropy beginnings. Journal of Cosmology, 10, In press. Russell, M. J., and Kanik, I. 2010). Why does life start, what does It do, where will It be, and how might we find it? Journal of Cosmology, 5, 1008-1039. 7. Babies are Born Very Young. The Synthesis of Change. Antoine Danchin, Ph.D.1, Gang Fang, Ph.D.2,1AMAbiotics, Génopole 1, Genavenir 8, 5 rue Henri Desbruères, Evry Cedex, France. 2Department of Molecular Biophysics and Biophysics, Yale Medical School, Yale University, New Haven, CT, USA Take a computer. Plug in the power supply. Insert a CD-ROM with the operating system. The computer boots up. This is the bold radical empiricism approach that Venter and colleagues took to make a synthetic cell (Gibson et al., 2010). Should there be concern? We think not. At this hot moment when people are excited about the breathtaking pace of technological progress, we should calm down and think again about the essence of synthetic life and its future. Biologists should perhaps learn from cosmologists. Since cosmologists cannot tinker with the Universe to try to see whether an idea would work, they resort to math, quantum physics, computer models, and prolonged observation using a variety of space telescopes. Facing the question of Life, they would begin by defining what life is, how it may differ in different environments, and then explore where it came from (Joseph and Schild 2010; Russell and Kanik, 2010). Hoyle in his Black Cloud, took the extreme Copernican view: rather than extrapolate directly from life as observed on Earth, he explored the concept of life at a different scale and with matter (a dust cloud) that is quite different from the life forms we know. Life elsewhere in the cosmos may be completely different from life on Earth (Naganuma and Sekine 2010; Rampelotto 2010; Schulze-Makuch 2010), and some alien life forms, if they are not carbon based, or lack a genome, may appear to us as synthetic. Some might say that life is signified by behavior, the ability to replicate itself, to gather information, and to change. However, is a living entity which changes, which evolves into something else, still the same entity? Does the characteristics of life require life to become non-life in the process of living? This was understood some three thousand years ago by the prophetess of Delphi, Pythia. She asked passers-by the question: “My boat is made of planks. They rot away; I replace them. After some time, all have been replaced: is it the same boat?”. This is my boat, yet its matter has been entirely changed… Life is the Delphic boat. We can knock out a gene, replace a gene, and now we have the capacity to replace a whole natural chromosome by a synthetic chromosome. However, a difficult problem remains: it is a fiction to say that the synthetic chromosome is assembled according to our design: we had to refer to what already exists, to the genetics of life forms which has been subject to billions years of evolution. We cannot say yet that we know how to make synthetic life. To understand what life is, we must understand the relationships between entities, whether they be material processes, or abstract. To this aim we can benefit from careful reviews of how extant living beings have evolved, evolving from single celled organisms to multicellular organisms capable of dealing with sophisticated environmental challenges in the process of gaininginformation. Zurek (1989) proposed that living organisms are "information gathering and utilizing systems". We should try to understand the nature of information gained through evolution and its relationships with the four standard currencies of reality: matter, energy, space and time. Venter's group laid a technical footstone, and now the big challenge for Synthetic Biology (SB) is to construct cells and organisms in a rational way. It must take into account the particular genetic setups required not only to manage information but to gather it from the environment. Comparison between computers and SB might help us better understand the importance of information. Computers are machines manipulating (and creating) information. So, are computers alive? Computers behave. They gather information. They change with the addition of new programs. However, to be alive also requires self-replication. Can computers make computers? The engineering project RepRap (http://reprap.org) is building a 3D printer which will be capable of making 3D printers. This effort is not without similarity to that of SB. Computers making computers would be orthogonal life, i.e. construction of entities that would be based on the laws of life, but based on totally different material entities. SB defines life as the association of a machine (the cell, or chassis or hardware) and software (the genetic program, a string of symbols implemented as a molecule of a nucleic acid, the object synthesized and transplanted by Venter's group). Several processes are associated to that view: program from software must be expressed as components of the chassis, to make a progeny. This process manages matter and energy (via a general process, metabolism). It further requires reading of the program by nanomachines that transcribe portions of it, and subsequently translate it with reading heads into a variety of agents that run metabolism, construct the cell's nanomachines and the casings of the chassis, and recursively replicate the program. The popular view of SB restricts it to pieces of DNA, the nuts and bolts that carry the software of life. However, even if we ignore the hardware, life differs from computers: it spans over many generations in an unbroken line which leads to the first life on Earth, and possibly, to life on other planets (REF), until finally we arrive at the first living cell. However, since the establishment of that first cell, life has evolved in response to the information in its environment. Subsequent copies are not identical to the first cell. The most crucial evidence of the success of a SB experiment was that copies of the synthesized chromosome were carried by progenies over generations. The hardware, however, differed: the initial host cell build up is not found in the final hardware outcome. This implies a subtle but essential feature: the hardware reproduces a similar copy of itself, while the program replicates an exact copy of itself. The outcome of protein synthesis is a collection of proteins with similar, not the same, sequences and shapes. Progeny are not a replica of their parents, being young, not old, and so on. Understanding the mechanisms of aging, evolution, and reproduction of progeny are the key questions in coming research of SB. This is where the importance of information cuts in. Some information must be recovered from somewhere, or created de novo in a single cell cycle. If we accept that the genetic set up (the abstract entity transmitted by transplantation) is enough to produce this information, then we must find genes to code for that task. Analysis of bacterial genomes demonstrated that among functions persistent in all genomes were degradative functions that, surprisingly, used rather than produced, energy. Here is the reason: energy-dependent degradation enzymes are central actors in the production of young cellular structures, contributing to the creation of new living individuals. What we name natural selection is the physical principle stating that degradative processes use energy to prevent degradation of functional entities. These enzymes act asMaxwell's demons, accumulating information in a ratchet-like manner, without any prescience, but with strong anticipation properties. This view has the remarkable consequence, in terms of societal issues, that either we omit these genes, and construct factories that do what we wish them to do, but which then age (or evolve) and have to be periodically reconstructed. Or we keep them, with the drawback that there is no reason whatsoever that the myopic Maxwell's demons would follow our requirements. As a conclusion, accumulation of new information, and the changes which would ensue, should be the central topic in the future of SB. Last but not least, we may need to say something about ethics. Does transplantation of a synthetic genome really pose ethical questions? Should we worry, and if so why? For such questions, we must explore the knowledge that we are required to master to (re)construct life in order to gain a better idea of the economic and ethical issues that we have to confront before we start asking them. Life itself is far less predictable than SB, and this is where the danger resides. Joseph R., Schild, R. (2010). Biological cosmology and the origins of life in the universe. Journal of Cosmology, 5, 1040-1090. Naganuma, T., Sekine, Y. (2010). Hydrocarbon lakes and watery matrices/habitats for life on Titan. Journal of Cosmology, 5, 905-911. Rampelotto, R. H. (2010). The search for life on other planets: Sulfur-based, silicon-based, ammonia-based iife. Journal of Cosmology, 5, 818-827. Russell, M. J., and Kanik, I. (2010). Why does life start, what does It do, where will It be, and how might we find it? Journal of Cosmology, 5, 1008-1039. Schulze-Makuch, D. (2010). Io: Is life possible between fire and ice? Journal of Cosmology, 5, 912-919. Zurek, W. H. (1989). Algorithmic randomness and physical entropy. Phys. Rev. A 40, 4731–4751. 8.The Seeding of Synthetic Life Throughout the Cosmos. Chandra Wickramasinghe, Ph.D., Director, Centre for Astrobiology, Cardiff University, United Kingdom. The recent successful implantation of a digitally determined genome sequences into a bacterium – the synthesis of a computer designed microorganism – ushers in a new era of biotechnology. It would not stretch our imagination or credulity unduly to suggest that 200 years from now a successor to the Craig Venter Institute would be able to digitally reconstruct a set of the best possible sequences of the human genome. The eventual creation of "synthetic humans" is a natural extension of Venter's work (Holt 2010). Yet what does the breakthrough in genetic engineering and synthetic biology tell us about the origin of life? So far, the consensus appears to be "nothing at all" (Lane 2010; Nishida 2010; Trifinov 2010). If we are asking about Theorigin of life, that first ever primordial cell (Hoyle and Wickramasinghe 2000), then synthetic biology tells us nothing; except perhaps, that life may have begun as matter (Penny 2010). However, synthetic biology may have a lot more to say if the question concerns how life may have arisen on Earth and other planets. Nearly 50 years ago, Crick and Orgel (1973) acquiescing to the realization that life could never have originated on Earth (see Joseph and Schild 2010a), proposed instead that our planet was purposefully seeded with life by a technologically advanced race of extra-terrestrials via mechanisms they described as "directed panspermia." As conceptualized by Nobel Laureate Crick (1981), Earth was targeted to grow life including humans. Yet how could these "seeds" purposefully evolve into humans? More recently, Joseph (2009a) has proposed detailed genetic mechanisms through which bacteria, archae, and viruses, once arriving on this planet encased in planetary and cometary debris (Hoyle and Wickramasinghe 2000; Napier and Wickramasinghe 2010; Wickramasinghe et al. 2010), combined their genes to fashion multi-cellular eukaryotes. According to this genetic model of panspermia, these "genetic seeds of life" also contained the genetic instructions for the metamorphosis of all life on this planet, including humans (Joseph 2000, 2009a, Joseph and Schild 2010b). According to this theory, as viruses and microorganisms are cast from world to world via mechanisms of panspermia, they exchange genes with the denizens of these other planets, thereby building vast genetic libraries, which for the most part are stored in virus genomes. These gene depositories contain the genetic instructions for the replication of these alien life forms. However, what if this genetic seeding was purposeful as proposed by Crick? Venter et al's creation and the long-term implications for "synthetic biology" may be directly related to "biological cosmology" (Gibson and Wickramasinghe 2010; Joseph and Schild 2010a), and Crick and Orgel's (1973) proposal that Earth may have been purposefully seeded with life, i.e. synthetic life with genetically modified genomes. With the rapid pace of technological progress that we have witnessed in the past few decades, projecting into the future to foresee the nature of technology, would be a risky business. Advances in communications, computers, information technology and biotechnology have been staggering to say the least. The world just one century from now would be to us as unrecognisable as our world would seem to our great grand parents. And a few hundred years from now, is it not conceivable that synthetic humans might be built to order and to precise specifications: hair, height, personality, intelligence, sexuality... why not? As detailed by Holt (2010), "we are now able to copy organisms. Change them a bit. So where do things go from here? Could we create a more complex microbe? A yeast, perhaps, which is an organism with a cell structure more related to multicellular entities like ourselves than to bacteria. Various yeast strains have been sequenced, and a typical yeast genome is only about ten times larger than Mycoplasma mycoides JCVI-syn1.0. How about a fruit fly, ten times larger still, and with a well characterized genome sequence? Or, if we follow this train of thought about as far as anyone would care to, how about a person?" Envision, a few hundred years from now, tiny synthetic genetic packets of precoded humans, instant humans so to speak, made to order. Synthetic soldiers, laborers, sex partners, slaves, and so on, created to exact specifications. However, the nature of DNA is that it does not stay put. The universal nature of the genetic code makes it possible for genes to be transferred horizontally between species (Joseph 2009a; Joseph and Wickramasinghe 2010). Genes escape. Genes can exit one organism and insert themselves into the genome of other organisms. Is it possible for entire genomes to escape? In 1969 Sol Spiegelman was awarded a patent for a synthetic virus RNA. However, most of its synthetic genes disappeared from its genome. It is the nature of viruses to insert their genes into other organisms. So did this synthetic virus transfer its genes? We don't know. What we do know is that synthetic genes can exit the genome of a synthetic creation. Is it possible that synthetic genes have an even greater propensity to escape their synthetic genomes and insert themselves into other species, and perhaps, especially other synthetic organisms? Horizontal gene exchange is commonplace in nature and directly impacts evolution (Joseph 2000, 2009a). There is also evidence that microbes and viruses from space periodically infect life on this planet, and through horizontal gene transfer may contribute genes which influence the trajectory and nature of evolution (Joseph and Wickramasinghe 2010; Wainwright et al., 2010). Where do these microbes and viruses come from? Other planets. Some are lofted into the upper atmosphere of their home planets (Joseph and Schild 2010b), as is the case here on Earth (Joseph 2009b; Miyake et al., 2010; Yang et al., 2010), and when blown into space by powerful solar winds (Joseph 2009b; Joseph and Schild 2010b), or when cast from their planets encased in ejecta following meteor strikes (Hara et al., 2010) some are eventually deposited here by comets and stellar debris (Miyake et al., 2010; Napier and Wickramasinghe 2010; Wickramasinghe et al. 2010). Should synthetic bacteria behave any different? Might they also store copies of their synthetic genes in viruses? It can be predicted that synthetic bacteria will not remain confined to laboratories but will eventually become commercially available. Some of these synthetic bacteria will share their genes with viruses, and some will also inevitably be lofted into the air, then the upper atmosphere, and finally into space during episodes of increased solar wind activity. Will these synthetic bacteria have acquired synthetic human DNA through horizontal gene transfer? Will viruses also come to store synthetic DNA? Are synthetic life forms more likely than non-synthetics to horizontally transfer genes? Or, hundreds of years from now, might future packets of synthetic human DNA, once escaping the laboratory, also come to be lofted into space? Might they may be purposefully directed into space, to other planets, to seeds alien worlds with terraforming life, and future workers and slaves? If Crick and Orgel's (1974) theory of directed panspermia has any validity, it could be surmised that the delivery vehicles may have contained synthetic DNA with all the genetic instructions for the evolution of life on this and other planets. By the same token, the peoples of Earth could also engage in acts of "directed panspermia" if for any reason, in the future, there is cause to believe that life on Earth is doomed for extinction. In fact, our desire for immortality might well prompt an attempt to launch our genes out into space (Arnould 2010; Mautner 2010). Might synthetic human genomes serve this purpose? Be it directed or accidental, synthetic bacteria or packets of synthetic human DNA, or synthetic bacteria whose genome carries human DNA, once they escape Earth’s gravity, they would have numerous dynamical pathways available to them by which they can leave the entire solar system (Joseph and Schild 2010b; Napier and Wickramasinghe 2010; Wickramasinghe et al. 2010). And once free of the Sun’s gravity, synthetic bacteria, for example, can be propelled by the pressure exerted by starlight from one planetary system to the next. The well-attested survival attributes of bacteria would enable a surviving fraction of human-genome carrying bacteria to be carried to innumerable alien planetary systems – thus leading to an ever-expanding wavefront of human-genome carrying packets that can effectively colonise the entire galaxy. However, what if synthetic-human genome-carrying bacteria reach a planet on which higher life has already evolved. These alien (human) bacteria (and their viral counterparts) could lead to epidemics and pandemics of disease (Joseph and Wickramasinghe 2010). Survivors of such pandemics are then likely to incorporate the offending gene sequences in their genomes, and future evolution of life on their planet would be affected by such gene inserts, much as has similar events effected the evolution of life on Earth (Joseph 2000, 2009a; Joseph and Wickramasinghe 2010). The principle of mediocrity dictates that the Earth cannot be unique in its potential to disperse life in the manner we have discussed. Similar events may take place on innumerable life-bearing planets, and this may explain how life on Earth began and indeed evolved. Indeed, we must recall that the Milky Way galaxy is 13.6 billion years in age, which means that life could have begun to evolve on innumerable planets almost 10 billion years before Earth was formed; life which would have evolved, and which may have also created synthetic life, and synthetic human genomes, some of which was dispersed into space. Might the same be true of other galaxies? If correct, then the legacy of human life could be thought as having an eternal existence in the cosmos. Crick, F. H. C. and Orgel, L. E., (1973). Icarus, 19, 341-346. Gibson, C., and Wickramasinghe, N.C., (2010). The Imperatives of Cosmic Biology. Journal of Cosmology, 5, 1101-1120. Gibson, D.G., Glass, J.I., Lartigue, C., et al. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science DOI: 10.1126/science.1190719. Hara, T., et al., (2010). Transfer of Life-Bearing Meteorites from Earth to Other Planets. Journal of Cosmology, 7, 1731-1742. Holt, R. A. (2010). Are Synthetic People Next? Reflections on a Prosthetic Genome. Journal of Cosmology, 2010, 10, in press. Hoyle, F. and Wickramasinghe, N.C., (2000). Astronomical Origins of Life: Steps towards Panspermia. Kluwer Academic Press. Joseph, R. (2000). Astrobiology, the origin of life, and the death of Darwinism. University Press. Joseph, R. (2009a). The evolution of life from other planets. Cosmology 1, 100-200. Joseph, R. (2009b). Life on Earth came from other planets. Cosmology 1, 1-56. Joseph R., Schild, R. (2010a). Biological cosmology and the origins of life in the universe. Journal of Cosmology, 5, 1040-1090. Joseph, R. and Schild, R. (2010b). Origins, evolution, and distribution of life in the cosmos: Panspermia, genetics, microbes, and viral visitors from the stars. Journal of Cosmology, 7, 1616-1670. Joseph, R., and Wickramasinghe, N. C. (2010). Comets and contagion: Evolution and diseases from space? Journal of Cosmology, 7, 1750-1770. Lane, N. (2010). Intelligent Non-Design and the Origins of Life. Journal of Cosmology, 2010, 10, in press. Mautner, M. M. (2010). Seeding the universe with life: Securing our cosmological future. Journal of Cosmology, 5, 982-994. Miyake, N., et al., (2010). Identification of Micro-biofossils in Space Dust. Journal of Cosmology, 2010, 7, 1743-1749. Napier, W. M. and Wickramasinghe, N. C. (2010). Mechanisms for Panspermia. Journal of Cosmology, 7, 1671-1691. Nishida, H. (2010). Gene Transfer, Synthetic Organisms, and the Origins of Life. Journal of Cosmology, 2010, 10, in press. Penny, D. (2010). Life as a Natural Property of Matter.Journal of Cosmology, 2010, 10, in press. Trifonov, E. N. (2010). What is life? Evolution and Self-Reproduction. Journal of Cosmology, 2010, 10, in press. Wainwright M., et al., (2010) Are Microbes Currently Arriving to Earth from Space? Journal of Cosmology, 7, 1692-1702. Wickramasinghe, J.T., Wickramasinghe, N.C and Napier, W.M., (2009). Comets and the Origin of Life. World Scientific Press. Yang, Y. et al., (2010). Panspermia: Testing for the Interplanetary Transfer of Life. Journal of Cosmology, 7, 1703-1718. 9.Ethics, Knowledge, and Synthetic Life. Stephen Napier Ph.D., Ethicist, National Catholic Bioethics Center, Philadelphia, PA, USA. Craig Venter’s group has created what has been described as "synthetic life." What are the moral and ethical implications. I argue that the research is morally good in seeking understanding oriented to serving the human community and the environment. Theologically speaking his research does not tread on God’s ground or manifest vicious hubris. His research exudes the creativity and understanding that characterize flourishing rational beings. Research of this sort, to the extent that it respects human persons (of any age) and serves the human community, exercises a distinctive potency of human beings, namely rationality, and its many daughters; creativity and understanding. Suppose I take to sitting at my desk and memorize telephone numbers in the phone book while on company time. My boss enters the room and sees what I am doing and promptly asks, “What are you doing!?” I reply, “I am memorizing phone numbers.” “But why!?” comes the reply with an objectionable tone. My boss’s question is apposite and highlights the fact that some things are just not worth knowing while other things are. If I am getting paid to know things, I better come to know important and meaningful things. Even if I accumulate numerous true beliefs, I still do not necessarily have an epistemic state that is valuable. The scientific enterprise aims to know, or better, it aims to understand. And understanding involves not just knowing or memorizing piecemeal facts, but involves apprehending the nature of things, the universe, and ourselves. Knowledge pertains to this or that fact; understanding pertains to these facts and their interrelation and as such understanding is a valuable epistemic state. For bio-medical research this understanding is oriented to the good of the human person which is to say that the reason why we want to understand, is to benefit human beings, e.g., to treat or prevent disease. Anyone familiar with institutional review boards will know that they only approve research that, at least, holds out some benefit to humanity. The promise to gain knowledge If Tuskeegee (untreated syphilis), Willowbrook (deliberate infection of hepatitis), or Jewish Chronic Disease Hospital (deliberate injection of live cancer cells) taught us anything it is that the aimless acquisition of knowledge is dangerous. Indeed in this country, there have been numerous unethical scientific studies where children and adults have been injected with syphilis, cholera, tuberculous, influenza, malaria, hepatitis, cancer, yellow fever, dengue fever, and other pathogens all in the interests of science and knowledge, and without the knowledge or informed consent of the victim. Thus the creation of review boards to insure that research is ethical and does not cause harm. Scientific research in general and bio-medical research in particular needs to be oriented to the good: it must be at the service of the human person. When the good of the person is ignored or subordinated to the sole end of acquiring knowledge, trouble looms. Is there any reason to fear that the work of Craig Venter and colleagues (Gibson et al., 2010) may cause harm? Research on synthetic life is subject to similar ethical constraints. It realizes the goal of understanding, but it also needs to be oriented to the good of the human person. Craig Venter’s research does hold out considerable therapeutic promise. Consider being able to download the genetic sequence of deinococcus radiodurans, isolating the genetic sequence responsible for its several unique abilities, such as rapid repair of DNA damage through annealing, and using such a preparation for anti-senescence therapies, or developing a “vaccine” against a nuclear radiation. Of course, manufacturing whole genomic sequences presents significant risks to the environment and to the human person in the form of bioterrorism. Neither of these risks is new. And there is nothing intrinsically immoral about Venter’s research project; it resembles in many ways gene therapy in that it has, in some sense, altered the genome of a particular cell. That is the object of gene therapy, namely, to change the patient’s genetic make-up (to one that is not dysfunctional). Venter’s study is a technical achievement in that it successfully changed the genetic structure of a bacterial cell with a whole genetic code manufactured on a computer model. If the research is to move forward, the only ethical issues concern the potentially deleterious consequences of it, namely, dangers to the environment and the possibility of bioterrorism. Does this research tread on “God’s ground”? Does it manifest a vicious hubris? Venter’s research is creative, and it represents a deeper understanding of nature and our world around us. In a sense, those working in science recapitulate or duplicate a divine attribute, namely creativity. Far from ‘treading on God’s ground’ this research on synthetic life realizes distinct human potencies to a considerable degree, chiefly of which is rationality. St. Thomas Aquinas defined goodness as the realization of a thing’s distinctive potencies. In the case of human beings, that potency is rationality and its daughter’s: creativity (pertaining to the addition of knowledge), understanding (pertaining to the quality and depth of knowledge) and knowledge itself. Further understanding our world is a case of actualizing our rational potencies. Aquinas states, “goodness is spoken of as more or less according to a thing's superadded actuality, for example, as to knowledge or virtue” (Aquinas, 1920). Research can be contrary to reason if the research itself acts against certain basic goods, such as human life, or disrespects vulnerable populations. But Venter’s research project seems oriented to the good of the human community and did not harm human life in the process. Venter’s research is not an example of hubris, but rather seeks to perfect one’s reason through creative cognition and understanding. Thomas Aquinas, Summa Theologica, I q. 5 a. 1 (ad.3), trans. Fathers of the English Dominican Province, 1920, available online at "http://www.newadvent.org/summa/" 10. Artificial Hype: Has Anything New Happened? Have We Been Here Before? Anthony Mellersh, Ph.D., Department of Chemistry, University of Derby, United Kingdom. Craig Venter and colleagues are to be congratulated on a brilliant media and publicity campaign. Whilst not denying that the achievement of Craig Venter's team is a tribute to the "industrialization" of molecular biology and the scale on which DNA sequencing and synthesis can be done (Gibson et al. 2010), the question remains: "Has anything new happened?" Three aspects of this very successful publicity juggernaut seem to have captured the media's imagination: The first is the concept that a "new" bacterium has been artificially created. This is not strictly true, as the intact cytoplasm of one bacterium has been used to host the artificially copied DNA of another. The synthetic DNA was then demonstrated to exert a degree of control over the metabolism and replication of the host bacteria. Haven't we see this before? Oswald Avery was doing essentially the same science in 1944 when he demonstrated he could transform pneumococcal strains with DNA from other pneumococci. What makes Avery's work even more remarkable is at the time he published his findings, most scientists did not believe DNA was genetic material. DNA was dismissed as a simple protein consisting of repeating patterns of four nucleotide bases which had little biological specificity. In fact, most biologists believed that genetics could not even be applied to bacteria as they lacked chromosomes. Therefore, when Avery et al (1944) reported that DNA was responsible for bacterial transformation, and was analogous to genes, the work was dismissed and ignored, even by the Nobel foundation which later expressed a public apology for failing to award the Nobel Prize to Oswald Avery. Secondly, the media is mesmerized by the concept that this creation is "artificial". Despite Wohler in 1828 demonstrating that urea could be synthesized from chemicals readily available and that it was the same as biologically formed urea, there is a persistent belief that anything biologically synthesized has some sort of intrinsic mystique, just look at cosmetic advertisements. The Venter group's series of experiments does not even go that far. Is it even accurate to describe this creation as "synthetic"? The DNA was assembled using biological tools such as enzymes and living entities such as yeasts and a bacteria. It is not synthesis from basic chemicals mimicking the origin of life from a prebiotic world as some headlines would have us believe. Lastly, the media has been led to believe that Venter's work heralds a new dawn. The attendant hype is reminiscent of the 1970's and 80's when the public was told that bioengineering was going to solve all our problems. Nice little organisms were going to synthesize drugs such as interferon, antibodies and anything that we needed. Organisms could be designed to mop up our messes such as oil spills and heavy metal pollution. The press trumpeted the hype (much of which had been fed to them by multi-billion dollar corporations) that genetic engineering will produce endless oil from the increasing concentrations of carbon dioxide in the atmosphere. The human race will enter the age of miracles where the more oil we burn, the more the carbon dioxide we generate and then more oil we get. Alas, we soon learned the truth: microorganisms will not behave as simple slaves which enrich and save us. The media still echoes these beliefs today. Climate change will also be sorted. We can continue messing up the planet. This technology was ushered in by the mild unassuming Oswald Avery, so it is perhaps best to leave the last words to him: 11. Be Afraid: Synthetic Life, Genetic Pollution and Horizontal Gene Transfer. Rhawn Joseph, Ph.D. Emeritus, Brain Research Laboratory, Northern California. It has been claimed that more people have died in the name of religion, than for any other cause. But in truth, in the history of this planet, science and technology has destroyed more life and murdered more people. Science and technology have always been the best friend of the killer. Craig Venter and colleagues are among the latest to dazzle the masses with the wonders of science and technology (Gibson et al. 2010). But what did they create? The artificial genome of a parasite and a pathogen. Will their creation be a boon, or will it spawn mass death and disaster? In 1963, Kurt Vonnegut, Jr. published "Cat's Cradle" which detailed the invention of "Ice-nine" by one of the greatest scientists on Earth, Dr. Felix Hoenikker, one of the "Fathers of the Atom Bomb". "Ice-nine" was to serve a simple purpose, to freeze mud so tanks and soldiers could easily travel across wet and muddy surfaces. Ice-nine consisted of a stable polymorph of water which would remain frozen at temperatures up to 45.8 °C (114.4 °F) instead of melting at the standard 0 degrees Celsius (32 degrees Fahrenheit). Ice-nine was essentially a "seed crystal", brilliant in its conception, and "completely harmless," serving only to keep America strong by making it easier to win wars. Unfortunately, once Ice-nine escaped the laboratory and came into contact with liquid water, it first froze that body of water only to spread to nearby lakes, rivers and then the oceans, such that eventually the entire planet froze and became a solid block of Ice-nine. In 1971 "Cat's Cradle" earned Vonnegut a Master's degree from the University of Chicago. Have Venter and friends presented the world with a genetic version of Ice-nine? What if this synthetic microbe or its artificial genes were to escape the lab? Should we be concerned? Or just amazed? Perhaps our amazement should begin with Venter et al's choice of microbe: Mycoplasma mycoides. Mycoplasma mycoides is a parasite. Mycoplasma is by definition restricted to vertebrate hosts. Several species of Mycoplasma are pathogenic in humans. Mycoplasma pneumoniae, for example, can cause pneumonia and other respiratory disorders and can kill the host. Mycoplasma genitalium is associated with pelvic inflammatory diseases. The Mycoplasma genus is unique in that it lacks a cell wall which renders most common antibiotics completely ineffective. Therefore, Venter and colleagues have synthesized the genome of a parasite which attacks and causes disease in vertebrates and which can resist antibiotics. They created a synthetic genetic weapon. Certainly there are a variety of technical reasons why Venter et al., would synthesize the genome of a parasitic, disease inflicting pathogen which has the potential to not just sicken but kill. And perhaps he allowed it to replicate a billion times in the interests of science. But what if just one of these billion were to escape the lab and replicate another billion in a matter of hours? What if this "artificial life" were to shed its artificial genes? Impossible? Everything is under control? Too many times in the past we have been told: "trust me." In the 1990s plant biologists working for giant corporations assured the public that genetic engineering was safe, there was no danger of contamination. However, in March of 1996, it was reported by plant geneticists at the Riso National Laboratory in Roskilde, Denmark, that genes they had inserted into oil seed rape canola plants (to increase their resistance to the deleterious effects of herbicides), were subsequently transferred to nearby weeds which in turn became resistant to the various chemicals that were supposed to eradicate them. That is, genetic copies of the genes inserted into the oil seed rape plant, exited the genomes of these plants and invaded and altered the genomes of nearby weeds. Since the weed and the canola plants do not mate, then the most likely means of cross-fertilization occurred via free horizontal gene exchange. Not only were these weeds "spontaneously cross-fertilized" but the weeds passed these new genes and this herbicide resistant trait to subsequent generations (Mikkelson et al., 1996). Horizontal gene exchange is commonplace between bacteria, archae, viruses, and eukaryotes (which include humans). The "universal" nature of the genetic code makes every living thing on this planet ideally suited for acquiring and making copies of genes, transferring these genes to other species, as well as accepting foreign genes, and then later donating and transferring these genes, including their own genes, to yet other organisms (Joseph 2009; Joseph and Wickramasinghe, 2010; Koonin 2009; Koonin and Wolf 2008). Parasitic creatures are the most likely to acquire and transfer genes between species, and Venter et al synthesized the genome of a parasite,Mycoplasma mycoides, which targets vertebrates. For a variety of reasons Mycoplasma is resistant to various antibiotics. Horizontal gene transfer also plays a significant role in the acquisition of antibiotic resistance which can be conveyed to a new bacterial host. This is made possible via the exchange of plasmids (mini-chromosomes), and DNA which has been expelled from the bacterial cell and then transferred to the genomes of yet other microbes which then acquire the genes necessary to combat these toxic agents, even prior to exposure. Further, these genes interact with yet other genes to provide resistance even to newly invented antibiotics. Should we be concerned if Venter's creation escapes the lab and begins sharing its synthesized genes with other creatures? Advocates of the "benefits" and "safety" of genetic engineering, and those who mock any supposed threats and dangers associated with genetic pollution, need only point out that as yet there has not been a single catastrophe and no mass deaths associated with these "miracles of science." Yes, genes have escaped and have been incorporated into the genome of other species, but what of it? Perhaps the same argument can be made for nuclear proliferation. So what if terrorists or rogue nations get their hands on a nuclear weapon. Nothing to be afraid of. Nothing bad has happened -yet. Evolution is slow and is punctuated with bursts of speciation and mass extinctions (Eldredge and Gould 1972; Elewa and Joseph 2009). The evolutionary progression leading to humans took 4.6 billion years. Fully modern humans have walked this Earth for less than 50,000 years. If the 4.6 billion year history of Earth were a clock, then modern humans have existed for about 15 seconds. Yes, in that 15 seconds humans have not destroyed the planet, though they have destroyed innumerable life forms and have murdered hundreds of millions of humans. And yes, in the last 30 years, in the last few seconds, the wonders of genetic engineering has not wrought havoc upon this planet; nor has it created mass mutations and nightmarish monstrocities that threaten to destroy life. And yet, time marches on. So far the planet is safe. But what about in the next 15 seconds? Hubris! The evolution of new species does not take place in small steps, as Darwin claimed, but in leaps after long periods of stasis (Eldredge and Gould 1972; Joseph 2009). And with evolution, there is extinction. The dire consequences of genetic pollution coupled with the eventual escape and proliferation of synthetic organisms and their synthetic genes, may not be fully felt for another thousand years. So, yes, we have nothing to worry about. Hubris can rule the day. But for those of the future, it may already be too late. Elewa. A. M. T., Joseph, R. (2009). History, origins, and causes of mass extinctions, Journal of Cosmology, 2, 201-220. Gibson, D. G. et al., (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science, advance on line publication. Joseph, R. (2009). Extinction, metamorphosis, evolutionary apoptosis, and genetically programmed species mass death. Journal of Cosmology, 2, 235-255. Joseph, R., and Wickramasinghe, N. C. (2010). Comets and contagion: Evolution and diseases from space? Journal of Cosmology, 7, 1750-1770. Koonin, E.V. (2009). Evolution of genome architecture. Int. J. Biochem. Cell Biol. 41:298–306. Koonin, E.V., and Wolf, Y. I. (2008). Genomics of bacteria and archaea: the emerging generalizations after 13 years. Nucleic Acids Res. 36:6688–6719 Mikkelson, T.R., B. Andersen and R.B. Jorgensen. (1996). The risk of crop transgene spread. Nature Vol. 380, 31. 12. Is Craig Venter Playing God with Genetics and DNA? Ted Peters, Ph.D., Center for Theology and the Natural Sciences at the Graduate Theological Union, Berkeley, California. Has genomic Titan Craig Venter stolen fire from the sun? Along with his research team, Venter has announced the "Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome" (Gibson et al., 2010). From the bottom up, so to speak, the Venter team assembled the chemicals to make up the genome of a bacterium,Mycoplasma mycoides. Then the lab team transplanted the nucleus into a Mycoplasma capricolum recipient. The result is the creation of a new life form, Mycoplasma mycoides JCVI-syn1.0, a bacterium controlled solely by the synthesized genome. From now on we can expect the new cell line to replicate continuously. This is a major achievement in genetic technology. What motivated Venter and his lab team of twenty-five to work fifteen years to make this happen? Venter’s purpose has been to "understand the basic components of life," he told Charlie Rose in a May 21, 2010 television interview. Venter said he is trying to "get control over nature." According to Venter, this proof of concept will provide the resources for future inventions of synthetic life forms, forms that could provide the human race with more effective vaccines, food, and fuel. What are we hearing in the hallways of the ethicists and the corridors of the moralists? Do we hear whispers of "hubris"? "Prometheus"? "Frankenstein"? "Playing God"? Has Venter crossed the line between non-life and life? Has he provoked the ire of the gods who alone claim province over life’s origin? Will nature respond to this invasion with a counter attack, letting loose genomic chaos? First, let us ask: has Dr. Venter created life from non-life? No. Rather, he has assembled nucleotides—much as previous experimenters with recombinant DNA have done--into a new configuration to produce an entire genome, a genome that operates the cell’s machinery. One might observe that this is what nature has been doing throughout our evolutionary history. As Charles Darwin theorized, nature is constantly generating new species through the interaction of variation in inheritance with natural selection. Assembling mutations over deep time leads to new species. Venter has done in the laboratory what Mother Nature has been doing for nearly four billion years. New life builds upon previous life. A Berkeley bioethicist colleague, Gaymon Bennett, emphasizes that Venter has synthesized a genome; he has not created synthetic life. Or, to put it another way, no ontological or metaphysical change in our understanding of life or the origin of life has occurred here. Nevertheless, secondly, Venter’s achievement still looks a bit like that of Victor Frankenstein in Mary Shelly’s 1818 novel, Frankenstein: A Modern Prometheus. Shelly wrote her novel after hearing the wild speculations of Erasmus Darwin, Charles Darwin’s grandfather, regarding galvanism—that is, returning dead body parts to life. The fictional Dr. Frankenstein sewed together body parts from a number of corpses and, with a spike of electricity, enlivened the assemblage into a new living person. Dr. Frankenstein, overcome with feelings of scientific grandeur then announced to stunned onlookers: "Now I know what it feels like to be god." The new person got out of control, as we all know, letting loose chaos and death. Shelly condemns the hubris of Dr. Frankenstein because it mocks "the stupendous mechanism of the Creator of the world." Hence, our contemporary phrase for a scientist who crosses the line, "playing God," reminds us of Dr. Frankenstein and his unconscious ego ideal, Prometheus. The reason the Olympian god Zeus punished Prometheus was that the Titan—when stealing fire from the sun--had crossed the line and invaded the sacred realm of the immortals. The problem with Prometheus as well as with Frankenstein was hubris, too much pride. This led to a backlash. This led to punishment of Prometheus by the gods and revenge by nature for Frankenstein. In our modern world, nature has banished the gods for setting moral limits on the height that human ambition will be allowed to rise. Does Craig Venter exhibit hubris? Relevant to answering this question, one might note that two decades ago he hired his own biographer to chronicle the achievements which would eventually place him in the annals of history. He has donned the demeanor of the maverick, the entrepreneur, the rascal, the soldier of fortune. Yet, even this image has self-imposed limits. "I don’t mind being Bad Boy," Venter told his wife over lunch; but "I just don’t want to be Evil Boy" (Shreeve 2004). So, we must ask: is Venter just a bad boy or an evil boy? Will Mother Nature strike back with genomic chaos, punishing the mad scientist and perhaps the rest of us as well? Actually, to my reading, the degree of Venter’s own personal hubris is not at issue here. This is not an ad hominemmatter pertaining to this scientist as a person. Rather, the question has to do with whether or not nature has placed a "No Trespassing" sign in front of the genome. Does our DNA have a "Do Not Touch" sign on it? There is no philosophical or theological reason for keeping our scientific hands off DNA, at least as far as I can tell. Even though we can marvel at the wondrous elegance of genetic activity, neither animal genomes nor human genomes are intrinsically sacred. If a scientific researcher is going to risk playing God, I do not think that it is likely to occur at the point of genetic redesign. If a laboratory team wishes to synthesize a genome, I see no ethical issues arising from genetic technology as such. Ethical issues might arise, however, when we consider the purpose (motive) or consequences. Should such experimentation be pursued for the purpose of biological warfare, then moral discernment would be called upon. However, bio-weapon construction is not Venter’s purpose. Or, in light of the precautionary principle, we might want to ask about the likelihood of collateral damage, the likelihood of un-anticipated negative consequences. It is too early to make such a judgment on Venter’s work. Yet, ethicists should remain on alert, watching what will happen in light of this breakthrough. Although Frankenstein is not yet here, we just might remain on the look out. Shreeve, J. (2004). The Genome War, Ballantine, p. 238. 13. Synthetic Biology and Fear of Ignorance. Hans Ziock, Ph.D., Los Alamos National Laboratory, Los Alamos, New Mexico, USA Science and technology have bequeathed untold benefits upon society and civilization. There is no reason to believe that the same will not be true for the field of synthetic biology. The general, underlying goal of science, including synthetic biology, is to improve the human condition, while also fulfilling the quest for understanding that motivates all men and women of science. The desire to know and to acquire knowledge is what distinguishes us as humans. The work reported by Dr. Venter’s team (Gibson et al. 2010) on the artificial generation of a complete and functional bacterial genome represents a truly remarkable engineering achievement and epitomizes that spirit of science which has led to so many scientific revolutions which have ultimately conferred wonderful benefits upon society. Although one might claim that the team’s achievement follows from longer-term steady progress in the general field of DNA reading, synthesis, and manipulation (and was thus inevitable), it is a major milestone. This is especially true when one considers the remarkably short time frame in which it was realized. The work leads to many new doors that should be opened and possibilities that should be taken advantage of. As with all new achievements in knowledge and engineering throughout history, it is possible that the work of Venter and colleagues can be exploited for "good" or "bad," even if the initial goals are purely virtuous. However, as a rule, the net benefit of new knowledge and technological progress has been for the "good", even if there can never be an absolute guarantee. In fact, an ever-wider knowledge base also serves as a resource to prevent or ameliorate any undesired consequences. It is also important to consider the question of "good" or "bad" in the context of life itself. Life is a dynamic process involving competition, with winners and losers, i.e., those who evolve vs. those that go extinct. Furthermore, success is ultimately measured by survival of the species and not the individual. At the same time, the species is made up of individuals and hence maximizing their number (and survival) provides an intrinsic advantage and a measure of success, i.e., "good". In the still longer term, even a given species becomes unimportant, so long as members of it evolve to give rise to new species that continue to survive. In this context, "good" refers to continued survival and is best quantified by a large population size, whereas "bad" is quantified by a small population size, and failure by lack of continued existence of the species. Survival depends on the ability to cope with both the inanimate physical environment, as well as with other life. In fact today, other life presents the greatest challenge, as it is the fastest changing part of the overall environment. Thus competition will be a major factor, be it with other species or other members of one’s own species. The other major factors impacting survival are the ability to adapt the environment to ones own needs, to predict how the environment will change in the future and how to maximally benefit from the predicted changes, and to ameliorate any pending detrimental changes. The key for these abilities is acquiring knowledge about the environment and usually also involves building a map of one’s environment and the ability to change the environment as desired based on acquired knowledge. Past experience (i.e. knowledge) of ones own or that of others is the ONLY basis available for prediction of the future or altering the environment in the desired fashion and as such is absolutely critical for long-term survival. The larger the knowledge base and the faster the ability to use it, the better the chances for survival. Hence, knowledge is inherently good and essential for our survival. Furthermore competition means that failure to make use of it gives something or someone the competitive advantage to ones own detriment. History repeatedly shows that on a probabilistic basis new knowledge, and the technology enabled by it, were undoubtedly for the greater good. In fact, most of the world’s population would not exist today without our continual gain and exploitation of new knowledge. Thus on a historic probabilistic basis (which is all that we have), there is absolutely no reason to believe that the breakthrough achieved by Dr. Venter’s team will not also overall confer significant advantages to humanity. Possible examples include the creation of synthetic life forms that can economically produce biofuels and/or new pharmaceuticals, or which could combat pollution or pathogens. The technology enabled holds promise for curing genetic ailments such as diabetes, Huntington’s disease, ALS, and cystic fibrosis, and could be used to screen for genetic defects in the unborn leading to much prompter and robust treatment. To summarize, the achievement by the Venter group should be embraced and put to use in as timely a manner as possible. Failure to do so ignores what history has shown to be the best choice possible for the population as a whole, namely to seek out new knowledge and use it as it become available. 14. Evolution, Synthetic Life, and the Tin Woodman Dilemma. Lynn J. Rothschild, Ph.D., NASA Ames Research Center, Moffett Field, CA "The Wicked Witch enchanted my axe, and while I was chopping away at my best one day….the axe slipped all at once and cut off my left leg. So I went to the tin-smith and had him make me a new leg out of tin" (Baum, 1900). Unfortunate, but a woodman with a tin leg is not philosophically vexing. It does not even justify the journey to the Emerald City of Oz. What are we evolutionary biologists to make of the announcement from J. Craig Venter’s group (Gibson et al., 2010) about the artificial synthesis, partial biological construction and transplantation of the 1.08 MbpMycoplamsa mycoides genome (including "watermark" sequences) into a M. capricolum cells? Has the first origin of life on Earth in the last 4 billion plus years finally occurred? Thoughts of "Frankenstein" and vague feelings of evolutionary and philosophical unease discourage a clear verdict on whether this is in fact a new life. The right analogy can precipitate the "ah ha!" moment when an abstraction becomes concrete and thoughts crystallize. Take Van Valen’s (1973) Red Queen Hypothesis, based on Lewis Carroll’s Through the Looking Glass. Alice must run to keep up with the Red Queen just to stay in one place, and personifies the continual evolutionary arms race that occurs in nature. Evolution is part of life. To discuss the significance of the work of Venter Institute’s achievement, I propose "The Tin Woodman Dilemma." To recap: in The Wonderful Wizard of Oz, prior to Dorothy’s flight from Kansas, the Tin Woodman was a live woodman, Nick Chopper. Nick was a lumber jack, and chopped down trees in the forests of Oz, and this is how he earned his living. Nick was also in love. Enter the Wicked Witch, who enchanted his ax to prevent him from marrying. Instead of felling trees, the enchanted ax cut off his limbs beginning with his legs, and then his arms, head and ultimately his body. A lesser man (munchkin) would have been deterred, but Nick Chopper, one by one had all of his parts replaced with tin prostheses which became limbs and ultimately his head and body. Nick had become a man of tin. Yet, rather than feeling sad because of his change, Nick was proud of his new body. Dilemma: at what point is he no longer Nick Chopper but instead a new person? Clearly the arms and legs are not what defines a person. Nor in an era where the transplanting of hearts is common, can we say its their "heart." We are on shakier grounds with the head and body. Medical science has already achieved heart, kidney, lung and even face transplants, and has fashioned prosthesis for legs arms, and even sexual organs. Even brain tissue has been regenerated. In rare instances, patients have undergone multiple replacement procedures. However, at what point can we say that the recipient is no longer the same person? Is it genetic continuity? Physical continuity? Would they be the same person following a brain transplant and body transplant coupled with a complete reprogramming of memories? But then, during our lifetime individual cells and atoms are continually being replaced and memories change. It has been fashionable to include Darwinian evolution as a pre-requisite for defining life. Is this definition accurate? Surely in determining if a creation is life the evolutionary origins of all parts are not truly necessary. When we meet and if you pass the basic requirements of life, I am willing to call you alive, whether you evolved from nature’s primordial cauldron or were created during the last few minutes. To claim otherwise would be the equivalent of denying membership in a club based solely on genealogy, thus not allowing for independent origins of life elsewhere or even on the early Earth. Perhaps the "what is life" dilemma can be clarified by turning to the early evolution of life. Woese (2002) presented a compelling scenario, where early life evolved as a fluid pool of genes. As metabolic interactions became more interconnected, it was necessary to keep gene complexes together. Thus gene exchange was severely restricted in order to evolve something critical to evolution: the origin of individuality. The subject of sex is perhaps even more pertinent to the discussion. If sex is simply the exchange of genetic information, all sorts of sexual and parasexual processes (Rothschild, 2010) begin to resemble the Tin Woodman’s travails. A gene or two is inserted through gene transfer. This is not only well known in nature, but has been performed in laboratories for decades. In fact, during evolution, interspecies ("horizontal") gene transfer has been extensive among prokaryotes for "operational genes", though conspicuously scarce (but not absent) among the "informational" genes (Jain et al., 1999). Eukaryotes too have indulged in gene swapping. Exhibit A: the mitochondrian and chloroplast, both of which have sent genes to the nucleus to replace host genes. So what makes a cell? The operational molecules? The informational molecules? Extra-chromosomal elements? Although evolution has provided parallels to the accomplishments of Gibson et al. (2010), the answers to these questions are not clear cut, largely because of the fact that we lack a robust definition for what is life. Several centuries ago water was described by its properties: not sweet, not salty and so on. But this leaves great ambiguity as to what water actually is. The "natural kind" definition is simple: H2O. I agree with Cleland and Chyba (2002) who believe that the problem lies in the lack of a "natural kind" definition for life. In this vacuum we will continue to struggle with vague feelings of unease and the perennial challenge of defining life and thus, what constitutes the creation of a new life. Did the J. Craig Venter Institute play "God"? Certainly not. Their monumental achievement (and it really is) was to take the "operating system" that evolution had produced for M. mycoides, laboriously copy it with a few flourishes, and use it to run the "hardware" of M. capricolum. It is telling that they named the new cellMycoplasma mycoides JCVI-syn1.0, clearly coming down on the side that the "operating system" defines the cell. By this definition, the Tin Woodman is still Nick Chopper. At this point evolution will once again take over and we are left with an amazing model to study the actual relationship between cellular DNA and extrachromosomal elements. For example, in ciliates there are documented examples of cortical inheritance during which a row of cilia, reversed during cell division, is inherited from generation to generation (Beisson and Sonneborn, 1965). Will there be information, structural, like the cilia example, which will eventually be passed on by inheritance? Might the RNA of M. capricolum provide a tension in this new cell between the authority of its M. mycoides genome and enucleated M. capricolum host? It is time for the evolutionary, molecular and cell biologists to step up to the challenge of Mycoplasma mycoides JCVI-syn1.0. Carroll, L. (1871). Through the Looking-Glass, and What Alice Found There. Macmillan, 224 pp. Cleland, C. and Chyba, C.F. (2002). Defining "Life". Origins of Life and Evolution of the Biosphere, 32, 387–393. Gibson D.G. et al. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science, advance online publication. Jain, R., Rivera, M.C. and Lake, J.A. (1999). Proc. Natl. Acad. Sci. USA, 96, 3801–3806. Rothschild, L.J. (2010). A powerful toolkit for synthetic biology: Over 3.8 billion years of evolution. BioEssays, 32, 304–313. Van Valen, L. (1973). A new evolutionary law. Evolutionary Theory, 1,1-30. Woese, C.R. (2002). On the evolution of cells. Proc. Natl. Acad. Sciences, 99, 8742-8747. Carroll, L. (1871). Through the Looking-Glass, and What Alice Found There. Macmillan, 224 pp. Cleland, C. and Chyba, C.F. (2002). Defining "Life". Origins of Life and Evolution of the Biosphere, 32, 387–393. Gibson D.G. et al. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science, advance online publication. Jain, R., Rivera, M.C. and Lake, J.A. (1999). Proc. Natl. Acad. Sci. USA, 96, 3801–3806. Rothschild, L.J. (2010). A powerful toolkit for synthetic biology: Over 3.8 billion years of evolution. BioEssays, 32, 304–313. Van Valen, L. (1973). A new evolutionary law. Evolutionary Theory, 1,1-30. Woese, C.R. (2002). On the evolution of cells. Proc. Natl. Acad. Sciences, 99, 8742-8747. 15. Are Synthetic People Next? Reflections on a Prosthetic Genome. Robert A. Holt, Ph.D., Sr. Scientist, British Columbia Cancer Agency Genome Sciences Centre; Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada. There is nothing particularly thought provoking about a Teflon frying pan, but it has enormous utility when frying eggs. Teflon (the DuPont brand name for polytetrafluuoroethylene) doesn't exist in nature. It is a polymer, a chainlike assembly of simple, repeating, fluorinated carbon molecules that was first synthesized by DuPont scientist Roy Plunkett in 1938. It is the only know substance to which a gecko cannot stick. DNA, or deoxyribonucleic acid, is a polymer. It is a natural polymer, comprised of a chainlike assembly of four different constituent deoxyribonucleotides, commonly referred to as DNA bases A, G, C and T. Each base has considerably more structural ornamentation than the pedestrian fluorinated carbons of Teflon, and when appropriately paired and polymerized as they are in the genome of every living thing, they form an elegant double helical structure. Genetic information, the instructions for cells to make gene products that form the structural and functional components of cells, is carried in the particular order of bases in the double helix. The order of bases in the sum total of DNA that encodes our biosphere has been laid down over evolutionary time. The order is not immutable but it is resilient, left on its own. We have become very good at reading the order of DNA bases (ie. DNA sequences) to the point where an individual human genome comprising billions of ordered bases can be read in about a week. A bacterial genome, typically containing a million or so nucleotides can be read about as fast as the DNA can be purified. Like Teflon, the new bacteria, Mycoplasma mycoides JCVI-syn1.0, has its origins in polymer chemistry. The genome sequence of its forbearer, Mycolplasma mycoides LC has been known for some time. When we know the order of bases in a piece of DNA we can physically reconstruct it. The procedure involves chemically modifying a base to specify its reactivity, joining it to another base to create a sequence of two, then demodifying this product in readiness for addition of the next base. It is slow, expensive and error prone and can support only a few dozen additions. The approach hasn't changed much since the first chemical synthesis of DNA molecule, a 77 base fragment of a yeast gene, was synthesized by Har Gobind Khorana and colleagues in 1965. This being the case, the synthesis of a plethora of short DNA precursors, each a carbon copy of a particular fragment of the 1.08 million base Mycoplasma mycoides LC genome, and the assembly of these chemical precursors into the complete, accurate and functional genome of JCVI-syn1.0 is a tour de force in both polymer chemistry and synthetic biology. The Mycoplasma mycoides JCVI-syn1.0 genome is a prosthetic genome because like any other prosthesis, it is an artificial replacement of a missing body part, albeit an essential one in this particular case. Where will this remarkable new direction in chemical synthesis lead us? Unlike Teflon frying pans, JCVI-syn1.0 cells have zero utility. In fact, if anything they are more likely to have negative utility. It is well established that some types of mycoplasmas are infectious, and in the laboratory many a research project has been derailed by incidental mycoplasma contamination of cell cultures and considerable effort goes into making molecular biology labs mycoplasma free, to the point where an entire industry is dedicated to this problem. A google search for "Laboratory Mycoplasma Decontamination" returns 160,000 hits. Try it. So why would anyone want to dedicate years of R&D and tens of millions of dollars to build a mycoplasma? Why create the synthetic genome of a parasitic pathogen? To digress a little, synthetic mycoplasma is a legacy project. Initial studies begun over a decade ago focused on Mycoplasma genitalium because it was known to have one of the smallest genomes of any cellular organism - only half a million bases. It was anticipated that the small genome size, plus lack of a fortified cell wall, would make genome reconstruction and activation of more tractable. The reason to try to reconstruct and activate a synthetic genome was simply to show that it could be done. However, when the genitalium genome was built it could not be activated by transfer into a recipient mycoplasma cell, probably because its genomic composition was just too different from that of the standard recipient, Mycoplasma capricolum. To digress further, since capricolum was already known to be able to support transfer of the natural, but larger, mycoides genome the synthetic genitalium operation was scrapped and replaced by the now successful synthetic mycoides project. Although there have been claims that, being engineerable, mycoplasmas could now have commercial applications, this is is highly debatable. The fragile cell membrane that positions mycoplasmas so well as experimental organisms for microbial genomics makes them, at the same time, completely unsuitable for the heavy lifting of industry. These tasks are better suited to their more robust bacterial cousins. Although lacking any real world utility, Mycoplasma mycoides JCVI-syn1.0 is definitiely thought provoking. Why is this genome not just another synthetic polymer? What makes it more intriguing than polyester? At first glance it is probably clear to anyone that what sets this polymer apart is that unlike any former product of chemical synthesis it is supporting what is, undebatably, cellular life. Of course we don't have a clue how to do the design of an organism from scratch, to pick a particular order of A, G, C an T's that yields some startlingly new but entirely pre-designed outcome. But we are now able to copy organisms. Change them a bit. So where do things go from here? Could we create a more complex microbe? A yeast, perhaps, which is an organism with a cell structure more related to multicellular entities like ourselves than to bacteria. Various yeast strains have been sequenced, and a typical yeast genome is only about ten times larger than Mycoplasma mycoides JCVI-syn1.0. How about a fruit fly, ten times larger still, and with a well characterized genome sequence? Or, if we follow this train of thought about as far as anyone would care to, how about a person? This is the real impact of the JCVI-1. It is demonstration that once we know a genome sequence, we can rebuild the organism it encodes. Even, in principle, a person. From scratch. Using chemically synthesized DNA fragments. To be sure, the technology is nowhere near being up to the task of constructing or activating anything as large and complex as a human genome, but the point is just that. The hurdle would be a technical one. A problem of scale. For better or worse, contemplation of human existence need no longer be purely metaphysical. We should ask ourselves how we feel about that, and start to act accordingly. 16. Intelligent Non-Design and the Origins of Life. Nick Lane, Ph.D., Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK. It is not to decry Venter to observe that implanting a synthetic genome in a bacterial cell is not the same thing as creating an artificial cell. The distinction is far from trivial. While the synthetic genome did take over all cellular functions, ultimately replacing all the protein hardware, it could only do so by requisitioning the machinery of the host cell in the first place; and it could only do that because the strains of Mycoplasma used were closely related. Had this protein machinery not been in place, had the membrane potential not been charged, had the axes of growth not been specified by subtle gradients, all the technical wizardry would have been worthless. Venter’s team copied the exact nucleotide sequence of Mycoplasma mycoides (Gibson et al., 2010) Remarkably, even a single point mutation (a frameshift mutation in the gene for DnaA, which initiates DNA replication) prevented the cells from dividing, holding up the team for weeks (Gibson et al., 2010). In fact, it is plain why a shift in this particular reading frame would cripple the cell; but other large deletions and inversions of DNA had no obvious effect on cell growth. As with the human genome, little is known about what most of the Mycoplasmagenome codes for, or how it works. If not copied exactly, the default assumption is that it won’t work at all, for reasons largely unknown. The fears of ethicists are patently unfounded. Researchers cannot begin to create ‘superorganisms’ that will ‘take over the world’. Genomes can be synthesised by copying exact sequences of bacteria, and perhaps mixing and matching genes with useful functions, as has long been practiced by genetic engineers. But until proteins can be designed from first principles with a particular function in mind, there is no threat of intelligent design. On the contrary: only natural selection, with its ability to vary gene sequence and protein function in millions of places simultaneously, in billions of bacteria, over trillions of generations, has the power to produce a superbug; and it has already done so repeatedly. Venter’s intelligent mimicry merely highlights the power of natural selection. That bears on the origin of life, specifically the moment that natural selection takes over from abiotic kinetic and thermodynamic selection (Lane et al., 2010). There have been real breakthroughs lately, with the synthesis of nucleotides under prebiotic conditions (Saladino et al., 2008; Powner et al., 2009); the demonstration that cyclic nucleotides can spontaneously polymerize into RNA chains in aqueous solution (Costanzo et al., 2009); that free nucleotides and short polymers of RNA or DNA concentrate many thousand-fold in hydrothermal currents (Baaske et al., 2007; Budin et al., 2009); and that DNA replicates thousands of times a day under hydrothermal conditions, using only a polymerase enzyme (Mast and Braun, 2010). All in all, small genomes have been successfully synthesised and replicated under abiotic conditions. But far from a superbug, the best this is likely to achieve is a Spiegelman monster (i.e. his synthetic virus). Selection for RNA replication ultimately leads to the formation of a short stretch of RNA, less than 100 bases long, which replicates furiously: the binding site for the RNA polymerase (Oehlenschläger and Eigen, 1997). Only higher units of selection, such as cells, can break this loop, to enable selection for the whole suite of metabolic properties needed for real life. But research into the origins of cells has been splintered and sporadic. What comprises a minimum cell? Should it have a wall, and one membrane or two; composed of lipids or proteins? The fact that bacteria and archaea have totally different membrane lipids and cell walls – fundamentally different barriers between the inside and outside – suggests that there is a structural abyss at the base of life (Martin and Russell, 2003). The fact that bacteria and archaea are practically indistinguishable in size and shape implies that the basic principles of cell structure emerge naturally from chemical mechanics. Life probably began in alkaline hydrothermal vents (Russell and Kanik, 2010; Russell et al., 1993). The geological process of serpentinization would have provided abundant hydrogen and reduced nitrogen to drive the carbon and energy metabolism of cells by a geochemical metabolism analogous to the acetyl CoA pathway in modern methanogens (Martin and Russell, 2007; Russell and Kanik, 2010). The honeycomb of micropores form naturally catalytic cell-like structures, probably lined with lipids, hinting at the beginnings of cellular selection. The interactions between nucleotides and amino acids that gave rise to the genetic code, RNA, DNA and proteins (Copley et al., 2007; Yarus, 2010), and the advent of cellular selection from naked RNA or DNA (Koonin and Martin 2006), are all experimentally tractable in simulated vent systems. That will provide real understanding. Cell structure might have been critical to the origin of complex life too. All complex life on Earth is composed of eukaryotic cells, which arose just once in four billion years via an endosymbiosis. The power of natural selection, acting on unimaginable populations of prokaryotes over unimaginable spans of time, never once gave rise to morphological complexity: endosymbiosis was necessary, for reasons discussed elsewhere in this Special Issue (Lane, 2010). Given the irrelevance of exact genome sequence to the origin of complexity, it’s ironic that another of Venter’s impressive technical achievements – the microimplantation of DNA into tiny prokaryotes only 1 µM in diameter (Gibson et al., 2010) – may make it possible to design experiments into the origin of eukaryotic cells by creating prokaryotic cybrids. Budin, I., Bruckner, R.J., Szostak, J.W. (2009). Formation of protocell-like vesicles in a thermal diffusion column. J. Am. Chem. Soc., 131, 9628-9629. Copley, S.D., Smith, E., Morowitz, H.J. (2007). The origin of the RNA world: Co-evolution of genes and metabolism. Bioorganic Chem., 35, 430-443. Costanzo, G., Pino, S., Ciciriello, F., Di Mauro, E. (2009). Generation of long RNA chains in water. J. Biol. Chem., 84, 33206–33216. Gibson, D.G., Glass, J.I., Lartigue, C. et al. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science DOI: 10.1126/science.1190719. Koonin I, Martin, W. (2005). On the origin of genomes and cells within inorganic compartments. Trends Genet., 21, 647-654. Lane, N., Allen, J.F., Martin, W. (2010). How did LUCA make a living? Chemiosmosis in the origin of life. Bioessays, 32, 271-280. Lane, N. (2010). Life in the universe: chance or necessity?. J. Cosmol. (Aug, in press). Martin, W., Russell, M. (2003). On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Phil. Trans. Roy. Soc. Lond. B., 358, 59-85. Martin, W., Russell, M.J. (2007). On the origin of biochemistry at an alkaline hydrothermal vent. Phil. Trans. Roy. Soc. Lond. B., 367, 1887-1925. Mast, C.B., Braun, D. (2010). Thermal trap for DNA replication. Phys. Rev. Lett., 104, 188102. Oehlenschläger, F., Eigen, M. (1997). 30 Years Later – a new approach to Sol Spiegelman's and Leslie Orgel's in vitro evolutionary studies dedicated to Leslie Orgel on the occasion of his 70th birthday. Orig. Life Evol. Bios., 27, 437-457. Powner, M.W., Gerland, B., Sutherland, J.D. (2009). Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature, 459, 239-42. Russell, M. J., and Kanik, I. (2010). Why does life start, what does It do, where will It be, and how might we find it? Journal of Cosmology, 5, 1008-1039. Russell, M.J., Daniel, R.M., Hall, A. (1993). On the emergence of life via catalytic iron-sulphide membranes. Terra Nova, 5, 343-7. Saladino, R., Neri, V., Crestini, C., Costanzo, G., Graciotti, M., DiMauro, E. (2008). Synthesis and degradation of nucleic acid components by formamide and iron sulfur minerals. J Am Chem Soc, 130, 15512-15518. Yarus, M. (2010). Getting past the RNA world: the Initial Darwinian Ancestor. Cold Spring Harb. Perspect. Biol. doi: 10.1101/cshperspect.a003590. 17. Life as a Natural Property of Matter. David Penny, Ph.D., Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand. The paper by Gibson et al (2010) introducing a synthetic DNA genome into an existing cell is certainly an important scientific advance. Because this new artificial cell used the new DNA and grew and divided, just like a natural cell, it allows us to move ahead intellectually in our understanding of the origin of life, both on earth and wherever else life might be found. The result removes a few lingering doubts that there was something special about natural DNA, and must encourage many researchers to aim for the next steps in new, or synthetic, life. Scientifically, the origin of life has many approaches. I find it helpful (Penny 2005) to divide the studies into three complementary and overlapping categories. Firstly there is bottom up (the chemical approach from relatively simple molecules towards macromolecules, for example Costanzo et al. (2009 and Powner et al. (2009) and top down (simplifying from existing biology towards macromolecular systems). Then it is useful to divide studies into more theoretical/abstract ones as compared to the important experimental studies, and finally into the macromolecules involved in replication versus the fundamental energy sources and chemical pathways (e.g. Martin and Russell 2007; Russell and Kanik 2010). For myself, the biggest interest in the Gibson et al. (2010) result is that it is another step to showing that ‘life’ is a natural property of matter – given the right mixture of chemicals in the correct orientations, the system will have the property of self-sustaining catalysis and reproduction. For this question, one of my favorites is the early approach of Skoultchi and Morowitz (1964) who took the naturally dehydrated embryos of brine shrimp down to 2°K, left them at this near absolute zero temperature for six days, and slowly allowing them to warm back up to room temperature. When placed in sea water the embryos recovered, then grew and reproduced. Although they had earlier shown the same survival for the bacterium E. coli near absolute zero, to show it for a complex multicellular animal (possessing nerves and a brain) was certainly a major leap. It certainly allowed the conclusion that life was determined solely by the arrangement of the chemicals – life did not (for example) depend on any special arrangement of electron orbitals that would not arise spontaneously at normal environmental temperatures. Almost certainly, life was a normal property of matter. The current work with synthetic DNA extends this theme; we certainly expect living systems to be developed in the laboratory. There are other aspects where the more theoretical approach is also helpful. The results of Mossel and Steel (2005) show that for a complex chemical system it is almost inevitable that autocatalytic cycles will occur. Such cycles are probably essential precursors of 'life as we know it'. From the studies of Eigen and Schuster (1977), quite a lot is known about the limitations imposed from the fidelity (accuracy) of replication (or the lack of fidelity) on properties such as the size of the genome. It is very interesting that the principles found by studying the necessary conditions for the origin of life were later shown (Reanney, 1982) to help explain the structure and evolution of RNA viruses (which have a much higher error-rate than for DNA viruses. As an aside, we used to be concerned how we could demonstrate evolution through time, now we realize that we can’t stop evolution! How could we possible stop the influenza virus evolving? Theoretical work on the origin of life can lead to profound implications for other areas of science; there is no part of evolution that should not lead to testable predictions (Penny et al. 1991). It was expected that Gibson et al. limited themselves to known nucleotide metabolism, but it is still important to keep broadening our knowledge of the chemical systems that could form life. Certainly, our knowledge is increasing of some of the constraints on living systems. The work of Eschenmoser (e.g. 1999) as well as Sutherland and Whitfield (1997) shows, as an example, the limitations that arise from ribose (or deoxyribose) in nucleic acids. Certainly, other forms of self-reproducing complementarity are possible and, in principle, additional nucleotides could be used (Piccirilli et al. 1990), although Szathmáry (2003) points out that there even given complementarity of base pairing there are still limits on the minimal number of complementary pairings with nucleotides. It is expected that a primary sequence should specify a reasonably unique three dimensional structure of whatever macromolecule is involved. Where next with the present study? From my interests, I would like to see synthetic ribosomes added into the cell as well – that would eliminate even another possible escape route for those who do not accept life as a natural property of matter. As a first step, it could just be natural proteins and RNA molecules reassembled into ribosomes, but in the longer term it might be even better with proteins and RNA molecules synthesized in the lab. This would require a major effort, but the Gibson et al approach was also a major project. To come back to the original Gibson et al. (2010) paper. On the more practical side, it will most definitely accelerate the field of synthetic biology, though I have nothing particular to say on that aspect. The interesting part to me is that it is another step demonstrating that life is a natural property of matter. The present work needs to be extended even further. We must continue to learn more about the principles behind the emergence of life, both on earth, and potentially elsewhere. Eigen M and Schuster P. (1977) The hypercycle, a principle of natural self- organization. Part A, Emergence of the hypercycle. Naturwissenschaften 64, 541-565284, 2118-2124. Eschenmoser A. (1999) Chemical etiology of nucleic acid structure. Science 284: 2118-2124. Gibson DG and 23 others (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 10.1126/science.1190719 Martin W and Russell MJ. (2007) On the origin of biochemistry at an alkaline hydrothermal vent. Philos. Tran. R. Soc. London Ser B 362, 1887-1925. Mossel E and Steel M. (2005) Random biochemical networks, the probability of self-sustaining autocatalysis. J. Theor. Biol. 233, 327-336. Penny D. (2005) An interpretive review of the origin of life research. Biology and Philosophy 20, 633-671. Penny D, Hendy MD and Steel MA. (1991) Testing the theory of descent. In "Phylogenetic Analysis of DNA Sequences" (Miyamoto MM and J. Cracraft, eds) pp 155-183. Oxford University Press. Piccirilli, JA, Krauch T, Moroney SE and Benner SA. (1990) Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature 343, 33-37. Powner MW, B & Sutherland JD (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459, 239-242. Reanney DC. (1982) The evolution of RNA viruses. Annu. Rev. Microbiol. 36, 47-73. Russell, M. J., and Kanik, I. (2010). Why does life start, what does It do, where will It be, and how might we find it? Journal of Cosmology, 5, 1008-1039. Skoultchi AI, Morowitz HJ (1964) Information storage + survival of biological systems at temperatures near absolute zero. Yale J Biol. Med. 37,158. Sutherland JD and Whitfield JN. (1997) Prebiotic chemistry, a bioorganic perspective. Tetrahedron 53, 11493-11527. Szathmáry E. (2003) Why are there four letters in the genetic alphabet? Nature Rev. Genet. 4, 995-1001. 18. Origins: Genetics, Synthetics, and Primeval Life. Clémentine Delan-Forino, Ph.D., and Maurel Marie-Christine, Ph.D., Acides Nucléiques et Biophotonique, FRE 3207 CNRS, Fonctions et Interactions des Acides Nucléiques, UPMC Université Paris 06, France. Two years after the synthesis of the first artificial bacterial chromosome, that is the genome of Mycoplasma genitalium (Gibson et al., 2008), the Venter team again published thought-provoking news (Gibson et al., 2010). Craig Venter used Mycoplasma capricolum (its own genetic material deleted) as recipient cell in which to transplant and which would control by a chemically-synthesized chromosome (1 million base pairs) copy of the genome of Mycoplasma mycoides. During the last decade, Venter’s laboratory developed methods to transplant an entire “natural" chromosome from a donor bacterium to a recipient one (Lartigue et al., 2007). Then, they in vitro synthesized, without mistake, large pieces of DNA reaching 6 kilobases (kb), and assembled them, step by step, by enzymatic methods and recombination steps in Saccharomyces cerevisiae, in order to get a whole synthetic genome of almost 600kb in 2008. Look beyond an obvious profit-seeking motive and attendant philosophical and ethical questions, do these first successes in synthetic biology bring new perspectives in fundamental research, especially in the study of origins of life? The RNA World hypothesis, one of the major scenarios of evolution which has received wide acceptance, postulates that an ancestral RNA world (Crick, 1968; Orgel, 1968; Woese, 1968) existed originally and gave rise to the common ancestor which evolved into all present forms of life. This means that the functional properties of nucleic acids and proteins observed today would have been previously performed by RNA molecules (Gilbert, 1986). The difficulty to synthesize, in prebiotic conditions, RNA molecules able to self-replicate spontaneously leads to the possibility that a simpler alternative genetic system (AGS), could have appeared before the modern RNA. In a geobiological perspective, Steven Benner and collaborators have shown the way to stabilize riboseborate complexes, which might have helped to obtain the precursor of the current RNA backbone (Benner et al., 2010). Following this line of investigations, a synthetic minimal living system would be a very interesting way to test the different AGS or other third type of nucleic acid in order to study their biochemical evolution. These are promising paths for all the scientists studying origins of life at molecular and structural levels, considering that life originated from simple organics leading to simple biomonomers then to functional biomolecules. However, we are still far from the primordial living system. In this last advance, Venter “just" copied what exists in the contemporary world promoting a gene-centric view that restricts the range of perspectives in fundamental research. Indeed, Craig Venter wants to demonstrate that a simple synthetic DNA can take the full control of an entire unicellular organism. This obviously reminds us of The Selfish Gene (Dawkins, 1976), and its “survival machines" described as simple receptacles responsible for protecting and transmitting genes to progeny. We know today that heredity transmits considerably more than just genetic elements and how wrong is the idea of a self-sufficient DNA responsible for the entire phenotype of an organism. This has been demonstrated many times, thanks to studies in epigenetic both in prokaryotes and eukaryotes cells. Nowadays, cytoplasmic heredity is also a well-established substantial process. For instance Sun et al., (2005) demonstrated the importance of cytoplasmic factors in the development of cross-genus cloned fish by transferring carp nuclei into goldfish enucleated eggs (for a review see Maurel and Kanellopoulos-Langevin, 2008). Subsequently, these cloned fish presented somite development and numbers consistent with those of the goldfish recipient species, but not with those of the carp nucleus donor. Non-mendelian heredity process is also illustrated by studies on paramecium model system, which revealed that the developing macronucleus is epigenetically programmed by the maternal macronucleus through RNA-mediated, homologydependent effects, and proposing the maternal transcriptome as a third actor in cellular inheritance (Meyer and Beisson, 2005). In short, Craig Venter is a magician of the genome. He was one of the pioneers of DNA sequencing during the eighties and nineties. He kept demonstrating his talent in 2000, when he almost won over the huge public enterprise decrypting the human DNA, the "Human Genome Project". But Venter wants more. We know that “natural" unicellular organisms are already central tools in industry; therefore, a minimal synthetic life could lead to tremendous breakthroughs in pharmaceutical but also in the energy industry. This scientist undertook the conquest of the green Graal, a synthetic microscopic algae capable of producing alternatives to fossil fuels. For fifteen years, in parallel to the massive sequencing of DNA from many marine algae, Venter has cut away, step-by-step, the genome of bacteria with one final goal: to transform these cells in multipurpose factories infinitely programmable, banishing any random event. We must recognize the huge technical feat performed by Venter but we also have to keep in mind that technical advancements do not constitute a universal theoretical panacea. copycats of Nature, remains copycats and, at their best, become useful tools. A decisive step remains to design a “genetic" material capable to store information, replicate and act as catalyst in a plausible primitive compartment. This still needs to be done for the one who wants to (re)-create what we think to occur with the emergence of a primeval life. Dawkins, R. (1976). The Selfish Gene, New-York, Oxford University Press. Gibson, D.G., Benders, G.A., Andrews-Pfannkoch, C., Denisova, E.A., Baden-Tillson, H., Zaveri, J., Stockwell, T.B., Brownley, A., Thomas, D.W., Algire, M.A., et al. (2008). Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319, 1215-1220. Gibson, D.G., Glass, J.I., Lartigue, C., Noskov, V.N., Chuang, R.Y., Algire, M.A., Benders, G.A., Montague, M.G., Ma, L., Moodie, M.M., et al. (2010). Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science. Gilbert, W. (1986). Origin of life: The RNA world. Nature 319. Lartigue, C., Glass, J.I., Alperovich, N., Pieper, R., Parmar, P.P., Hutchison, C.A., 3rd, Smith, H.O., and Venter, J.C. (2007). Genome transplantation in bacteria: changing one species to another. Science 317, 632-638. Maurel, M.C., and Kanellopoulos-Langevin, C. (2008). Heredity--venturing beyond genetics. Biol Reprod 79, 2-8. Meyer, E., and Beisson, J. (2005). [Epigenetics: Paramecium as a model system]. Med Sci (Paris) 21, 377-383. Orgel, L.E. (1968). Evolution of the genetic apparatus. J Mol Biol 38, 381-393. Sun, Y.H., Chen, S.P., Wang, Y.P., Hu, W., and Zhu, Z.Y. (2005). Cytoplasmic impact on cross-genus cloned fish derived from transgenic common carp (Cyprinus carpio) nuclei and goldfish (Carassius auratus) enucleated eggs. Biol Reprod 72, 510-515. Woese, C.R. (1968). The fundamental nature of the genetic code: prebiotic interactions between polynucleotides and polyamino acids or their derivatives. Proc Natl Acad Sci U S A 59, 110-117. 19. Artificial Claims About Synthetic Life: The View from Relational Biology. A. H. Louie, Ph.D., Mathematical Biologist, 86 Dagmar Avenue, Ottawa, ON K1L 5T4, Canada The achievement of The J. Craig Venter Institute, "Creation of a Bacterial Cell..." (Gibson et al, 2010), is an exceptional feat in biotechnology. And for that, the team must be congratulated. They did not, however, create a bacterial cell, and they did not produce synthetic life. Their work is one step closer to the telos of an artificial lifeform, perhaps, but the final goal remains out of reach. They have clearly transformed one cell into another. But there is nothing new about the modification of existing organisms; people have been doing that for millennia, at least since the dawn of agriculture. In the 21st century, we simply have more sophisticated tools. The Venter achievement differs in degree, but not in kind. Instead of the now-commonplace partial modification of the genome by multiple insertions, substitutions, or deletions, they have synthesized the entire genome — but still just one component of the whole cell. What it ultimately comes down to, as it does in most contention, is definitions. In Gibson et al (2010), they admit as much: Craig Venter reportedly said in an interview after the publication of Gibson et al (2010): "This is the first synthetic cell that's been made, and we call it synthetic because the cell is totally derived from a synthetic chromosome, made with four bottles of chemicals on a chemical synthesizer, starting with information in a computer." Note the unbridgeable gap between "synthetic cell" and "synthetic chromosome". I think Craig Venter was closer to the mark in 2007, when (in a quote attributed to him) he likened the process to "changing a Macintosh computer into a PC by inserting a new piece of software". In 2007 it was prophesied that artificial life would appear within months. Now, three years later (to continue the imperfect machine metaphor), the Venter group may have replaced the operating system, but they have not built a whole new computer from scratch — nor will they be able to in any foreseeable future. Craig Venter has synthetic genome; George Church at Harvard has synthetic ribosome. Are we once again proverbially "within months" of a truly artificial lifeform? For fundamental logical reasons, this kind of 'synthetic biology' — a mechanistic, algorithmic, and by-parts fabrication of life — will not work. Biochemistry has progressed so far and so fast in the past century that people find it hard to imagine that the process cannot continuead infinitum. The main problem is that the reductionist biology-is-chemistry approach has been so successful in solving biological puzzles, that although everyone can recognize that a living system is not just a machine, there is a great reluctance to admit that the two are different in kind and not just in degree. Relational Biology Biology is a subject concerned with organization of relations. A living system is a material system, so its study shares the material cause with physics and chemistry. But physicochemical theories are only surrogates of biological theories, because the manners in which the shared matter is organized are fundamentally different. Hence the behaviours of the realizations of these mechanistic surrogates are different from those of organisms. This in-kind difference is the impermeable dichotomy between predicativity and impredicativity. The study of biology from the standpoint of this 'organization of relations' is a subject called relational biology. It was founded by Nicolas Rashevsky in the 1950s, thence continued and flourished under Robert Rosen (For a comprehensive exposition on relational biology, see More Than Life Itself (Louie 2009)). The principles of relational biology may be considered the operational inverse of reductionistic ideas. The essence of reductionism in biology is to keep the matter of which an organism is made, and throw away the organization, with the belief that, since physicochemical structure implies function, the organization can be effectively reconstituted from the analytic material parts. Relational biology, on the other hand, keeps the organization and throws away the matter; function dictates structure, whence material aspects are entailed. Stated otherwise, an organism is a material system that realizes a certain kind of relational pattern, whatever the particular material basis of that realization may be. The relational pattern that makes a natural system alive turns out to be the impredicativity that is 'closure to efficient causation'. There is an alternative to physicochemical and algorithmic means in the quest for the fabrication of life. The important and consequential Venter achievement is an impressive one in technology, but no synthetic life, alas, has been made. An achievement is diminished if it is accompanied by overreaching claims of success, when such hyperbolic 'accomplishment' is illusory, and not entailed from what has actually been done. Louie, A. H. (2009). More Than Life Itself: A Synthetic Continuation in Relational Biology. ontos verlag, Frankfurt. 20. Synthetic Dreams and Genetic Destiny. Vipin Chandra Kalia, Ph.D., Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi, India. Evolutionary events manifested through changes in genetic material of living organisms enable us to visualize the acts of Nature. Genetic engineering and synthetic biology may enable humanity to gain control over Nature for the common good. The different frames of evolution are represented by nucleotides on a double helical circular DNA material. Synthetic biology creates copies of what evolution has wrought, so that humanity may control evolution and guide its trajectory in ways which benefit humanity. Assuming microbes to represent an intermediate stage in the complexity of life, an anticlockwise rotation along the helix shift the equilibrium towards the simpler forms of life – viruses. A clockwise movement along the evolutionary ladder takes us to more complex forms – the eukaryotes. This bidirectional evolutionary sequence of events can be linked to adaptation of genetic material to changes in environmental conditions. In a simpler three stage evolutionary scale, viruses primarily need a host - microbes or eukaryotes to sustain, whereas eukaryotes live as free living organisms and may act as host(s) to viruses and microbes. Microbes make up most of the biomass of this planet. They have also contributed to the evolution of the biosphere which sustains us all. Thus, by gaining control over microbial genetic machinery such as through the synthesis and manipulation of the bacterial genome, offers the opportunity to gain control over nature and to control and reverse changes in the biosphere which may threaten us all. We can assume microbes, based on their lifestyles, to represent the intermediate stages between viruses and eukaryotes. Microbes largely live as planktonic cells or as organized communities such as in soils or within biofilms. These lifestyles, which are quite evident in Vibrio cholerae, Xanthomonas campestris, Pseudomonas aeruginosa and Staphylococcus spp., have specific characteristics, which are crucial for their survival (Cotter and Stibitz, 2007). Within the biofilm, these microbes act as multicellular organisms and communicate among themselves to express phenotypes which require their collective actions (Bassler, 2002). Changes in genetic makeup are reflected in the variability within an organism. Polymorphisms of the nucleotides leading to variability, arise due to substitution, insertion or deletions (Gupta and Gao, 2009). This process is aided by diversity generating retro-elements, horizontal gene transfer, etc (Medhekar and Miller, 2007; Lal et al., 2008). By understanding the basic of genetics and biology, and putting them to use through synthetic technology, gives us the opportunity to jump start the evolutionary process, gain control over our genetic destiny, and to create synthetic interacting microbial communities and other life forms which can benefit us all. Combinatorial recombination events have the potential to generate genetic diversity, which is difficult to retrieve and quantify by presently available molecular techniques. Metagenomic approaches have provided some relief to the immense efforts needed to tap and elucidate the biodiversity, which seems to exist in nature (Handelsman, 2004; Venter et al., 2004; Tringe et al., 2005). It will not be too immature to state that NATURE has created all forms of life which are necessary for its existence and persistence. Therefore, by logical extension, it make sense to manipulate what nature has provided, such as through genetic engineering and synthetic biology, for the common good. Nature has provided the genetic blue print and a few visionaries, such as Craig Venter, have learned to read it. Now our innovative minds combined with available techniques and knowledge bases can help us to discover what seems to be an impossibility today and will be called a wonderful discovery tomorrow. Dr. J. Craig Venter has the passion, faith and courage to dream the impossible and put in efforts to make it come true. Dr. Craig Venter and his colleagues have created a microbial cell which is regulated by a chemically synthesized genome. This creation has opened up avenues for producing compounds useful for humankind (Gibson et al., 2010). He and his colleagues followed a reductionists approach to look for the minimum genomic machinery required for survival of microbes such as Mycoplasma (Glass et al., 2006). Attempts to determine the ability to tolerate losses in genetic material have been successfully attempted in Escherichia coli and Bacillus subtilis (Hashimoto et al., 2005; Ara et al., 2007; Morimoto et al., 2008; Singh et al., 2009). However, by discovering the minimal number of genes necessary, also provides the opportunity to insert additional genes to perform specific functions. By taking minimal gene sets from those with the smallest genomes, and by inserting synthetic copies into larger microbes with a greater genetic capacity, enables scientists to in fact increase synthetic genetic capacity to provide a wider variety of functions more effectively and efficiently. What can Venter's synthetic life do for us, which NATURE cannot? The most imperative needs are generation of fatty-acid derived fuels, which represent the naturally occurring petroleum (Steen et al., 2010) and bioproducts such as carbohydrates – hemicellulose from plant biomass (Steen et al., 2010) and associated enzymes - cellulases and hemicellulases (Picataggio, 2009) for third generation carbon neutral biofuels (Carere et al., 2008). There is also the dire necessity of reducing CO2 emissions by recycling this gas to produce fuels or chemicals – isobutyraldehyde and isobutanol (gasoline substitute) by over expression of ribulose 1,5-bisphosphate carboxylase / oxygenase. If this can be accomplished it would serve the dual purposes of reducing global warming and eliminate the unnecessary exploitation of precious biomass (Atsumi et al., 2009). It would allow the introduction of alien genes through conventional genetic engineering techniques in the laboratory or through horizontal gene transfers (HGT) in nature. The mosaic organisms acquire genes for better survival and transforming the non-producers (of a specific molecule or product) to acquire the status of producers (Kalia et al., 2007). Synthetic biology aims to engineer E. coli to produce biodiesel, fatty alcohols, and waxes from simple sugars (Picataggio, 2009, Steen et al., 2010) and terpenoids by manipulating mevalonate pathway (Martin et al., 2003). Secondly, E. coli does neither synthesize polyhydroxyalkanoates (PHAs, Bioplastics), nor accumulates such polyesters as carbon storage compounds. However, it could be transformed as PHA producer by expressing the entire PHA operon from Ralstonia eutropha(β-Proteobacteria) and by constructing a novel pathway by simultaneous expression of butyrate kinase (Buk) and phosphotransbutyrylase (Ptb) genes of Clostridium acetobutylicum (Firmicute) and the two PHA synthase genes (phaE and phaC) of Thiocapsa pfennigii (γ-Proteobacteria) (Liu and Steinbüchel, 2000). Phylogenetic studies revealed large scale HGT during the evolution of PHA biosynthetic pathway, where by probable transfer of PHA synthase gene - phaC responsible for polymerization of monomers can transform the presently reported non-PHA producers – Streptomyces coelicolor, Corynebacterium glumaticum, Clostridium perfringens, Desulfitobacterium hafniense, Staphylococcus epidermidis, Brucella suis, Coxiella burnetii and Leptospira interrogans to novel PHA producing organisms (Kalia et al., 2007). As a short term survival strategy, bacteria acquire resistance to antibiotics and loose certain other essential biological functions, leading to lower degree of fitness than the parental strain (Courvalin, 2008). Through genetic engineering we are likely to determine the possibility of persistence or reversibility of resistance (Courvalin, 2008). What about dangers? We need to carefully watch those organisms which have the potential to develop antibiotic resistance and whose genes then jump to new hosts: Agrobacterium tumefaciens, B. suis, Metarhizobium loti andSinorhizobium meliloti (van Baarlen et al., 2007). Genetic engineering has the potential to reproduce biological phenomenon which are occurring in nature and over which we have virtually no control. However, through synthetic biology, we may finally be able to take control and direct our own genetic destinies. Dr. Venter has opened the door and all of humanity may be the beneficiaries. Dr. Craig Venter is a bold visionary who does not fear failing by attempting the "impossible." Dr. Craig Venter dared to dream and to act on these dreams, and his success will lead to even greater discoveries which someday will reward us all. |
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