Synthesis and the Organism: Biology, Chemistry, and Engineering

Workshop Report

Synthesis and the organism: biology, chemistry, and engineering

Dominic J. Berry

Report and analysis of an interdisciplinary workshop that took place on 28 November 2017.

Organised as a collaboration between the Engineering Life project (ERC 616510-ENLIFE), the Flowers Consortium (EP/J02175X/1) and the Chemical Heritage Foundation.

Hosted by the Chemical Heritage Foundation (now the Science History Institute), Philadelphia.

Dominic Berry asserts their moral right to be identified as author. Permission is granted for noncommercial reproduction, copying, distribution and transmission of this publication or parts thereof so long as full credit is given to the coordinating projects, organisation, and authors; the text is not altered, transformed or built upon; and for any reuse or distribution, these terms are made clear to others.

The views expressed in this publication are those of the workshop participants and the author. Institutional affiliations are provided for purposes of identification only and do not imply endorsement of the content herein.

We would like to thank all the workshop participants for their contribution to the con- structive and engaging discussions and for their contributions to the review process. My considerable gratitude to Dr Dmitriy Myelnikov for designing and producing this report to such a high quality, particularly as this is now the second of our reports to which he has dedicated his skills. The first, authored by Deborah Scott and Dominic Berry, Genetic resources in the age of the Nagoya Protocol and gene / genome synthesis, can be found at the Engineering Life project website: www.stis.ed.ac.uk/engineeringlife

The workshop was funded by the ERC and EPSRC, and was further supported by the Science History Institute.

ERC 616510-ENLIFE EP/J02175X/1

None of the participants in the workshop should be considered as committed to the arguments and views contained herein.

This report was written thanks to further ERC support.

ERC 694732-NARRATIVENSCIENCE. Introduction from Engineering Life and the Science History Institute

Jane Calvert Engineering Life This workshop on the history of DNA synthesis was one of a series of interdisciplinary workshops organised by the Engineering Life project. The project investigates the movement of ideas, practices, policies and promises from engineering into the life sciences. Its focus is on synthetic biology, a field that aspires to engineer biological systems. Although DNA synthesis is essential to synthetic biology, it often remains in the background in discussions of the field. By bringing it to the foreground this workshop contributed to the Engineering Life project in several ways. Importantly, it provided a new way of thinking about the history of synthetic biology, which often traces its origins to the early 2000s, when its engineering agenda was articulated. Focusing on synthesis allowed us to connect synthetic biology to a much longer trajectory of DNA synthesis, starting in the 1950s. The workshop also highlighted the importance of chemistry, alongside biology and engineering, in DNA synthesis and in synthetic biology more broadly. It also raised challenging questions about the differences between synthesized and non-synthesized DNA; about the importance of provenance, inherit- ance and genealogical relationships, and what happens when these are bypassed by chemical DNA synthesis. Relatedly, thinking about the distinctiveness of synthesized DNA drew our attention to the nature of DNA itself. Synthesis produces a material entity, a molecular sequence, but DNA is more than this in also being a carrier of information and a product of evolution. By foregrounding these historical and conceptual dimensions of DNA synthesis the workshop allowed us to think afresh about current large-scale whole genome synthesis projects involving yeast and human genomes. Finally, I would like to say how valuable it was to hold the workshop at the Science History In- stitute, where the unique historical expertise in chemistry, engineering and the life sciences greatly enriched our discussions. 1 Jody Roberts Science History Institute The Science History Institute was proud to partner with the Engineering Life project team at University of Edinburgh to make this unique workshop possible. At the core of our institution’s mission is creating tools to make the past accessible in ways that can foster important conversations across constituencies about the place of science in our society. As the Chemical Heritage Foundation has morphed into the Science His- tory Institute following its merger with the Life Sciences Foundation, we are particularly excited about occasions for highlighting and exam- ining the connected histories of these molecular fields. The history of DNA synthesis provides an almost perfect exemplar for charting out new directions for collections, knowledge production, and public en- gagement about these critical breakthroughs that continue to impact all of our lives. The workshop focused on an often forgotten or overlooked aspect of laboratory science: the role of new instrumentation as a driving force for breakthroughs. The presentations and conversations at this workshop traced the ways in which laboratory technique becomes codified in an instrument; how the commercialization of an instrument trans- fers skills and capabilities to users across new geographies; and how this mobilization of users yields the sort of breakneck breakthroughs that have come to define contemporary discourse in and about synthetic biology and biomedical research. By convening a group of practitioners, observers, and researchers from fields in and around synthetic biology, we simultaneously captured the before and after moments of instrumental development and caught a glimpse of how this technology continues to shape how and where research is done, what questions can be explored, and what might become possible in a not too distant future. In settings such as this it’s natural to ask the question: how will this history be preserved? We were delighted to facilitate a process of discovery connecting our museum at the Science History Institute to the participants of this workshop to begin what is always a long process of imagining and then initiating a collecting initiative that can serve as a representative collection of this work. On behalf of the Science History Institute, I am delighted to have had the opportunity to collaborate with the Engineering Life project. Their work has created an uncommon space for thoughtful deliberation, inspection, and perspective needed for finding aligning emerging science with social needs. 2 Executive Summary

This workshop attended to the ways in which methods for the chemical synthesis of organic materials has mattered, and continues to matter, for biological science and technology. It adopted a fundamentally historical approach with a focus on the synthesis of DNA, and was informed by accounts from scientific practitioners, social scientists, museologists, philosophers, and historians. The workshop’s investigation was inspired by a focal point: the efforts of a small international community of scientists and engineers who from around the 1960s picked up the challenge of synthesizing nucleotide sequences without having to rely on finding desired sequences in existing organisms. This was the making of sequences through chemistry, technology and engineering. While the historiography of biotechnology is vast, the capacity for DNA synthesis itself has largely gone unnoticed, the vast majority of work focusing on techniques for recombination, its meanings, broader social significance, and reception amongst diverse pub- lics. By staying focussed on the particularities of biological molecules as synthesised the workshop aimed to break new ground, drawing in material culture, engineering studies, and their historical, philosophical and sociological intersections. While DNA synthesis was the focal point, these activities needed to be understood in a longer and broader context, right up to the present. Speakers accordingly focussed on a range of periods, and highlighted different features when it came to synthesis and the organism, each with an emphasis on different kinds of scientific, commercial, or organic actor. Indeed it is no doubt thanks to the diversity of the kinds of actor involved that scholars in the history of science have yet to grap- ple with the cases addressed here, the majority staying within either chemistry, biology, or engineering. This workshop recognises that synthesis sits in an uncomfortable research space for historians and philosophers of science. It was dedicated to addressing this discomfort and producing materials for the systematic international investigation of nonbiological, or perhaps ‘mechano-chemical’ DNA synthesis, the philosophical questions it provokes, the historiographical revisionism it invites, and the social relations it changes. 3 Part 1 of the report incorporates short summaries of the papers given (each of which was 20 minutes in length) and reports of the question period. Part 2 includes the biographies of our participants. In an annex we include copies of the workshop documentation. For the author of the report the following themes seem to deserve particular attention:

1. Decomposition and recomposition At various different points in the history of science, experimenters have been prompted to celebrate the strategy of repeated rounds of analysis and recombination, followed by further analysis and further recombination. In biology for instance we might think of William Batesons’ analogies between decomposition and recomposition in chemistry and the same practices in genetics, or Wilhelm Johannsen’s emphasis on the usefulness of composing and decomposing pure lines to understand heredity. From a very abstract perspective, one devoid of any specific experimental content, it can be difficult to distinguish between all the different kinds of epistemic strategy that marry together induction and intervention in this way. For instance, is there anything additional implied by the ‘bottom-up’ approach in minimal cell research, or the ‘design, build, test’ cycle emphasised in synthetic biology, beyond Francis Bacon’s sixteenth century commitment to combining ‘works of fruit’ with ‘works of light’? The extreme and ahis- torical nature of this juxtaposition is intended to puncture much of the inflationary rhetoric used by present proponents of particular experimental designs. What we learn from the papers presented in this workshop, is that arguments about the epistemic value of decomposition and recomposition must first be made meaningful through the specifics of the material being decomposed and recomposed. A focus on the specifics of DNA, what it does, where it comes from, its various roles in experimentation and analysis, is a methodological commitment that also al- lows us to analyse and assess broader experimental designs and epistemic strategies that are argued to relate to them. Obviously this kind of methodological commitment can be extended to materials well beyond DNA.

2. Values and value making Throughout the workshop different speakers made different claims as to what things were valuable, or became valuable, and introduced different kinds of value, from financial, to social, experimental, moral, and many things in between. The making of DNA and its becoming an experimental commodity is therefore at one and the same time a 4 Fig. 1. Left to right: Dr. Jody Roberts (Director of Science History Institute’s Institute for Research and managing director of SHI); Dr. Dominic Berry (Research Fellow, Engineering Life Project); Marv Caru- thers (Distinguished Professor of Biochemistry and Chemistry at the University of Colorado, Boulder and pioneer in DNA synthesis); Dr. Robert G. W. Anderson (President and CEO of Science History Insti- tute), in the biochemistry and biotechnology section of the SHI museum. Thanks to Samantha Blatt of the SHI for taking this photograph and thanks to the SHI for permission to use it. history of making values. In this respect the history of DNA synthesis can be immediately related to ongoing research on values and valu- ation, historical interpretation of the relations between science and technology and economic change, public and private property, intellectual property, and cultures of innovation. Remembering that different stakeholders will have different concep- tions of what is valuable, and what can be valuable, provides excellent grounds for the motivation of historical research and analysis. Indeed a communities’ responding to and learning how to value material- semiotic objects is often at the heart of an historical enquiry. Being explicit about this opens up interdisciplinary paths between historical and social scientific research, while providing richer materials for histories of the sciences. It also further emphasises the need to draw in a wide range of stakeholders, including scientists, industrialists, economists, social historians, civil society, and so on, all of whom will have their own views as to what is valuable, most valuable, and why.

5 3. The history of biology meeting the history of technology The intersection of the history of biology and history of technology has been subject to considerable renewed attention in recent years. At present historians trained in each subject are increasingly learning how to apply their historiographical approaches to cases thought to lie outside their primary, perhaps even appropriate, research contexts. DNA synthesis provides an ideal case study for those contributing to or skeptical of this agenda, for it is impossible to tell its history without addressing biology and technology (and chemistry and engineering) simultaneously. How historians can and should respond to these kinds of context is currently being debated, and DNA synthesis can provide a range of provocations. To different people DNA is an experimental tool, epistemic object, commodity, chemical and physical and biological material, natural resource, economic resource, political arena, and many more other things that we commonly only research through attention to its recombination. By attending to the fact that there are different methods for the making of DNA, we can grasp the different meanings of its making, and revise history accordingly.

6 Contents

Introduction from Engineering Life and Science History Institute 1 Executive Summary 3 Summaries of workshop presentations:

• Session 1: Introduction 8 • Session 1: Whole genomes/organisms 10 • Session 1: Group discussion 18

• Session 2: Extending synthesis 20 • Session 2: Group discussion 29

• Session 3: Objects and epistemics of synthesis 33 • Session 3: Group discussion 40

Attendee biographies 43 Annex: Workshop documentation 47 Summaries of Workshop Presentations

Fig. 2. Model of the Structure of Penicillin, by Dorothy Hodgkin. By Museum of the History of Science, University of Oxford [CC BY-SA 3.0], via Wikimedia Commons.

Session 1: Introduction to the Worskhop

Dominic Berry Introduction

This workshop constitutes part of the ested in studying synthetic biology: trying Engineering Life project, which is run by to understand what’s going on with that Prof. Jane Calvert in Edinburgh. We are range of sciences, the developments un- an interdisciplinary team of researchers, derway, and the ways in which it is signifi- including social scientists, geographers, cant for broader society. For myself, as a historians, all of us with quite different historian of science, my role on the project backgrounds, dedicated to researching is to try and historicize contemporary sci- contemporary science as it is practiced in ence, to try and bring history to synthetic the present. The broad umbrella that we biology, and in the process bring the value are interested in is biological engineering, of the history and philosophy of science and within that, we are particularly inter- to the present. For me that is all that this 8 workshop is made of and dedicated to, try- The history of DNA synthesis is at one and ing to explore the past in order to better the same time chemical, biological, tech- understand and appreciate the present. One important thing to recognise about nological, and engineered our workshop today is that it is deeply interdisciplinary. We have people from a another, allowing you to look through the whole range of backgrounds, interests, perspex, eventually coming to appreci- expertise, their own reasons for finding ate what the 3D structure must look like. something like DNA synthesis interesting. I think this helps as analogy to visualise That interdisciplinarity is important for my understanding of historical change. at least two reasons. One, the phenomena But what are we trying to understand the that we are all here to discuss, DNA syn- structure of, what is our penicillin? thesis, is itself a deeply interdisciplinary There are some interesting questions phenomena. There were lots of kinds of about how to actually describe the topic actor involved, and lots of different exper- of our workshop. Is DNA synthesis right? tise involved. Another reason to make this I have proposed mechano-chemical in the an interdisciplinary event, is that there is workshop proposal, in order to recognise lots to do! We need as many people as we the variety of features that make this kind can get in order to pool together this his- of synthesis distinct from what is going on tory. So I hope from our discussions we can in cells, but what do you think of that? For learn what kinds of institutions we want to lots of purposes today we are going to be go and investigate further, which archives able to say synthesis or chemical synthesis, to try and find, which people to try and fol- but does that capture everything going on low up, who we need to convince to leave in those instantiations, and are there oth- their papers to an archive, to build the ar- er interpretations? It’s also the case that chive that we need. Another question that perhaps we are actually wanting to talk is close to the heart of the Science His- about something else, and the synthesis tory Institute, is what kinds of objects we frame ultimately does not work. One could might want to collect in order to preserve have easily organised todays workshop the material history of something like around ‘model organism research and bio- DNA synthesis. I am hoping we can get lots tech’, with DNA synthesis becoming one of ideas here. When you take a topic like amongst a number of technologies that DNA synthesis, we have the opportunity mattered, or we could have gone for ‘histo- to think large and be ambitious about what ries of the commercialisation of university we want to do with that history. research’, and again DNA synthesis would Not everyone here is used to thinking have become one of a number of examples. historically, and those of you that are, we Why chose DNA synthesis then? Well don’t all think historically in the same way. if you’re part of a project focussed on syn- So with the rest of my introduction I want thetic biology, then DNA synthesis is a to give you an insight into how I, myself, very quick way to start forcing some his- understand historical change, and the tory into contemporary practices, because kinds of history that I see today contrib- synthesis is essential to everything that uting to. Not so that I can convince you it’s synthetic biologists get up to. So if we the right one, but so you can appreciate can learn more about the history of DNA some of the quirkier aspects of the work- synthesis we are de facto learning about shop. In order to do that I am going to lean the history of synthetic biology, even if it on an analogy from the history of x-ray is not necessarily on the historical terms crystallography. that synthetic biologists understand them- When Dorothy Hodgkin was working on selves. Another reason to choose this focus, the structure of penicillin, she adopted the is that in terms of the history of biotech- practice in x-ray crystallography, of map- nology, DNA synthesis has been neglected, ping out the data on sheets of perspex. even though it does come into parts of sto- These would then be layered one on top of ries that are very well known, such as the 9 Human Genome Project or PCR. DNA syn- exploration easier for other historians in thesis has not had this kind of dedicated the future. attention that we’re going to give it today. Returning now to Hodgkin, I want us to The time is ripe for people to start doing so, be thinking of those perspex sheets, lay- drawing in people who have been working ered on top of one another, and the over- in fields associated with DNA synthesis, all structure that emerges, as we try and and start collecting the materials that we piece together a history of DNA synthe- would need in order to preserve it. Lastly, sis. We are perhaps trying to find ways to I think this approach to the topic sets us perform x-ray crystallography on the past, up with some nice historiographical chal- at least, that is an image that feels right, lenges. The history of DNA synthesis is at to my mind, as being close to what it is to one and the same time chemical, biologi- think historically about a subject. Some of cal, technological, and engineered. As good the parts of the structure will be directly as the discipline of the history of science connected, other parts disconnected, other is, it is not necessarily good yet at dealing parts meeting for a while before going off with that kind of historical space. So an- to have lives of their own. But you come to other reason to have this workshop is to grasp the whole by putting everything into produce materials that will make such an place.

Session 1: Whole genomes / organisms

Alok Srivastava & Elihu M. Gerson Synthesis of Viable Genomes and Organisms: Understanding Wholes

What do synthesis experiments add to our I will be arguing that synthesizing does understanding and our capacity to explain more than explaining; explaining and things? How new kind of work do synthe- making both develop capacities for pulling sis experiments do? Similarly, a parallel systems apart and putting them back to- question is what do synthesis experiments gether; and that making is more than ma- add to technology and how do they do it? nipulating. When it comes to making the In this paper, I focus on a particular class chemist holds a different standard than the of synthesis experiments called Total Syn- one that biologists have typically adopted. thesis projects. I will discuss two cases and That making is more than manipulating in both of them, I will use the standards and is a way to reconcile two different kinds of total synthesis projects as practiced by of complexities: descriptive complexity, chemists to elucidate their contributions. and interactive complexities. By descrip- The Nobel Prize-winning chemist Gob- tive complexity, I mean that explanations ind Khorana highlighted the integrative and mechanisms delineated in the same nature of working on chemical experi- phenomena by different disciplines do not ments in biology in the opening sentence easily coincide. For example, for the gene, of his Nobel lecture: “Recent progress in the informational picture, the chemical the understanding of the genetic code is biosynthetic picture, and the physiologi- the result of the efforts of a large number cal picture don’t line up by themselves— of workers professing a variety of scien- like Dorothy Hodgkin’s perspex sheets do. tific disciplines.” (He received the prize By interactive complexity, I mean that the in 1968 for his work on “interpretation of explanations and mechanisms work across the genetic code and its function in protein multiple dimensions of explanation. For synthesis.) For myself what matters here example, the chemi-synthetic picture of is the idea of individual researches pro- the gene is only a subset of the full pheno- fessing and practicing a range of scientific type generating aspect of the physiological disciplines and thereby synthesizing those gene referred to by the geneticists. These disciplines. descriptions and explanation can line up in 10 practice if the independent diagrams we Making is more than manipulating and is hold bring you to do something new in the a way to reconcile two different kinds of lab, but those diagrams themselves can’t line up one on top of each other to be part complexities: descriptive complexity, and of the same whole. interactive complexities. Before I begin, I also need to explain the particular standing of total synthesis between the material entity and its biolog- experiments and projects in contrast to ical behaviour? The Khorana lab success- synthesizing a part of a whole or demon- fully demonstrated a reconciliation of the strating the mechanistic operation of a chemical gene, the informational gene that part. Experiments demonstrating the com- Francis Crick would recognize, and the plete chemical synthesis of biologically vi- physiological gene that even Thomas Hunt able wholes such as genes and genomes Morgan might recognize. In comparison, are examples of Total Synthesis experi- what kinds of reconciliations were at- ments. Total synthesis projects are a long- tempted by the Venter Institute’s project? standing institution in the professional Their goal was to produce the minimum world of chemists and have been adopted viable organism as defined by the minimal subsequently by biochemists, molecular genome, the minimal set of cellular parts biologists and most recently by synthetic and pathways and the minimal physiologi- biologists. This has been applied to DNA, cal capacities required to keep a cell vi- biosynthetic pathways, biochemical com- able. These three descriptions and mech- plexes, genes, regulatory pathways, and anisms—genome, parts and pathways, now genomes, with the hope of getting to and physiological capacities—needed to organisms. One of the points of the talk is be defined exactly and reconciled in their to distinguish the claim of synthetic organ- project. The second half of the discussion isms versus synthetic genomes. What this will attempt to delineate the accomplish- synthesis means is different according to ments and limitations of their attempt. the type of scientist involved. Biochemists There are at least three aspects of total hold themselves to having reconstituted synthesis work. The first is articulating purified components that comprise DNA established explanations and manipulation polymerase activity or RNA polymerase techniques from decomposition studies activity. Molecular and cell biologists they i. e. pulling things apart and saying ‘this reconstitute complexes in vivo. And syn- thing caused that’. In this aspect, you are thetic biologists are taking it to recompose putting the pinch points between your whole systems. manipulations and explanations to say In this talk, we also want to introduce ‘we have mechanisms here that we can two distinct types of coordinative arrange- work with and recapitulate what nature ments entailed by the work of assembling does.’ Second, you need to show that once parts into viable wholes—scaffolds to hold your identified parts are recomposed, they the organization of parts while under con- behave as expected. Third, when the target struction and brackets to hold together phenomenon has multiple dimensions you parts or capacities that are not linked but have to reconcile different explanations, must operate near each other. and the associated manipulations and I will be working with two cases of total mechanisms, in order to show your synthesis projects. First is the accomplish- perspective is complete. In the case of ment in 1979 of the Khorana lab demon- Khorana and the gene, the informational, strating the first total synthesis of a gene chemical and physiological dimensions and showing its biological activity. The of the gene were reconciled in the total other is the claim from March 2016 of the synthesis project. total synthesis of a minimal genome—they The Khorana Lab combined tools from are careful to avoid saying ‘organism’, but chemistry and biochemistry. The direct do the chemist’s standards of total syn- chemical synthesis was done to obtain the thesis projects allow such a distinction small oligonucleotides, but enzyme-based 11 Fig. 3. Visualisation of a historical arc showing passage through stages of decomposition, manipulation and re-composition. Copyright retained by Alok Srivastava and Elihu M. Gerson. biochemical reactions were used in the a historical transition in development and construction of the longer length DNA of integration of the multiple disciplines de- the gene. And also the complementarity of veloping explanations and manipulations duplex DNA was used to bind pieces with of that target phenomenon. This historical each other in the correct order to construct arc shows the passage from a phase of de- the whole length gene. Khorana called their composition work into a phase of re-com- method the chemical-enzymatic method position work through a transitional phase for synthesizing the gene. Through several of reconciliation work. The decomposition stages, the whole gene is assembled—and phase accumulates discoveries of parts in their diagram, they depicted each loca- and their inter-relationships into a stack tion where enzymatic activity is complet- of possible explanations and manipula- ing the synthesis with a bump. To demon- tions. During the reconciliation phase, this strate the expected behavior of the gene stack of explanations and manipulations they inserted the synthesized gene into a are rationalized with respect to the assem- disabled version of its home organism—a bly of the whole and its behaviour. As the bacteriophage (bacterial virus) lacking a elements of this stack begin to fit together copy of this essential gene. This disabled some of the explanations are found to be version of the bacteriophage is unable to lacking and are replaced and some of the complete the final stage of its life cycle in missing manipulation capacities are speci- bacteria—to break out of the cells—which fied and discovered. As the elements of the is visualized through the formation of stack begin to fit with each other the total plaques on a lawn of bacteria. The syn- stack reduces. The successful execution of thetic gene successfully restored plaque the Total Synthesis Project marks a recon- formation behaviour and reversed the dis- ciled and complete repertoire of explana- ability of the bacteriophage. tions and manipulations. The first total The execution of a Total Synthesis synthesis of a gene and the demonstration project of a target phenomenon also marks of its biological behaviour reconciled the 12 chemical, informational, and physiologi- In the Khorana case, a range of ways to cal explanations and manipulations of hold the sequence of the gene together the gene. This full package of repertoires of manipulations underlying such a dem- was utilized, such as the written sequence onstration is portable and transportable. of the gene, the maps, and protocols In this aspect, the successful execution of a total synthesis project of a whole marks used to represent the arrangements of the passage through a bottleneck in tech- the intermediate parts and to guide the nology development. The tour-de-force efforts offer to all the workers in related sequence of assembly. disciplines a complete circuit of explanations and manipulations for the making gene together was utilized, such as the and remaking of genes at the chemical written sequence of the gene, the maps, level and the behavior of genes at the bio- and protocols used to represent the ar- logical level. rangements of the intermediate parts and Historically, the first successful total to guide the sequence of assembly. synthesis of a gene depended on an array Brackets, on the other hand, are used of earlier completed work produced by a to hold capacities together when they are range of different disciplines. We might needed in the same space or time. Some ca- list the central dogma of molecular biol- pacities of the elements of a whole interact ogy, gene structure, physiological activi- and need to be kept in place but blocked ties of the cell, and chemical-enzymatic from interacting during assembly and characterizations of the cell’s proteins as some capacities that are not linked need to capacities available to this project. Impor- be kept together so that their joint action tantly also, the chemical-enzymatic expla- can drive the assembly. These situations nations and manipulations of processes are articulated with brackets. An example such as DNA polymerization and RNA is the role of blocking chemistry in these polymerization had already been worked experiments to deal with the many active out in in-vitro & cell-free experiments be- centers in a chemical part of a polymeriza- fore this project. These repertoires offered tion reaction. Blocking agents being added the starting stack of explanations and ma- to selective sites of a molecular part in nipulation at the start of the reconciliation one reaction to selectively enable a spe- work involved this total synthesis project. cific reaction and sequentially removed in Reconciliation work during re-compo- subsequent reaction steps to enable other sition and re-assembly projects empha- specific reactions are examples of - brack size the role of unique classes of capacities ets employed during bench-work. This called scaffolds and brackets. These are co- class of coordination devices articulating ordination devices to enable work within DNA Synthesis in the laboratory has been and across multiple levels of the phenom- a critical technology in the growth of DNA enon. This coordination includes the social synthesis and it was crucial in the develop- level of the lab personnel and interacting ment of the capacities packaged in auto- disciplines and the physical level on the mated-mechano-chemical DNA synthesis. lab workbench and the test-tube. Scaffolds Now turning to the Venter study. Their are required while a configuration of tar- claim was that they had designed and syn- get phenomena is being assembled. Suit- thesised a minimal genome. The intended able scaffolds that hold the configuration goal of their project was to design and together during and through the interme- demonstrated a minimal and completely diate stages of assembly. The capacities of defined cellular organism. They aimed to the scaffold are not built out of the mecha- achieve and demonstrate a reconciliation nisms inherent in the phenomena but are of three intersecting models and mecha- recruited from outside such as the labora- nisms of the minimal viable genome: the tory environment. In the Khorana case, a minimal set and network of genes, the range of ways to hold the sequence of the minimal set of cellular parts and pathways 13 and the minimal physiological capacities was not a design process, this is trial and of the cell. error, trying multiple hundreds. By this An early accomplishment of the Ven- process, they arrived at one genome that ter Institute was to achieve the capacity was viable. This accidentally successful to build genome length molecules of DNA genome had 473 genes compared to the from small pieces in surrogate chemical original 525 genes. Moreover, one-third of and biological environments. They also the 473 genes are without assigned biologi- accomplished the ability to replace the na- cal functions in the available knowledge of tive genome molecule of a host organism microbial molecular biology. with the synthesized genome and re-boot The Venter Institute study misses the the physiological life of the host cell with standards of a total synthesis project as the transplanted genome. To achieve this practiced by scientists in significant ways. the Venter laboratory behaves like a surro- The parts and their relations remain un- gate cell and is organized to take on several known for at least 1/3rd of the genes in steps carried out by the cell. Several parts the viable genome. So if we compare the and sub-assemblies having to be specified, Venter institute’s study to Khorana lab’s organized and held correctly along the achievement, we can see that the Venter step-wise process of making and piecing study could not achieve reconciliation of them together. The lab here is made up of a the multiple perspectives. Firstly they lack system of scaffolds and brackets that let it a complete list of defined parts on each of substitute for cellular processes. The Ven- the three perspectives: the minimal set and ter Lab acting in this manner as a surro- network of genes, the minimal set of cel- gate cell is able to routinely specify, make lular parts and pathways and the minimal and assemble a full bacterial genome, physiological capacities of the cell. As a re- transplant into the host cell and reboot its sult, their project failed to get going on the physiological activity, all in three weeks. reconciliation work typical of a total syn- However, in their pursuit of minimiz- thesis project. In sum, the contrast in the ing the list of parts and capacities to sup- accomplishments of these two projects un- port a minimal organism the Venter group derscores that making a working system hit significant failures. The implemented from scratch constitutes a distinctive kind genomes based on previous work from of knowing, and making cannot substitute top labs such as the George Church group for explanations. defining the minimum list of genes and pathways to support a cell. This minimum ↠↠ Bibliography: gene set included 166 genes and the trans- Wimsatt, W. C. (1972, January). Complexity and planted organism did not reboot and could organization. In PSA: Proceedings of the biennial not be enlivened. Fresh attempts through meeting of the Philosophy of Science Association bioinformatics efforts by two separate (Vol. 1972, pp. 67–86). groups at the Venter Institute built alter- Khorana, H. G. (1979). Total synthesis of a gene. Sci- ence, 203(4381), 614–625. native lists of genes. But the designed ge- Hutchison, C. A., Chuang, R. Y., Noskov, V. N., nomes from these two efforts again proved Assad-Garcia, N., Deerinck, T. J., Ellisman, M. unviable and could not be resuscitated by H., ... & Pelletier, J. F. (2016). Design and syn- additional strategies. At this point they thesis of a minimal bacterial genome. Science, went back to traditional genetics, and used 351(6280), aad6253. transposon-mediated deletion analysis of Coyle, M., Hu, J., & Gartner, Z. (2016). Mysteries in each gene, to discover the set of essential a minimal genome. ACS Cent. Sci., 2 (5), 274–277. genes required for viability. Through this Gerson, E. M. (2008). Reach, bracket, and the limits process, they obtained a reduced gene set. of rationalized coordination: Some challenges But when they built this, it did not live. for CSCW. In Resources, Co-Evolution and Arti- At this stage they put back genes that facts (pp. 193–220). they had left out, one by one, to test each Caporael, L. R., Griesemer, J. R., & Wimsatt, W. C. additional gene for contribution to viabil- (Eds.). (2013). Developing scaffolds in evolution, culture, and cognition. MIT Press. ity. This was a purely empirical effort. It 14 Jane Calvert Synthetic yeast: a tale of sixteen synthetic chromosomes

The aim of the synthetic yeast project is to of the codons in E. coli. The synthetic yeast redesign the genome of the yeast species project is an order of magnitude larger Saccharomyces cerevisiae. The project is of- than previous bacterial genome projects. It ten referred to as Sc2.0. Several of the chro- also aspires to change the genome in many mosomes have already been synthesised, ways. and these results were published earlier in 2017 in Science, so some of you may already When the scientists first set out with the be familiar with it. There are two main rea- goal to design a new yeast, they could sons why it is relevant to our discussion today. First, it is the kind of project that peo- not easily decide what to do, because the ple only take on thanks to the capacities for number of possibilities was so large. What DNA synthesis. It reflects the kind of sen- timent I heard expressed by the synthetic they decided to do was to design a yeast biologist Christ Voigt at the Synthetic Biol- that could teach them biology. ogy 7.0 conference: “Now that we have the ability to synthesise anything, what we do In passing I should mention that some we build and what do we design with that people see this as on a path towards the capacity?” I am not necessarily endorsing synthesis of the human genome, which I his view that we can synthesize anything, won’t discuss myself, but Rob Smith will but I am highlighting the kind of sense of address this at the end of the day. possibility that DNA synthesis often in- While this overview is the kind of his- spires. The second reason I wanted to dis- tory people usually recapitulate for the cuss this project is because of one of the synthetic yeast project, others do go back questions which this workshop was organ- further. One of the people on the project ised around, one that resonated with me: traces a history of synthesis back to the ‘what are the relations between organisms first synthetic gene in 1979, and then from in receipt of synthesised DNA and those there the first synthetic plasmid in 1990, al- inheriting it from biological production or lowing for a broader and bigger trajectory receiving it from another organism?’ of the history of synthesis. By bringing this The synthetic yeast project places itself into my talk I want to point out that there in a trajectory with previous whole ge- are many different ways to think about the nome synthesis projects. These normally trajectories of synthetic genome projects, start with the polio virus in 2002. Peo- and that at least some members of the syn- ple usually then tell a story which goes thetic yeast project want to see themselves through the J. Craig Venter Institute’s work as part of a longer history than just syn- we heard about in the first talk. So in 2008 thetic biology narrowly understood. there was the Mycoplasma genitalium ge- Because yeast is the largest genome to nome, which is one of the smallest known be synthesized so far, it has been organised bacterial genomes, then there was the 2010 as a large international project with many Mycoplasma mycoides work that Alok spoke different countries involved. The chromo- about. Up to this stage the genomes had somes are distributed around these differ- maybe included a few ‘watermarks’ but ent locations as we see here. The empirical basically the genome sequences were the work that I will draw on throughout my same as the wild type. With the 2016 paper talk has involved spending time visiting we were introduced to a reduced genome, these labs, attending their conferences, which was very different from the original and interviewing the practitioners. I will sequence, so we began to see people us- discuss three things today. I will start with ing synthesis to change existing genome the synthetic yeast project as a whole, be- sequences. That same year there was also fore moving on to specific discussion of an attempt to systematically recode many the synthesis of some of the chromosomes 15 Fig. 4. Timeline of the production of synthetic genes and genomes, originally published in Sackler Forum 2015 Trends in synthetic biology and gain of function and regulatory implications. Reprinted with permission of Patrick Cai. which have distinctive characteristics, and They did this by adopting three design then finally arriving at the question of principles: (1) maintain the fitness of the species identity and how this project may yeast, (2) maintain genomic stability, (3) in- challenge it. crease genetic flexibility. To achieve these As a whole, the synthetic yeast project is aims they are making a range of changes to often described as a ‘refactoring’ project, the genome, such as removing the introns, which is a term that comes from computer shortening the telomeres, and reducing software engineering, meaning to ration- the number of codons. The final synthetic alise and clean up software code. Synthetic yeast will be 8% shorter than the wild type. biologists say they are doing the same to One of the most interesting design fea- the genetic code. One of the earliest exam- tures, with the aim of increasing the flex- ples was the refactoring of bacteriophage ibility of the yeast genome, is the so called from 2005. Refactoring is interestingly dif- ‘SCRaMbLE’ system. This enables large- ferent from recombination, because it re- scale genome rearrangements, including quires an overview of all the changes you deletions, inversions, and duplications. It want to make, it is not just about putting provides a new kind of experimental space different bits of DNA into a recipient cell. for exploration, and also potentially leads In addition to being a refactoring pro to new yeast variants with industrial sig- ject, the synthetic yeast project is a design nificance. This scramble system has been project. When the scientists first set out introduced across the whole genome. with the goal to design a new yeast, they The building process started out around could not easily decide what to do, because 2007, when they began to order the DNA the number of possibilities was so large. sequences that they needed from com- What they decided to do was to design a mercial companies. But they found this yeast that could teach them biology. was taking too long and was prohibitively 16 expensive. So they decided to adopt a strat- There are perhaps things we need to dis- egy of relying on undergraduate labour, cuss about the parallel histories of se- introducing a course called ‘Build a Ge- nome’ at Johns Hopkins University. The quencing and synthesis undergraduates were supplied with oligonucleotides produced by a synthesiser, The next chromosome I will discuss is which they then combined into ‘building the ‘neo-chromosome’. The reason for con- blocks’. The process has been a stepwise structing this chromosome is to increase one of increasing scale, from so-called the stability of the genome overall. The mini-chunks, to chunks, to mega-chunks. scientists have taken the tRNAs, which Mega-chunks are integrated into the yeast are considered the most unstable parts of genome through homologous recombina- the genome, and they have put them all to- tion, which is something that the yeast gether in one chromosome. The downside do naturally. It’s a stepwise process where is of course that you therefore have all the the synthesised DNA replaces the natural unstable elements in one place. DNA sequentially. Because of this new chromosome, The aim, as one of the scientists put it, it might look as though the overall was to ‘create a living yeast cell whose DNA synthetic yeast will to have an additional traces back to an oligo synthesiser, and be- chromosome. But this is not the case, fore that to a computer programme rather because they are going to combine than a parent cell’. This is very reminiscent chromosome I and II. This will be done of the Venter Institute’s statements they partially to keep the same number of released in 2010 stating that their syn- chromosomes, and partially to increase the thetic Mycoplasma ‘was the first cell to have stability of the refactored and shortened a computer for a parent’. These examples chromosomes. At NYU they ran an matter for our discussion, because they experiment to see how many chromosomes show how evolutionary and genealogical could be combined, and found they could relationships are cut, raising questions reduce the number of chromosomes about provenance. substantially. This is a finding that might Having discussed the project as a whole, prompt questions regarding the identity I will now discuss a couple of the individ- of organisms and chromosome number, ual chromosomes in more detail. I’ll start because chromosome number is one of with chromosome III, which was the first the ways in which we commonly identify to be synthesised by Johns Hopkins and organisms. NYU in 2014. It was also the first yeast In respect to species identity, I now want chromosome to be sequenced, in 1992. This to talk about chromosome 12, which was draws attention to the fact that there are synthesised at Tsinghua University. An perhaps things we need to discuss about important point here is that China is a very the parallel histories of sequencing and important country for the synthetic yeast synthesis. Chromosome III is sometimes project, with Tianjin University and BGI referred to as the ‘sentimental favourite’ also involved. An interesting feature of of yeast geneticists, because it contains the chromosome 12 is that it has the ‘barcode’ genes responsible for sexual behaviour. It for species identity. This barcode is used is also one of the shortest chromosomes, to identify Saccharomyces cerevisiae, which which was another reason for choosing to is a redundant and repetitive region in the synthesise it first. Because it was the first wild type which we use in order to iden- chromosome to be synthesized, when they tify the species. But because it is redun- came to publish their work, the authors de- dant and repetitive the synthetic genome scribed the synthesis of the chromosome. project has deleted it. Does this mean that This situation put pressure on authors of the synthetic yeast is no longer the same the future chromosome papers, who had to species? This was a question that the sci- think of additional contexts and stories in entists themselves raised. I see it as related which to situate their work. to broader questions of species identity. 17 Lastly I will explain three of the chromo- they decided to do. This points to the kind somes that have come late to the project, of experimental space that is opened up by which are not particularly distinctive, but the project itself, and indeed a few of the they raise questions for large genome syn- other labs have also decided to create their thesis projects. Macquarie University in own neo-chromosomes. Australia has two large chromosomes, and The final chromosome I will discuss is when I asked what was special or interest- being synthesised by the National Univer- ing about their chromosomes they did not sity of Singapore, the last group to join the identify any particular features. But what project. This is chromosome XV, which is is interesting about their work is that they a very large chromosome. Here I want to have a collaboration with the Australian draw attention to the fact that size mat- Wine Research Institute. With AWRI they ters and that building large chromosomes are building a ‘pan-genome neo-chromo- can be a laborious and mundane task. This some’. They are taking the genes that are contrasts with rhetoric in synthetic biol- found in industrial strains, for instance the ogy that sees design and construction be- ones that are found in wine-making yeast, coming two separate spheres, with design and putting them into a separate chromo- requiring all the creativity, and construc- some. This is not strictly part of the syn- tion being the boring bit, being taken over thetic yeast project, but is something that by machines in the future, or so it is hoped.

Group discussion Marv. Has the neo-chromosome been syn- Jane. They do sequence it regularly to thesised already, and has it been made sta- try and check, but I am not sure how long it ble? takes for mutations or changes to happen. Jane. Yes they made it stable, it was a lot The publication of the papers in Science, in of work, not yet published. Required lots one of them they were keen to point out of knowledge of tRNAs, had to get flank- that it was a perfect copy of the design and ing regions from different yeast species, came out exactly as it was meant to, but I it actually has 9 different species involved do not know how long it stays like that. in the neo-chromosome in order to make Lijing. It seems that the two projects, it orthogonal to the rest of the system. Khorana and the synthetic yeast, are two They also are building it to have a different modes of synthetic biology happening SCRaMbLE mechanism built in. at different times, and are reflective of Marv. But when you put it into the total two different views at these times of how genome, with all the tRNAs are on that one biology works. One way to synthesise a chromosome, somehow one of those con- gene is to figure out each piece of the en- structs has to figure out how to be stable in zymatic process necessary, and through order for the cell to survive. But you won’t trial and error, asking new questions that know which one that is, just one of those build postdocs and people’s careers over neo-chromosomes will have to be stable. time. But in recent years we see a move to Jane. There is an interesting project a more global conglomerate and large in- looking at the chromosome structure in ternational collaborative approach, both to 3D and how they fold. The image of the sequencing and synthetic biology. We also neo-chromosome in comparison to the see this shift in ‘big data’ biology. How do other ones, it just looks like a tiny curled the speakers see their cases fit into a larger up thing. I do not know what that implies historical context? about how it will coexist with the others. Jane. I agree that the parallel of Marv. That leads me to ask, the one that sequencing and synthesis is very works, i.e. that gets inside the cell, does important. I think it also matters that some it still have the same sequence as the one of the people involved in the synthetic they made, or has it been recombined in a yeast project like to connect themselves to way that is surviving? the longer history of gene synthesis, where 18 other synthetic biologists might focus on Marv. Well I see design and synthesis a turn of the millenium context, and a going hand in hand. You go from synthe- renewed emphasis on the importance of sis to design, from synthesis to design, engineering for biology. Venter has been and you get to the end product of your doing the mycoplasma work for a very long process. time indeed. Roger. This to me is also how technology Alok. The cell is very complicated. The works. People try things and then see what number of tasks that it does is large. The works, change it, and see what works. fact that 17 chromosomes are being at- Jane. Synthetic biologists do talk about tempted across the globe, people are learn- wanting control. They want to be able to ing what it takes, and organising their design it and for it to work as intended. project to find what it takes. I think the Marv. Another question I had was to do scale of project is matching the scale of the with the labour involved. And the reliance task structure. Also if we compare the two, on undergraduate labour. Well in indus- the Venter project is working on some- trial synthesis, even with the best chemis- thing 1/6th the scale of the yeast genome. tries, there is roughly 1 mutation every 500 Marv. This is not a synthesis story, nucleotides. So you have to put them to- but Spiegelman in the late 60s, I think it gether in blocks, then clone and sequence was bacteriophage R17, he put it under them in order to find the one that is right. the pressure of time. He asked ‘if I keep That’s where the labour comes in. Now, if shortening the amount of time, what will you could improve the chemistry to bring happen?’ And the answer is he was able this up to 1 mutation in every 2000 nucle- to reduce the time it took to replicate that otides, you might be able to get away with genome in the test tube from, I don’t know a lot less labour. what the numbers are, let’s say an hour to Dominic. I felt that in both papers there five minutes. This organism learnt how to were always tensions about what to val- do it by shortening the chromosome and ue at a given time. So in the first paper it only putting the essential parts in, and the was explained how so much of this was a rest was discarded. Now in those days they chemical enterprise, but then to synthe- could not sequence it properly so they had sis the gene they really had to rely on the no idea what the sequence was. biology. Could you both say more about Jane. Time is very interesting also in the these tensions? The times when labour is Venter Institute’s work, because they de- labour, and not that great, and times when cided to move from the Mycoplasma geni- labour is engineering and something more talium to the Mycoplasma mycoides because impressive. Or the times when a particular the former was very slow growing. phenomena is worthy of attention or not Alok. Indeed the genitalium was slow worthy, because by alluding to it you might growing to the extent that it did not have a just actually expose your ignorance. Or the defined doubling time. There is also a ques- times when having an explanation seems tion of how much of the physiology we are to matter, and when it doesn’t. able to map and play with. We do not un- Jane. One of the heads of the synthetic derstand the physiology that produces the yeast project is famous for some work on doubling time, so this is not engineering transposons, but in this genome they are in the hands of Venter because they do not getting rid of them. So in their case they know how doubling works. What is nice once valued these components of a chro- about the Spiegelman example is that you mosome, but are now deleting them, which do not claim to know how doubling time I think is a good example of something’s shifts from an hour to five minutes. But if value changing. you let the cell replicate under pressure it Marv. Do they know if they can delete will shuffle the mechanisms and make it all those transposons? happen, and you can come along and read Jane. A lot of the deletions go wrong, out the sequence. But you are not design- and they find they have to put them back in ing or claiming to explicate. again. Likewise with introns. 19 Marv. I would imagine that you’re going huge amounts of labour to achieve to get a lot of people groaning very loudly something in biology is not new. The first when they realise that in order to use the tRNA that was chemically synthesised synthetic yeast to explore a particular with all the modified bases, that was done function, you’re going to have to resynthe- in China around 1978–81/2. They had sise x-number of chromosomes to recover literally a factory outside of Shanghai the function you want to look at. Or the that did nothing but take natural tRNAs groans will come when they try and make and fractionate them and isolate all the the whole thing actually survive. modified bases that went into a tRNA. A Alok. The question brought attention massive effort, 500, 1000 people? I don’t to differences between chemists and biolo- know. Once they had enough of this gists, and the chemist recruiting the biol- material to put into a synthetic gene, they ogy’s unknown ability to complete the syn- shipped it to the Shanghai Institute of thesis. The other tension here is between Biochemistry and they then incorporated explaining and manipulating, and putting these modified bases into the right sites. a technology in a box. Manipulation is a lot So this was lots of labour too, it wasn’t high of fun, it gives you an enormous amount of school students but it was workers in a novelty, but then there is bookkeeping to factory. do for explanation. Jeff. So the ability to mechanise the Jeff. Something has changed to simplify process matters. But doesn’t this require these procedures to the degree that under- fundamental advances? If we look at Emil graduates or high school students can con- Fischer trying to synthesise proteins, he tribute to these international efforts. could never do it because he hasn’t figured Marv. High school students these out the correct technique, so it wouldn’t days will usually be highly skilled when matter how many people he put on the job, it comes to ligating and cloning. Having he’s not going to get there.

Session 2: Extending synthesis

L. Scott Cole Selling DNA Synthesis: Applied Biosystems’ DNA Synthesis Business from 1989–1992 This morning I’ll be discussing the dissem- My presentation has three sections. ination of automated DNA synthesis tech- First, I’ll be talking about DNA synthesis nology. That’s what we did at a company platforms and technology. Second, I’ll take called Applied Biosystems, or ABI, where an inward-looking view of the company, I worked in the DNA synthesis group from i.e. the people, processes and culture at about 1989 to 1992. Briefly, my background ABI. Lastly, I’ll take an outward view, i.e. is in molecular biology. That’s what I stud- focused on ABI’s customers, applications, ied as an undergrad and in grad school, and competitors. I will present each with then I went to business school with the respect to two time periods: (1) 1983–87, idea of working in the biotech industry. which I call “market entry and develop- My first job was as product manager for ment”, and (2) 1988–1992, which I call the DNA synthesis business at ABI. I start- “rapid market growth.” The turning point ed there after the company had launched corresponds with the commercial intro- its first DNA synthesizer in 1983. So, for duction of PCR technology, which drove the earlier part of the brief history I’ll be growth in DNA synthesis. The reverse is presenting today, I’ll be relying on inter- also true: automated DNA synthesis ena- views I conducted recently with other ABI bled PCR technology to flourish. employees involved in DNA synthesis be- What is a DNA synthesiser? Curt Becker, fore me. one of ABI’s first employees called it a ‘glori- 20 Fig. 5. Clockwise from top, (i) Andre Marion (left) and Sam Eletr; originally published in Springer, Mark (2006). ‘Applied Biosys- tems: Celebrating 25 years of advancing science’, American Laboratory News. (ii) Bill Efcavitch (left), Steve Lombardi, and Scott Cole (right); photograph courtesy of Scott Cole. (iii) Michael Hunkapiller; photograph courtesy of Scott Cole. fied Coke machine’ since it’s fundamentally gent consumption. Again, this is because a liquid delivery system. A DNA synthesiz- the phosphoramidites are so expensive. er builds DNA strands (“oligonucleotides” Second, they care about “coupling efficien- or just “oligos”) in disposable cartridges cy.” This refers to the chemical efficiency called “columns.” A column contains a of each base addition and determines the solid support matrix—basically, very small ultimate amount and quality of the oligo glass beads—upon which the oligos are and the potential length of an oligo. Con- synthesized base by base. The instrument sider that if coupling efficiency is even performs successive cycles of chemistry. 90% at each base addition, the 10% loss Every cycle adds a new base to the growing compounds with every base addition cycle chain. At the end, the instrument performs and it becomes difficult to make even small a round of chemistry to cleave the synthe- oligos. Finally, customers care about “cycle sized oligos off the glass beads so they can time.” How long does it take to make an be used in an experiment. oligo and therefore how many can I make Automating DNA synthesis involved at in a day? least two challenges. First, the chemical Let me provide some context regarding bases in their precursor form, “phospho- ABI. The company was founded in 1981 ramidites”, are very expensive. This puts a thanks to two complementary academic premium on using very small amounts of efforts: those of Marvin Caruthers’ lab chemicals in each synthesis cycle. Second, at University of Colorado, which focused a few of the non-phosphoramidite rea- on DNA synthesis chemistry, and of Lee gents used in the synthesis cycle are toxic. Hood’s lab at Caltech, which focused on au- A DNA synthesizer is designed to sit on a tomation. In fact, many of ABI’s early em- lab bench and not in an air flow hood, so ployees came from these two labs, and also the synthesis process has to be completely from Hewlett Packard, which was the larg- contained. est instrument company in the Bay Area at From a customer perspective, there are the time. ABI’s first product was a protein at least three important performance met- sequencer. The second was the DNA syn- rics. First, customers want very low rea- thesiser. 21 Let me quickly give you a sense of ABI’s What is a DNA synthesiser? Curt Becker, early team and culture. The company one of ABI’s first employees called it a had two founders: Sam Eletr and Andre Marion. Sam was a former H-P engineer: ‘glorified Coke machine’ by all accounts very technically-oriented, competitive, demanding and even intimi- the company successful and made ABI an dating. But he was highly respected and exciting, dynamic, passion-filled place to really set the company’s fairly aggressive, work. demanding culture. André was also an en- Sam and Andre’s early vision was, in gineer. He worked with Sam at H-P and their words, to sell the picks and shovels was the quieter of the two. A third key per- to the miners in the biotech gold mine. son early on was Mike Hunkapiller. Mike The other pitch the founders made to was a post-doc in Lee Hood’s lab at Caltech early investors was that ABI was going and joined the company pretty soon after to offer everything required for molecu- it was founded. Mike would eventually lar biological research. That meant that become ABI’s president during much of for both proteins and DNA, ABI would the 90s and beyond. The fourth person I’ll develop platforms for both synthesis and mention is Bill Efcavitch, a chemist from sequencing. And it did. It launched these Dr. Caruthers’ lab who was the head R&D platform capabilities in the following or- person in the early years and beyond. der: protein sequencing, DNA synthesis, In short, the early team was engineer- peptide synthesis, and DNA sequencing. ing-focused and very competitive, with The commercialization of these four types some strong personalities. ABI was not a of platform delivered steady, rapid growth. “marketing-driven” company. Marketing As one platform would begin to plateau in as a corporate function was not highly re- the market, a new one would pop up and spected. To be successful in marketing at take its place, and so on. These successive ABI, really throughout the company’s ex- roll-outs culminated with DNA sequenc- istence, you had to not only be able to keep ing, Celera Genomics and the sequencing up with the technical folks, you sometimes of the human genome, which I probably had to be capable of challenging them on won’t have time to talk about. technical matters. But focusing again on DNA synthesis, ABI’s culture and strong market posi- the company launched its first DNA syn- tion gave it a reputation in the market as thesizer, the 380A, in 1983. It was large being an arrogant company. A 2000 New and weighed a ton. It was a workhorse. It York Times article about ABI said that in had three columns, so the user could make its customers’ minds, “ABI” stood for “Ar- three oligos simultaneously. In 1983, many rogance Beyond Imagination.” I more re- of the customers of DNA synthesizers were cently heard a story—so this is second organic chemist “tinkerers.” They weren’t hand—that when the protein sequenc- using the phosphoramidite chemistry that er, the company’s first instrument, was would eventually dominate the market, launched, a salesperson would visit a po- but a type of chemistry that was more tential customer lab and if that lab didn’t “tinkerable.” Many of these users had their place an order within three hours he or she own “recipes”—their own unique versions would leave. Again, I can’t vouch for that, of DNA synthesis chemistry—that they but it wouldn’t surprise me. Another quote wanted to implement on the instrument. from that same New York Times article was The applications at the time that required from the director of a large genome se- synthetic oligos included studies of DNA- quencing center (who was also a DNA syn- protein interactions and also reverse ge- thesis customer) who said about ABI that, netics. The latter required both a protein ‘It’s not that the customer is always right, sequencer, which was ABI’s first product, the customer is always wrong’. These and a DNA synthesiser. If you could get quotes highlight some negative aspects of the first bit of the sequence from a protein, ABI’s culture, but that culture also made you could create an oligonucleotide that 22 corresponded from a DNA code standpoint In 1983, many of the customers of to its gene. The researcher could then use DNA synthesizers were organic chem- the oligo to find the gene and clone it. That was a way to use both of these instruments ist “tinkerers.” They weren’t using to do something that at the time was very the phosphoramidite chemistry that novel and important. Competition during this earlier period would eventually dominate the mar- came mainly from Beckman, Biosearch, ket, but a type of chemistry that was and Advanced ChemTech. Beckman had a tight relationship with Caltech. So it more “tinkerable.” wasn’t easy to establish a relationship with Caltech and get the licenses required to in the US. Their Cyclone was really a pretty commercialize DNA synthesis technology. good DNA synthesizer. Most of ABI’s intellectual property licenses Then, in 1985 the market changed with were also made available to Beckman early the introduction of a technique called PCR, on. [From the audience: Arnold Beckman which is essentially a way to make very was on the Caltech board]. That’s right, large quantities of any relatively small and there’s a Beckman building and Beck- stretch DNA. Think of a photocopier. PCR man everything down there. At the time, was important to our business because any Sam Eletr made the argument to Caltech time a researcher wanted to do PCR they that large companies like Beckman with needed to make two small oligos of unique a lot of products wouldn’t put that much sequence. So, labs were now constantly effort into selling or developing Caltech’s needing small oligos. PCR was invented machines, whereas ABI was small and in 1983, presented at a conference in 1985, hungry and would focus on it much more. in 1987 it was starting to become commer- And probably that ended up being true. cially available. Then it absolutely took When the 380A launched, the compet- off and this was a game changer for DNA ing instruments were smaller and less ex- synthesis. Again, the relationship between pensive than the 380A, and in some ways PCR and DNA synthesis was synergistic. were more flexible. By comparison the PCR drove DNA synthesis sales. But DNA 380A was like a Mercedes: big, solid, heavy synthesis was required for PCR technology and expensive. One aspect of the 380A and to spread as fast as it did. other ABI instruments that we always em- To take advantage of the PCR oppor- phasized was their “valve blocks.” These tunity, in 1989 we launched the 391 PCR- valve blocks replaced the flexible tubes MATE. This was basically a 381 that was that transported liquids on competing in- rebranded, updated with a more modern struments. They were developed at Caltech user interface, and cost-reduced a bit. We and were unique to our instruments. They also sold it as “user-installable” for about resulted in very low liquid volume waste, $3,000 less than the same instrument in- less mixing, and better cleaning between stalled by an ABI service technician. We cycles. We would always claim that we had did this to better compete with our lower the most precise, frugal liquid handling priced competitors. Really, though, the 391 technology on the market. was never installed by a user because no But, again, those other instruments salesperson wanted to risk having a cus- were much less expensive, and some labs tomer mess up the install. So, the 391 was just didn’t have the money for a 380A or, pretty reasonably priced if you bought it as later, the very similar 380B. So, in 1985 ABI user-installable and then took advantage launched a smaller synthesizer called the of your salesperson’s offer to help! 381. It had one column and was much less The 391 helped us ride the PCR wave. expensive. The idea was to stop Pharmacia Then, in 1991, we launched what became in the places they were strong, namely Eu- the very popular 392 and 394 instruments. rope and Japan, and to fight the company These were basically one and the same in- that by then was called Milligen Biosearch strument outfitted with either 2 or 4col- 23 Fig. 6. Left, a photograph of a 380B model, launched in 1985. It looks very similar to the 380A; image courtesy of Scott Cole. Right, Bill Efcavitch overseeing the installation of the 380A in the Caruthers lab, 1983; photograph courtesy of Marvin H. Caruthers. umns, and either 5 or 8 phosphoramidite of the companies were offering high qual- positions. And everything was upgradable ity reagents. ABI always had a policy that after purchase. In other words, if the cus- if customers used non-ABI reagents, they tomer only had enough money for a 392, would void their instrument warranty. they knew that when they got more grant Customers didn’t like this. It was the epito- money they could upgrade their instru- me of ‘Arrogance Beyond Imagination’. But ment to 4 columns. And, just as important, it helped us maintain most of our reagent both the 392 and 394 finally had columns business. Our other selling point around in multiples of two, which makes sense that time was our “whole product” ap- for PCR since a PCR amplification always proach. ABI emphasized that in addition to requires two oligos. This was constantly a instrument and reagents, a DNA synthesis sales issues with the 391 versus its mostly supplier had to provide strong service and 2-column competitors: “You call it the ‘PCR support. Given our market dominance, we MATE’ but it only has one column!” had the largest and best service and sup- By the late 1980s, oligos for PCR repre- port organization by a long shot. Customer sented about 90% of the demand. And by conservatism also helped us. Customers this time typical DNA synthesizer cus- felt safe going with the market leader. tomers were no longer organic chemist There’s an old saying: “Nobody ever got tinkerers. Customers were now molecular fired for buying an IBM mainframe com- biologists. ABI had become far and away puter.” The same was said about ABI. the market leader because of their instru- Now for a quick internal perspective. ments’ performance and reliability but During the time I’ve been talking about, they were expensive for an individual lab. processes within the company remained So, departments started setting up what pretty flexible. If a product manager had to became known as “core labs.” These were get around things or do something quickly, centralized facilities managed by a small he or she could. And the technical knowl- staff. They enabled shared purchase and edge within the company was unrivalled. shared use of expensive instrumentation The main Foster City (California) campus among several or many labs in a depart- housed employees who knew an enormous ment. amount about the various technologies In the early 90s, competition was still relevant to DNA synthesis and who knew coming from some of the same companies how to design, develop and manufacture I mentioned earlier. But now there were very high quality instruments and rea- also competitors that only offered DNA gents. Being near Silicon Valley, ABI had synthesis reagents. Companies wanted to access to a lot of experienced engineers take away our reagents business, and some and scientists. And globally we typically 24 had more than 80% market share. That Our other selling point around that time meant we had the most salespeople talk- was our “whole product” approach. ing to the most customers. Tech companies often get the best new product ideas from ABI emphasized that in addition to customers. Up to a point, success creates instrument and reagents, a DNA synthesis more success. After 1992, commercial oligo services be- supplier had to provide strong service and gan to take off. Researchers stopped buy- support ing as many synthesisers and instead ordered them through the mail. And, around Time is up, so I’ll conclude by quickly this time, ABI started focussing more on emphasizing a few the points I made ear- DNA sequencing. As I said before, sales lier. First, I want to emphasize the impor- of a new instrument platform can grow tance of the culture and community in the very quickly for several or more years, but success of ABI’s DNA synthesis business. eventually start to plateau. That’s when it’s Second, I hopefully conveyed the degree important to launch a new kind of instru- to which commercializing a platform like ment that has greater growth potential. an automated DNA synthesizer requires So, the objective at this time was mainly to a highly multi-disciplinary scientific and protect our DNA synthesiser business. We engineering team. Finally, history shows did this by continuing to innovate: offering how various research technologies are smaller columns for less expensive synthe- interlinked, both technically and in the sis on the 392 and 394 and also by releasing market. Recall the synergy between ABI’s of a much higher throughput instrument: protein sequencer and DNA synthesizer in the 3948. There was also growing interest early reverse genetics applications as well in other applications, such as large-scale as the mutual dependence of DNA synthe- RNA synthesis for pharmaceutical appli- sis and PCR for each of their proliferation cations, at least their research divisions. and success.

Marvin H. Caruthers The Chemical Synthesis of DNA, RNA, and Certain Analogs

I am intending to give you some more of of slides on this topic, and I started with the history of DNA synthesis, to give you Lord Todd. It was published in the Journal of some stories and go from there. I would the Chemical Society. Todd was best known like to start with a quote from Frederick because he determined that DNA and RNA Sanger, where he is discussing his work on were made of ribose and deoxyribose sug- DNA sequencing. “Most of the significant ars, and the linkages were phosphate 3–5, work has been summarized in a number sugars were linked to the nucleoside bases, of reviews and articles. In these there was, and he defined the structures of all these of necessity, a good deal of simplification components, the bases included. This was and omission of detail, both for reasons mainly in the 1940s but some of the work of space and, sometimes, to make a good in the 1930s, and was the main focus of and logical story. With the passage of time his Nobel prize. When he completed the even I find myself accepting such simpli- synthesis in 1955, in his Nobel lecture two fied accounts”—I too will be giving you a years later, he states “synthesis can serve simplified overview of several topics along not only in the elucidation of structure, the way, through the history of DNA syn- but can in many instances open up wider thesis. vistas regarding the significance and func- In 2005 I had the honour at the 50th an- tion of biologically important compounds”. niversary of the first synthesis of a dinu- In other words, unlike most organic chem- cleotide in Cambridge, of presenting the ists, at least 99% of them, who were using introductory talk, which I gave as a history synthesis just to attack organic synthesis of DNA synthesis. So I have a whole lecture problems, such as a 20 or 30 step proposal 25 Fig. 7. Har Gobind Khorana in 1970. Associated Press, file 700602089. to synthesise some natural product, and gene for this particular transfer RNA, with once it was synthesised move onto the next the sequence that came out of Holley’s lab. one, rather Todd’s focus was building these Why did he want to do this? new molecules with a focus on biologically The following quotation comes from a important compounds that could be used jubilee lecture in 1968, ‘why would anyone to attack biology. He was saying this as ear- want to synthesise a gene?’ His objective ly as 1955, long before the concept of bio- was to develop methods where you could organic chemistry which became popular precisely define the sequence of DNA that in the 1980s and 90s. you put into a piece of synthetic DNA. He Then Khorana came along. He got his says: “We would like to know, for example, PhD with George Kenner in Liverpool, what the initiation and termination sig- moved to do a postdoc in Prelog’s labora- nals for RNA polymerase are, what kind of tory at the ETH in Switzerland, and then sequences are recognized by repressors, by moved to Cambridge to work in Todd’s host modification and host restrictive en- group, where he developed the method- zymes and by enzymes involved in genetic ologies for forming pyrophosphates and recombination and so on.” He goes on, “ the synthesising ATP and coenzyme A. And next long-range aim must be the develop- then he moved onto the problem of syn- ment of methods for the total synthesis of thesising oligonucleotides. The first major biologically specific DNA duplexes”. He involvement with them was using repeat- was using the synthesis of this gene as a ing trimers, and tetramers, and dimers, template to develop the technologies to de- to help elucidate the genetic code, and for fine sequences of DNA. This was the pur- that he shared the Nobel prize with Mar- pose of this work. shall Nirenberg. Later on, I myself got into It is worth commenting how much work the Khorana lab in the late 1960s, and the it took to chemically synthesise a 20mer project that was under way at that time was at this time. For instance, one part of the trying to synthesise a gene. At the time we duplex for this part of the tRNA gene was started this project in 1965 there was only synthesised by Hans Weber, and it was a one specific RNA sequence that had been two year project. It took him two years to carried through and that was Bob Holley’s make that 20mer in the mid to late 1960s. work on yeast tRNA alanine. So Gobind All the assemblies of the gene were ac- set up the lab and started to synthesise the complished by synthesis plus ligation, ar- 26 riving at the final product of the 77 piece Our lab has the honour of being one of the duplex DNA. But the point is that this was first two labs to show that synthetic DNA a template for developing methods for sequence defined synthesis of DNA. We felt has biological function. Both my lab in it was quite an achievement successfully Boulder and Arthur Riggs in collabora- putting together a 77 base pair duplex. We then published the 13 papers correspond- tion with Saran Narang, had synthesised ing to this total synthesis as one complete the lac operator sequence, both by differ- issue of the Journal of Molecular Biology which came out in December of 1970. Sub- ent methodologies but we got the same sequently a commentary that came out in sequence Nature, from a cell biology correspondent, states “the thirteen articles from Horana’s express and look at its biological activity. group which comprise a complete issue Here we looked at lambda phage virulence. of the Journal of Molecular Biology surely There is a story here I want to tell you about. set something of a record....Every step of We sat down in one afternoon in 1969 I this synthesis has obviously been execut- think, to lay out the synthesis of this struc- ed with consummate skill and the whole tural gene. We spent 2 or 3 hours doing this constitutes perhaps the greatest tour de because Gobind had a history of going to force organic and biochemists have yet La Jolla in January, there was a small group achieved.” I think I would agree with that, that Francis Crick put together where they and Gobind’s whole view was on the very would come and talk about their research horizon of what you can do, so everything every year, and Gobind wanted to present you do there is a tour de force, it is never the plan for synthesising this gene at that done simply. But then here comes the meeting. After spending a few hours talk- zinger: “Like NASA with its Apollo pro- ing about how to synthesise it, we turned gramme, Khorana’s group has shown it can to the discussion of how we were going be done, and both feats may well never be to express this gene. Well at that time we repeated”. Many times when I am present- didn’t know anything about promoters, ing in England, if I know there is a Nature or terminators, how to get this gene into a editor in the room, I try and bring this slide cell, or anything like that. So we sat around up. and talked about it for a while. The only I also want to add a quote from a paper clue we had to go on, was that Ray Wu at that Khorana gave in 1968: “I wish to con- Cornell had just sequenced, by a very diffi- clude by hazarding the following rather cult methodology, the sticky ends of phage long-range predictions. In the years ahead, lambda. We kind of thought ‘maybe there genes are going to be synthesized. The next is some way we can attach this to the sticky steps would be to learn to manipulate the ends of lambda and try to transfect it, sit information content of genes and to learn down on our knees and hope and pray that to insert them into and delete them from something would come out of that’. We had the genetic systems. When, in the distant no way of knowing how to incorporate this future, all this comes to pass, the tempta- synthetic gene into a bacterium and have tion to change our biology will be very it be expressed. So Gobind was listening to strong.” That was 1968, at an international all this, and this is what is important, after biochemistry meeting in Japan, he had this about 25–30 minutes had gone by he stood as part of his talk. Of course we are already up - in other words the meeting was over - doing that with yeast and several other or- and he said ‘well let’s synthesise the gene ganisms. first, and by the time we get it synthesised The point here is that we could not ex- we will know how to express it’. In other press that tRNA gene biologically. So in words, science is going to move far enough 1968 we started work on the synthesis of along that we will know how to express it, Tyrosine Suppressor tRNA. The idea this and that is the way that Gobind did his sci- time was to synthesise a gene that we could ence. 27 Fig. 8. Slide depicting the process of synthesising DNA through the solid phase approach. Image courtesy of Marvin H. Caruthers.

After Gobind’s death in 2011, myself two labs didn’t know that the other was and Robert Wells in our retrospective, we working in that area. Bob and Milt wrote wrote: “Gobind was a dedicated, driven, up their work and published it all the same focused, and humble scientist. He was year in JACS as Bruce Merrifield’s work. fiercely loyal to all whom he mentored and Unfortunately Bob did not share that Nobel worked with, and unyielding in his drive prize, it was given entirely to Merrifield. toward the highest scientific ideals and But Bob turned his attention to DNA syn- goals. He repeatedly attacked immense thesis and figured out a new method for and challenging problems, likely with lit- making DNA, again on a polymer support. tle idea of how he would eventually solve Myself and a number of other research- them—but solve them he did.” That was ers in the lab worked on other methods for Khorana. synthesising on a polymer support as well, I was fortunate that I worked with Bob and all this came down in the middle to Letsinger as a graduate student. When I late 1960s. Here I quote from a short article spoke to him, as you’re interviewing for I wrote about Bob: “Over the years, as I ob- places to pursue your work, he was try- served how others direct their programs, I ing to develop methods for synthesising consider myself one of the most fortunate macromolecules on polymer supports, and of graduate students. Somehow, I found a I thought that was really a neat idea be- mentor who was patient, who allowed stu- cause nobody had ever tried that before. I dents to explore their potential, and who specifically chose North Western to work focused his research on extremely chal- with Bob, and so as soon as I arrived I be- lenging problems.” That was Bob. gan working in his lab. At that time he had We went ahead, and our lab has the hon- a postdoc in his lab, Milt Kornet, who had our of being one of the first two labs to show just synthesised a dipeptide on a polysty- that synthetic DNA has biological func- rene support, and we were pretty excited tion. Both my lab in Boulder and Arthur about that. A month or so later, Merri- Riggs in collaboration with Saran Narang, field published his Tetrapeptide synthesis had synthesised the lac operator sequence, in JACS also on polymer support, and the both by different methodologies but we got 28 the same sequence. And then in collabora- I had a new graduate student, Mark Mat- tion with Jack Sadler down in the medical teucci, who wanted to do a project more school in Colorado, and Saran in collabo- on organic chemistry. So I suggested we ration with Art Riggs at City of Hope, we try and develop a methodology for synthe- independently cloned this operator into E. sising DNA on supports. Mark picked up coli and got expression. This was presented this challenge and was focussed on using at the Cold Spring Harbour Symposium in control pore glass and adding nucleotides 1976. Their group published in Nature, and one at a time, and then in collaboration we held off until 1977 to publish in the first with Serge Beaucage who developed as a issue of the new journal Gene. This was the postdoc the phosphoramidite synthans, we first piece of synthetic DNA that showed developed this chemistry for synthesising biological activity that had ever been pub- DNA. This is perhaps where I should stop, lished. From there using the chemistries but I had wanted to explain how I got in- that Bob Letsinger pioneered various labs volved in applied molecular genetics and started synthesising biologically interest- from there into Applied Biosystems, but I ing DNAs. Shortly thereafter, Genentech have run out of time. in collaboration with Art Riggs at City of Hope, published the synthesis and clon- ↠↠ Bibliography ing of human insulin, so both the synthe- Caruthers, Marvin and Robert Wells (2011). ‘Har sis and the biological activity. By that time Gobind Khorana (1922-2011), Science. 334:1511. two graduate students from my lab had Caruthers, Marvin H. (2012). ‘Gene synthesis with gone on to become two of the first four em- H G Khorana’, Resonance. 17:1143–1156. ployees at Genentech, Dave Goeddel and Caruthers, Marvin H. (2013). ‘The chemical synthe- Dan Yansura, both of whom were part of sis of DNA/RNA: Our gift to science’, The Jour- the expression team. nal of Biological Chemistry. 288:1420–1427. My lab got involved in solid-phase Caruthers, Marvin H. (2014). ‘Robert Letsinger: chemical synthesis around 1976 or therea- The father of synthetic DNA chemistry’, Pro- bouts. In those days we were very much ceedings of the National Academy of Sciences of involved in protein - DNA recognition. But the United States of America, 111:18098-18099.

Group discussion Dominic. It seems there is a wide variety of around eagerly waiting for someone to ways to synthesise DNA, and it can be hard develop methodologies for DNA synthe- to understand the differences between sis. They couldn’t care less in those days. them. Are there ways you could charac- They weren’t interested. For example the terise what makes different chemical ap- first Gordon conference I went to in 1975, proaches distinctive? by that time I had worked in Khorana’s lab, Marv. Well to be honest they’re all pret- Letsinger’s lab, and so I was given the re- ty archaic so I wouldn’t worry about it. sponsibility of reviewing DNA synthesis Dominic. But historians think archaic at that time. And so I did. Then that night things are pretty cool! I was sitting around a table having a beer Anonymous 1. I also would push back on and one of the individuals who was attend- the question, because everyone is using ing that conference, he said “Marv, why the phosphoramidite chemistry, the only do you want to learn how to synthesise difference is what is the hardware to build DNA? There’s no reason for it. Sure, Kho- those oligos. rana used it to solve the genetic code and Lijing. What was considered the signifi- now he’s made his gene. So what else are cance of tackling tour de force questions in you going to do with it? Why are you wast- biology, and how was this kind of activity ing your time learning how to synthesise rewarded in biology? DNA. You’re a bright guy why don’t you Marv. I have to tell you that molecular do something more interesting?” That was biologists, biochemists, were not sitting the mentality. He was not alone. You go out 29 in the world and apart from the aficiona- Alok. The beginning of the solid-phase dos who were working on DNA chemis- synthesis chemistry, is what was be- try and struggling to figure out a way to ing called the ‘hardware’. This hardware make it, and in those days we had not even though, might be more seen as a platform started on the phosphoramidite method for integrative buildup. Because the hard- yet. There was no interest in DNA chemis- ware story is about 96 well plates, beads try at all to speak of, even though Khorana don’t give us the next performance curve was out there preaching how, ‘once we can and so on. So the platform unlocked a new make DNA of a defined sequence we’re go- regime of yield, scale, and variety. Is as- ing to be able to do all of these other ap- sembling the platform another example of plications’. But nobody was really listening tour de force kinds of project? to him. Anonymous 1. I think you are getting Roger. What did you say to him when he onto something. When you are thinking of asked? making a synthetic gene. Building your oli- Marv. We had started out research in gos is only one part of the project. You then Colorado trying to understand how the lac need to assemble them, fishing out the er- repressor interacts with lac operator, and rors. only 1 in 1000 base pairs going wrong lambda phage’s C1 repressor and Cro re- is pretty good but it’s not perfect. so you pressors interact with their binding sites still have to clone and pick the perfect on phage lambda. So we were making these ones. To do that and scale up to 100,000s, DNAs synthetically using the old chemis- you need to automate everything. tries. So we already knew that there were Marv. When we first got this chemis- certain applications that you could direct try going, all biochemists, biologists, mo- your chemistry towards once you had it lecular biologists used it. They were ‘oh developed in biology. There were a few of wow we can make 20mers’. And they were us around like that, for example Sanger very happy with that for at least ten years. in collaboration with a former postdoc- Honestly it was a few people who started toral student from Khorana’s lab had syn- going around to, not so much Applied Bio, thesised at Cambridge a 12mer that they but other companies asking ‘can you make were using for priming sequencing work 100mers because we have some projects on ϕX174. This was the precursor to all the that require 100mers?’ Then maybe even DNA sequencing techniques that we use larger, 300mers etc. It was actually these today. So they were using primers in 1975– people coming and asking for larger com- 76 to develop what they called and present- pounds. And they were driving things ed at the ’77 Gordon conference ‘plus mi- along, wanting larger compounds meant nus sequencing for DNA.’ They were doing we needed better yields, driving chemistry that with DNA primers. So if you go and and instrumentation forward. look in the right places there were labora- Anonymous 1. And this has an effect on tories that were starting to use synthetic price. In 2000 a fully made gene would cost DNA to attack important problems. Not a $20 a base, now it’s 9 cents a base. Wait a lot but there were some. And if you looked few more years and it will be 2 cents a base. at Khorana’s paper you understood why he Marv. And people didn’t realise what was doing this. As I showed in that quote, you could do with larger DNAs until you there were a large number of biological could give them access to it. problems that required synthetic DNA to Alok. Can I make a comparative point attack them. But the biological community, then? The organism genome platform they just weren’t interested in those days. which the Venter Institute is developing, Unless you teach them something, doesn’t which the yeast SC 2.0 Cre-lox system, is a matter if it’s sequencing or synthesis or wet-ware equivalent to hardware? whatever, once they are taught this they Marv. This is what we’re saying. It’s the say ‘oh yeah that was obvious of course we development of the ability to make longer are going to use it’. Until you make it avail- sequences that is leading to the current able it’s like “why are you doing this?” revolution in what you can do with them. 30 Jane. Everyone touched on sequencing tegrating very different technologies to as well as synthesis, could you say more achieve a goal. about how they are related? You asked about the Bay area. ABI had a Marv. The current methods of sequenc- lot of relationships with folks at Cetus and ing require synthetic DNA. And that was then Roche. It’s complicated, but Perkin- the way it was for Sanger’s first method. Elmer who had the market for PCR, bought You need synthetic DNA to sequence DNA. ABI, so when that happened ABI also had Anonymous 1. One pushes the other. It’s PCR, at least for the research market. as with any human endeavour. If you can The universities in the Bay area for some read, that’s good. If you can write, that’s reason we never seemed to get along with. good. If you can do both then that’s great. I don’t know why. We had reasonable re- At the moment I think synthesis is a little lationships with Berkeley and LBL, but bit behind, and we need to catch up the other than that, we didn’t. Relationships writing to the reading. with several non-Bay area universities and Scott. To go back to the era I was talk- organisations ended up being important, ing about, I described how PCR drove the though. Thinking now of DNA sequenc- DNA synthesis business, and DNA synthe- ing, not DNA synthesis, the key relation- sis drove the ability to do PCR. Ultimately ship we had was with TIGR (The Institute what made ABI’s automated sequencer, for Genomic Research) and TIGR’s found- which was the dominant sequencer at er, Craig Venter. He had the attitude that the time, was the use of a cycling method he was going to work with us and not try in the chemistry. So you can draw a path to beat us. Most of the genome sequenc- from synthesis to PCR, PCR people start ing centres wanted to develop technology thinking in terms of cycling, and going to a to avoid buying from us. Craig’s attitude cycling version of the chemistry that made seemed to be “My competitors don’t like DNA sequencing robust. you so I’m going to be your best friend. Dominic. At ABI you mentioned there You supply the technology and we’ll focus were quite a lot of engineers working on what we’re good at.” That, I think, was there, and I was wondering how much bi- smart. Because of their attitude and ap- ology they would end up having to learn? proach to us, TIGR was always an early test And could you say more about the relation- site, they would get insights into technolo- ship between ABI, the Bay area, and uni- gies in development, and they got other versities? kinds of preferential treatment. Scott. This is true for DNA synthesis, Being close to Silicon Valley was re- but even more so for DNA sequencing. ally important, and that classic H-P cul- DNA sequencing, for example, requires ture and attitude, embodied in Sam Eletr, marrying expertise in chemistry, fluo- Andre Marion and a few other very early rescent dyes, molecular biology, optics, engineers, was the basis for ABI’s early gel matrices, firmware and software. You culture. have an organisation of people who are Marv. It’s worth commenting that what good at their own discipline, and who are really drove the development of modern also learning how to interact with other molecular biology and biotechnology was scientist and engineers whose parts of the fact that in the mid to late 70s the the platform touch their own. Engineers technologies for DNA sequencing, DNA don’t become experts in chemistry, for ex- synthesis, recombinant DNA technologies, ample, but everyone has to be conversant cloning, restriction enzyme modification, and reasonably knowledgeable in multiple they all came down within a 3,4,5 year domains, and that just comes through in- period. All of them. And that revolutionised teraction with co-workers. As an organi- biology research undoubtedly. And they all sation the ability to develop products in a came together at the same time. If any one multidisciplinary way becomes a source of them had come up by itself, and then of competitive advantage. A company like only 15 years later another one came along, ABI becomes very skilled over time at in- it’s a whole different story. We wouldn’t 31 be sitting here talking about what we’re Dominic. Would you say different things talking about. But they all came together to the different customers when you were at the same time and all at once the world visiting them? exploded with new ways of attacking Scott. Not generally. This is an industrial serious and important biological problems. sale. Platforms have specifications. You’re What we’re talking about in terms of DNA comparing your product’s performance to synthesisers and protein sequencers and your competitors’. It always seemed like so on, this is all part of that movement, there is a striking amount of animosity because all at once people needed these between companies in the instrumenta- compounds, products, and technology to tion industry. This is probably because po- do new state of the art biology. So they tential customers have set budgets, every were pushing the development of these company knows when a given lab intends techniques. to purchase a DNA synthesiser, the same A story that you don’t know about Ap- three companies and sales reps will be in- plied Bio, we actually started that compa- vited in to make their pitch. One will win ny, Lee Hood and I, with these venture cap- everything. The others come away with italists as an outgrowth of the group that nothing. But every customer wanted high started Amgen. We decided to go forward quality DNA, cheap and fast. So there were with starting Applied Bio, and we hired similar sales points to be made with most Sam Eletr. The point is that what Sam customers. did, these machines the DNA synthesiser Dominic. Would you be able to create and protein sequencer, were in such high an example for us, to do with the kinds demand that he went out and he acquired of thing they may say about you, and you contracts from 20 individuals or labs or about them? companies, 20 on the DNA synthesiser and Scott. Oh, we would show gel data of our 20 on the protein sequencer and told these very clean oligos. They would argue our people ‘OK if you want to be in the queue, valve blocks weren’t as good or as impor- you’re going to have to pay half the price tant as we said they were. They would blow of what we’re going to offer these on the out of proportion any reagent problem market. We haven’t designed them yet, and that we might have experienced recently, we certainly haven’t manufactured them and we would do the same. We’d talk about yet. But just to get in the queue you’re go- competing instruments’ lack of reliability. ing to have to put down 50% of the selling Fear is an important motivator, especially price’. And with that he built the company. if you’re the market leader. You want to There was so much demand in those days create doubt. You don’t say it directly, but for these machines that he could do that. it’s understood that if you, the customer, Roger. I was wondering more about cus- buy a competitor’s instrument for $20,000 tomer bases, and a broader historical ques- less you’re taking an almost personal risk tion about science funding and changes that it might not perform. An instrument that happened in this revolutionary time purchase is a highly visible decision within in the late 70s to early 80s. Who is buying a department. So those kinds of arguments most of these products, is it mostly univer- played a role. But most sales situation in- sities, or private companies, pharmaceuti- volved technical debates about issues that cal companies that have their own research to outsiders would seem like pretty modest institutions? differences. Marv. All of the above. Marv. Before Scott’s involvement at ABI, Roger. But who was the bulk? they had the market for DNA synthesis for Scott. There was no bulk. Industrial, five or so years, almost entirely exclusively. pharma stuff, biotech, academic, medical Pretty much in protein sequencing too. So centres. they built up a client basis which was basi- Marv. And the manufacturer of the ma- cally everybody in the industry, and then chines could not keep up with the demand. the Biosearches of the world and Milligens It was that simple. came along. 32 Scott. Even when I was there we always the market and have 80% at least before had roughly 80% of the market share. Beckman gets their first prototype built’. Marv. I mean, when we started Applied And of course that’s the way it was. Be- Bio I was pretty upset that we had to cross- cause we were a small startup, we weren’t a license our patents to Beckman. And Sam big monolith of a company called Beckman said ‘Oh don’t worry about it, we’ll be on instruments.

Session 3: Objects and epistemics of synthesis

Erin McLeary, Stephanie Lampkin, and Amanda Mahoney The material heritage of DNA synthesis?

We saw this workshop as a great opportu- So one story we might want to tell, would nity to think about, say, if we were to build be to take the reagent bottles, and the more a museum to showcase this history what recent machine, and perhaps tell a history would we collect? What artefacts, what of automation. stories would we collect, who would we be Alok. GE acquired a company a few telling them for? We want to work through years ago called Amersham, Amersham these questions with the group. had the AKTA HPLC system, which got For instance, if GE were to offer us an extended to compete with ABI to produce ÄKTA Oligopilot for free for our imaginary their synthesiser. So there is a certain his- museum, why might we want to collect it? tory of taking a platform and growing it Scott. Is it an early DNA synthesiser? into an application that has generated its It’s actually a pretty recent one, and I think own market. So we could see this in a mu- it’s an affordable synthesiser for non-spe- seum as an example of how technologies cialist labs. But if it is not immediately get combined. familiar to people, is it the kind of object That’s a great comment first because the museum would want to collect? What it brings in a corporate history that most about then something like reagent bottles, people would know nothing about. which everyone can recognise? Would we Alok. Those knobs and that stack of box- want to make space in our museum facility es is well known to people. to take care of these, and would we want Because it’s HPLC? the actual chemicals? Alok. Yes. Going back to the oligopilot—how do we So how would we preserve this history? think it would look in an exhibition? Not Alok. Well I would maybe walk along everyone is particularly interested in the Amersham’s HPLC line and then show history of DNA synthesis. What would we “well the next thing they did was…” need to tell a history of it? Dominic. And you could trace it back Scott. But I don’t know how it fits into to some of the first synthesis machines that story, so I guess I want to know because reworked HPLCs were used what the story is. I’m wondering why it widely. came from GE, I’m curious. Certainly our museum has a number of This instrument came into our presenta- HLPCs so we could tell that story. tion simply because I googled ‘DNA syn- Marv. Maybe if you contact Applied Bi- thesis instrumentation’ and this was the osciences and see if you could get hold smallest instrument I could see, I did not of one of their first. Then you could find want to pick a large one. It also was not someone who was working in a smaller mentioned in any of the studies I have lab who couldn’t afford it, and get one read, it wasn’t cited as being used, so I of their systems that was not really de- chose it as an odd example. It helps illus- signed as such but was being used to syn- trate the kinds of choices that museums thesis DNA. After that you might have a have to make. bunch of arrows going to the applica- 33 tions of DNA, such as PCR, and sequenc- If we were to build a museum to showcase ing, you might want to show a sequencer this history what would we collect? What or a little PCR thermocycler, something like that. You would then have a little artefacts, what stories would we collect, story where you start with manual DNA who would we be telling them for? synthesis, then going through the Ap- plied Bio machine and then these appli- Let’s consider an alternative object, cations that come out of it. what about a Controlled Pore Glass Col- So you’re thinking about sourcing, how to umn? Benefits of this are it is very cheap, find these instruments. very small, easy to put on a shelf. Jeff. A couple of years ago I was at the Marv. So if you look at that Oligopilot, Deutsche Museum in Munich and they that’s a large column for making DNA. have a really big collection of these early If you look at these little CPG columns devices. Subsequent to that I went to where you have a few milligrams of London and they only had one thing on Controlled Pore Glass, and in that pre- display. vious column you’ve probably got 15-20 Anonymous 1. One way to make it less grams. boring would be to show those four bot- How do you get a lay person to a museum tles, blue, yellow, pink, and green, those excited about CPG? are ACTG, through the tube at the end Anonymous 1. The problem there is, in comes a long letter of DNA. Putting chemistry, if you’re a chemist, you go in things together on a machine. in the morning, you put A together with So you’re connecting this kind of grey box B, and in 5 minutes you have something, with DNA, which is something most peo- and then you spend the rest of the day ple who know a little about science will purifying. With this, the product, is at- understand. Another thing to notice here tached on a bead, so you just filter out is that this Oligopilot is connected to a and save yourself a day of purification. computer. So software is vital to using this This seems like a very good example of type of equipment, and software is a whole how the day-to-day work of science has other can of worms for both preservation, changed, and how something as small and interpretation, and exhibition. How do we seemingly mundane as CPG can have a keep software available for scholars and do huge impact. we share it with visitors?

Jeff Johnson Factors shaping research in synthetic-chemical biology in the postwar West-German context (1945–1990): Report on a work in progress I am primarily a historian of the social the last third of the nineteenth century the and institutional context of science. What Germans were famous for developing a re- I will try and explain is why the Germans markably successful academic-industrial were not more central to the history of symbiosis, in the dye industry and early DNA synthesis. We mostly hear about the pharmaceuticals in the form of organic UK and the US, but what’s happening with compounds. So you had companies like the Germans? There are a number of fac- Bayer, BASF, and Hoechst, that dominated tors that might help to explain what was the market for those simple organic com- going on, including the influence of indus- pounds back in the early twentieth cen- try, politics, history, and particularly Na- tury. After the war, what was going on? I tional Socialism. They all created a culture looked at a couple of the key German bio- that was in many ways intended to retard chemists and their relationship to industry the development of this field. in the immediate postwar era. These are I want to start with the academic-indus- Richard Kuhn and Adolf Butenandt, both trial connection in the postwar era. From of them directors of highly prestigious 34 Fig. 9. Slide highlighting key developments in the organisation of biochemical research in Germany in the late twentieth century. Slide produced by Jeff Johnson, who also provides permission for its reproduction here.

Kaiser Wilhelm institutes, the predecessor The Director of the Bayer pharmaceu- of today’s Max Planck Society, which spon- tical division, Heinrich Hörlein, after the sors a total of around 80 institutes in vari- war took it as his job to help restore Ger- ous fields. These are focussed on research man success in biochemistry. So he ar- with no obligations to teach. The myth ranged industrial subsidies for both Adolf goes that all of these people do just basic Butenandt for very large amounts at the research without attention to applications. time (approximately US $36,000 annu- I have found that in both of these individ- ally for several years from 1949), and also ual cases, right after the war it was feared a smaller subsidy for Kuhn, to ensure that that they would out-migrate, because the they would decline calls from abroad and conditions in Germany after the war were remain in Germany. Both of them also had so devastated, and finances so limited that lucrative consulting contracts with indus- they were both entertaining lucrative of- try which in my view may have helped fers, particularly the United States was a keep their attention on the kinds of small possibility. Kuhn could have gone to the molecules that could be manufactured in University of Pennsylvania with a lot of these companies, rather than looking at bi- funding, and there were companies such ologically active molecules which required as Wyeth laboratories, willing to support production technologies that we think of his work on areas of interest to him. For today as genetic engineering, but which in example, in regard to the immune factors the 50s few Germans were thinking about. that he was finding in breast milk, Kuhn One question we can ask is ‘to what ex- was collaborating with one of the Penn tent were the Germans really responding professors (Paul György in the medical to the new kinds of technologies that were school) who had been an immigrant from emerging in the United States and else- Germany but had formerly collaborated where?’ I am not sure that they were, even with him in the 1930s before the Nazis took in 1973 when they brought together three over. In conjunction with his work with Max Planck Institutes and made a massive György, Kuhn had a consulting contract complex for biochemistry in Martinsried, with Wyeth (through its parent company, outside of Munich. They had 11 different American Home Products) until 1955. departments, and that was soon expanded. 35 They were doing all sorts of things, but to mated processes for DNA sequencing and what extent were they doing the kind of synthesis. fundamental work in recombinant DNA What about someone who seems to be and other things that led to Nobel prizes talking about precisely that kind of bio- elsewhere? I have not been able to look at technology industry? Consider the exam- all the data yet, but they seem to be focuss- ple of Ernst-Ludwig Winnacker, who to my ing on other questions, and this was in part knowledge was the first person to intro- because the German biochemists had not duce the term ‘synthetic biology’ into the yet been able to make the transition into German language, though if you go back to a closer relationship to molecular biology. 1915 you had Emil Fischer, the Nobel prize Even the Institute that one would expect winner, using the term ‘synthetic chemical to be doing this, the Institute for Molecu- biology’. I asked Winnacker if he had read lar Genetics, it had the problem that it Fischer’s papers, but he didn’t think he had was a descendent of the 1930s Institute been influenced by that. In 1983 Winnacker for Anthropology, which had been associ- did use the term ‘synthetic biology’ specifi- ated with Nazi racism and experimenta- cally to describe DNA synthesis. What’s in- tion. The claim I have been hearing is that teresting is that he used this in the English association with chemistry helped these form in quotation marks, as if he had got it groups distance themselves from their sta- from somebody else. We know he studied tus as the heirs of Nazi past. So it was in abroad and was actually in Berkley, so I’d many ways a negative motivation to be do- be interested to know if people in Berkley ing molecular genetics, which had impact maybe in the 70s were using language like on their overall funding success and public relations. (Note from September 2018: One question we can ask is ‘to what extent my subsequent work has revealed that the were the Germans really responding leading scientists who were planning the Max Planck Institute for Biochemistry at to the new kinds of technologies that Martinsried in the late 1960s discussed the were emerging in the United States and possibility of locating the future European Molecular Biology Laboratory (EMBL) in elsewhere?’ I am not sure that they were, their complex. The EMBL’s planners chose even in 1973 when they brought together instead to locate the EMBL in Heidelberg, but physically separate from the Max three Max Planck Institutes and made Planck Institute for Medical Research. The a massive complex for biochemistry in new Heidelberg EMBL was not completed until 1978, however, five years after the Martinsried Martinsried MPI). What about contrasting with the kinds synthetic biology at that early point. of devices produced by ABI? If we look at Winnacker was the man who as profes- a brochure from the MPI for Biochemistry sor at Munich University founded the LMU in the late 1970s, we see instrumentation Gene Centre in Martinsried in 1983-4, ten such as an automated protein sequencer years after the founding of the Max Planck from the Department of Protein Chemis- Institute there. The difference is that this try, which could sequence peptide chains was a university institute and for the first with 50-60 amino acid components. Were time offered a formal connection to allow any of the people there, people who could the Max Planck people to have more ac- have potentially collaborated with busi- cess to students, which would then allow ness people to found something like ABI them to train the next generation. The in Germany? Or were there cultural issues MPI had groups, called Nachwuchsgrup- that kept them separate? As I said before, pen (next-generation groups), which were the industrial people were focussed on for developing young scientists, but I am other kinds of products and were not so still unclear about their formal connection much interested in trying to develop auto- with the university after 1973. Butenandt 36 and his MPI colleagues taught in the LMU impact on the reputation of the chemical medical faculty, because Butenandt was si- industry. Ultimately in 1990 came the first multaneously professor and director of the German law on genetic engineering which university institute for physiology chemis- focussed on the use of a regulatory com- try, as well as director of the MPI. After mission, similar to NIH, but much more Butenandt resigned his professorship in elaborate. They had to approve every ap- the LMU to become president of the MPG plication, all done by the Central Com- in 1960, however, MPI-LMU relations were mission on Biosafety, for experimentation no longer as close. The subsequent move to on genetically altered organisms and the the remote location in Martinsried would release of GMOs into production and the have further disrupted the MPI’s ability to environment. I think this had a stifling ef- train doctoral students who could then re- fect in Germany. produce and further develop new research Bayer, for instance, really moved all of techniques. Winnacker helped to restore their active research to the United States. the connection to the university. They preferred to stay outside of their I also wanted to look at the politics. So country when working on genetic engi- in the early 1980s, just as we have the take neering or genetic diagnoses, in part be- off of ABI and the biotech industry in the cause of the PR problems involved. US, in Germany they were fighting over Marv. There is no question that this the dangers of genetic engineering. The Green movement in Germany set back Green party really took off in 1983, when German science, no question about it. they won their first Bundestag seats, by in- You couldn’t go there and learn anything corporating attacks on genetic engineering new in modern molecular biology, they into their policy. And they got even more couldn’t do it, because it was against the votes in 1987 following a few important law to do any recombinant research in publications. One was Benno Müller-Hill’s Germany in the 70s, 80s, and 90s. In fact book Tödliche Wissenschaft (Murderous Sci- all the major pharma and chemical com- ence), in 1984, in which a geneticist who panies set up labs in the US to do their had trained in the United States in DNA research components. They abandoned technology exposed the fact that a lot of his Germany. colleagues were essentially Nazis who had I was in the Bayer archive, so was able to covered up their past. This was not good for get their data on the research facility they public relations for bioscience in Germany. opened in 1988 in West Haven, Connecti- In addition you then had the Bundestag cut (near Yale University), through their Commission, in which Winnacker played American subsidiary Miles Laboratories, an active role, on ‘Chances and Risks of but I would love to find out about the other Gene Technology’. Around the same time companies. the Bhopal disaster had a very negative

Robert Smith Visions of value and the making of mega-chunks

What kinds of social relations, patterns of information drawn from (very early) work and technologies are being imagined qualitative analysis of publicly available and configured around DNA synthesis to- documents, technical articles, videos and day? Are any of these distinct from the ex- recordings of events and workshops that amples we have heard about so far? To behave been run by the Engineering Life gin to address these questions, I will focus team, as well as my own notes from par- on Genome Project Write, a proposal made ticipation in the GP-write project, most by prominent scientists to synthesise the recently as a member of the Ethical, Legal genome of organisms such as mammals, and Social Issues Advisory Group. including humans. GP-write is a project ‘in the making’. It Methodologically, I am building on is, arguably, more of a vision or phenom- 37 enon than a realised project. A quick look GP-write is a project ‘in the making’. It is, on the website and related reporting will arguably, more of a vision or phenomenon draw your attention to questions about whether the object of synthesis is a human than a realised project. A quick look on genome, whether or not that goal should the website and related reporting will be represented in the name (HGP-write or GP-write), about whether this is a sin- draw your attention to questions about gle project or a consortium of different whether the object of synthesis is a human projects and partners, or even whether it is a ‘Grand Challenge’. It is so early in the genome, whether or not that goal should making that none of these things are stable be represented in the name (HGP-write and it is unclear what actors will coalesce or what project will emerge. I want to pro- or GP-write), about whether this is a pose that there is utility in studying such single project or a consortium of different emerging phenomena because it might allow us to ask what synthesis is for – what projects and partners, or even whether it kinds of work is required, what kinds of is a ‘Grand Challenge’. social order are produced, what kinds of benefits might emerge and for whom, what So, how do we ‘know’ GP-write? What kinds of culture might produce all of these kind of histories of GP-write are being things? And, importantly in the workshop told? I think two are visible. context, what kinds of synthesis are being imagined and put to use? ↠↠ GP-write as Sc 2.0-2.0. One intui- At the outset it’s important to acknowl- tive origin story builds on the lineage of edge that there are substantial challenges genome-engineering projects that precede with studying contemporary phenomena GP-write. These projects are generally told like this. One that is particularly relevant in terms of building capacity to synthe- to this context is the notion of a ‘politics of sise larger and more genetically-complex novelty’ , which is a rhetorical switch that organisms, as in the slide Jane presented. is often present when people talk about The most recent of these projects, Sc 2.0, emerging science and technology. Synthet- is coming to an end and many of the most ic biologists are particularly good at this. prominent people involved in Sc 2.0 are One example is Craig Venter’s unveiling of also involved in the proposed GP-write the minimal genome in 2010. He goes to a project. And much of the required techni- lot of effort to emphasise that this feat was cal infrastructure, namely the ability to ‘new’: The team inscribed messages into synthesise and construct large chunks of the DNA to make it clear that what you DNA is imagined to be foundational for see is different. But at other times people any GP-write project. flip to talk about how what is being done is not really new, ‘something we’ve been ↠↠ GP-write as HGP-2.0. There are obvi- doing for centuries’. Acknowledging that ously many links to be drawn between there is a politics of novelty has several the way people talk about GP-write and important consequences. One is that you the way they talk about genomics projects can see immediately that language and the more-widely. The synthesis and sequenc- way that particular phenomena are framed ing of increasingly complex organisms is significant. Another is that this framing is one example. But the most striking will vary in relation to different situations parallel that was initially being drawn is – the longer view is often adopted under in an origin story that connects GP-write situations of (perceived) controversy, for to the Human Genome Project. Much has, instance. A final important consequence is obviously, been written about this project that historical scholarship will be vital to and there are many histories to be told be able to tease apart contemporary phe- of it. And it is therefore worth asking nomena. which history of the HGP is being told by 38 proponents of GP-write. Here, the domi- In this reframing I think what we might nant narrative is one coupled to so-called be seeing is an uneasy blending of the two ‘Carlson Curves’. These are images, first articulated by Rob Carlson which map the origin stories to produce a third narrative, cost per base against time for sequencing one which is about the value of synthesis and synthesis of DNA. While sequencing has fallen, synthesis remains high. It is more broadly, and one which partially argued – reasonably –that huge transfor- rolls back from the human mations and societal benefits flow from this reduction in cost of sequencing. It But in the second, one that confers social is claimed that this fall in price per base value and is arguably a much more explicit pair was a direct result of the funding of attempt to create a visionary project, the ‘a’ Human Genome Project; thus, funding human is the necessary organism. Of a second Human Genome Project, one to course, societies value these organisms ‘write’, will produce similar benefits. differently and the point at which most people will have heard about this project I started by emphasising questions about is in relation to a 2016 meeting, an the relationship between GP-write as pro- intentional attempt to build momentum posed, the kinds of cultures that it emerges by coinciding the launch of a Science article from and the kinds of social ordering those with an international meeting. Instead, for proposals might do. This line of work em- various reasons, it was reported as a ‘secret phasises that to ‘get synthesis done’ will meeting to talk about creating a synthetic mean enrolling a wide range of people, human genome’. resources and money. Narratives and vi- This reporting ricocheted around the sions are central to this process. What can world, was described as a plan to create be said about these narratives in this vein? designer babies, has been interpreted by What are they doing? some in the project as a ‘firestorm’ and has One of the first, tentative, things that had tangible consequences for the pro- can be said is that these stories is that posal. For instance, in the 2017 meeting or- they are doing different, but intertwined, ganisers were very careful to foreground things. One origin story blends epistemic, discussion around social, legal, and ethi- organisational and technical histories. It cal issues, with an aim to make sure these helps to make GP-write a credible proposal things were part of the project. More in- by making it feasible. The other acts as a teresting though are the consequences for way of conferring value: If the HGP pro- the scientific components and the vision. duced widespread societal benefit by driv- HGP-write has been re-framed as (the ar- ing economic reductions in sequencing guably broader) GP-write. In this refram- costs, another (H)GP will do the same. But ing I think what we might be seeing is an this second narrative is arguably one that uneasy blending of the two origin stories is more about creating a visionary ‘big sci- to produce a third narrative, one which is ence’ project. Indeed, Andrew Hessel, one about the value of synthesis more broadly, of the core members of the consortium, and one which partially rolls back from the has been explicit about this in public talks human. I think, potentially, in this broader and interviews. project there might be space for more di- A second thing is that they might enrol verse forms of synthesis than the cloud- different organisms and in different ways. lab highly automated vision attached to In the first narrative, one that locates the HGP-2.0, but I think this may come at GP-write as part of a string of genome the expense of a discussion of the value engineering projects, there are many of more widely putting DNA synthesis to organisms that would be credible, obvious work. and scientifically valuable to choose from.

39 Group discussion Jane. Could you clarify your very final Anonymous 2. A question for Jeff. I have point about the kinds of synthesis? been interested in the agro industry in Ger- Robert. The narratives that are being many, and the sources I have been mostly told are also attached to different visions looking at are Syngenta, the Swiss com- of doing synthesis. For example, in pany. I was reading that they had a large publications of the early Sc 2.0 work, advantage due to the way the Third Reich which was the creation of one artificial impacted industry and Syngenta were able chromosome, talks about how the synthesis to fill this gap. So were they perhaps able to work was done by teams of undergraduates. take over the role that Germany had before The more recent processes are synthesis, in Europe? using a combination of yeast and machines Jeff. I can’t say too much about what was to synthesise very large chunks of DNA. going on in Switzerland. One company cer- The vision of the human synthesis is tied, tainly, Hoffman–La Roche, was subsidising for example by Hessel, to a cloud-based Adolf Butenandt, so there were some con- foundry model. The work that each of nections between German biochemists and these different approaches takes will be the Swiss. I also know Richard Kuhn had different and will do different things. Most good relations with Ciba. The Swiss were obviously, the UG synthesis approach has certainly very conscious of what was going a pedagogical aspect. But additionally, on in Germany. what kinds of questions are answerable Many of the papers have suggested the by building an organism as opposed to a synergies between technological and sci- genome? One of the things that I want to entific innovation, and how these changes do is separate out the different forms of often make it possible to make brand new synthesis. What kinds of questions are markets. To what extent can these things solved by building an organism as opposed be seen as determined by technology? My to a genome. sense is that for these markets to develop Anonymous 1. Today companies can it requires things to come at the right time, synthesise the mini-chunks for synthetic creating tools for people who may not genomes, that is the easy part. The hard know the possibilities, but somehow when part is putting them together into the big the tool is presented they are inspired to chromosomes. And then for humans and think more broadly. mammalian types the next hard part is to Jody. Robert highlighted this bifurca- methylate all that DNA and then to pack- tion of when we say something is new, to age it on histones. So there is more than make an economic market, and when we just the synthesis itself. say ‘this is nothing new we have been do- Anonymous 1. I understand there is a ing it for thousands of years’. We say those Chinese group that is also trying to get to- simultaneously to two different effects, gether, even with the same GP-write name, while masking questions we should be ask- do you know if there is any coordination? ing. There might also be something deeper, Robert. I don’t know what coordination regarding the ability to understand histor- there is but I think that there is a parallel ical precedent, and does it hide the extent geopolitical aspect that is worth unpack- to which economics is really driving almost ing in the narratives around these propos- all of this. What is valuable is often what is als. This kind of thing can happen with valuable to the state. If we look at the his- big flagship projects. So, for instance in tory of Justus von Liebig, to take an exam- Europe there is the Human Brain Project. ple, there are some interesting historical But since its launch there have been like precedents for how we have thought about 30 flagship large projects that are all doing analysis and synthesis, which might help similar things with very little coordina- us rethink what is going on here in biologi- tion. And in America there was the launch cal chemistry. For we might interpret what of the BRAIN initiative, which was a direct he was doing as chemical, but it was also response to the Human Brain Project. clearly biological. He was also mobilising 40 large numbers of students to get his chem- thetic chromosomes into the cell and the istry done, in ways that seem to mirror cell is quite sick. Anonymous 1 also talked these contemporary biology cases. about the problem of methylation and the Marv. On the ethics of synthesising ge- chromatin, I don’t think it’s going to be so nomes. We can now synthesise the equiva- easy. lent of a human genome every day. One of Marv. You’re right, it’s not just DNA, these days in some place in the world they but still. are going to start synthesising a human Anonymous 1. There is a biosecurity and genome, and it will be unlike in the early biosafety angle. So people trying to syn- 80s when the Asilomar conference was or- thesise Ebola for instance. So if it’s to send ganised. In those days you dealt with North to a P. O. Box in North Korea, we won’t do America, Western Europe and Japan and it, but if it’s to send to the CDC in Atlanta, that was it. So if you get those countries well we do it all the time. You can screen to agree on a set of guidelines, you pretty and understand intent from looking at the much get all of them. Now if you look at the sequence. 80% of the companies that make people working on the yeast genome, it’s DNA from scratch have signed an agree- all over the world. So even if one country, ment where they screen every sequence. or one group of countries come up with On the question of creating life, people are ethical standards for synthesis of the hu- currently struggling with 500 genes. It will man genome, how do you deal with that on be a long time before we make a human a worldwide basis? It’s an important ques- from scratch. What will happen sooner tion that I don’t know how to answer. It’s is editing of humans. So we need to think tough but we could literally the synthesise of somatic mutations as one thing, and be the DNA for the human genome in one day. much more careful about germline muta- Jody. One of the questions I was think- tion. The whole idea of genetics is that we ing about was scale. Is the ethical ques- are all different, and we can’t lose that di- tion that you can synthesise so fast, or is it versity. about who we think we need to talk to the Jeff. Is there a set of general principles ethics about? for deciding who gets what and on what Jane. There was an international sum- grounds? There must be a large grey area mit on human genome editing a couple of when you are not sure. years ago, in 2015, and one of the challenges Anonymous 1. There is a government there was how do we have an international defined database of sequences that are regulatory system. This conversation is defined as dangerous. If someone orders happening in those spaces which overlap one of those sequences the synthesiser with DNA synthesis. has to screen the user, and if they are Jeff. And that conference did produce authorised to use it it is fine. So if they guidelines. had a Professor from Harvard ordering Marv. But with the Asilomar confer- smallpox, and they call the Dean and ask ence almost every country that was capa- what this Professor is doing. If they say ble of doing recombinant technologies in the Professor is working on something the early 1980s bought off on the guide- completely different from smallpox, then lines. But just try and do that today. With they would have a question. Most of the the exception of North Korea you can syn- time, when they get a flag, like a toxin, thesise a human genome in almost every they call them up and talk, and explain it is country in the world. because the thing they ordered was a toxin Jeff. That does raise some interesting and they go ‘ah, we had no idea, thank possibilities that someone is potentially you I will do something else’. But it’s the going to exploit. government database which most people Jane. One of the points of the choice of agree is the right database. yeast is that it is a very simple organism, Alok. If I could write a sequence for a especially in comparison to the human, toxin grafting onto a protein, and disguis- they have only managed to get three syn- ing the amino acid sequence so that I got 41 1/10th of the scaffold of a harmless protein, are going to be able to make more and more how would you know? themselves? Anonymous 1. Mostly you are likely to Anonymous 1. It looks to me that DNA lose the activity. So even if you got it, it is synthesis is moving towards centralisa- unlikely to be more dangerous. Companies tion. Less and less people want to have to also spend a lot of time talking to govern- synthesise themselves, they want someone ment agencies, such as the FBI, about the to make it all cheaper and faster for them. spread of biological weapons. What they The next pandemic is more likely to come are really worried about is not how some- from nature. one gets the sequence, the hard part is Marv. I think when it comes to large ge- making a large amount, and weaponising nomes it will always be large companies. it without killing yourself. It is really only But when it comes to smallpox you could states that are large enough to weaponise do it with an ABI synthesiser and take a these things. month making DNA. Alok. This works for large companies Anonymous 1. But the hard part is to like you. But isn’t it the case that as the ma- weaponise it. How to make a lot of it and chines and chemistry gets cheaper, people spray it over a large area.

42 Attendee biographies

Dominic J. Berry David J. Caruso Dominic is a historian David is the Director of and philosopher of sci- CHF’s Center for Oral ence, integrating meth- History. His current ods and ideas from sci- research explores the ence and technology relationship between studies. He is a member of Jane Calvert’s government, private funding, and the de- ‘Engineering Life’ project, which inves- velopment of biomedical research in the tigates the ideas, practices, policies and United States from the end of the 20th cen- promises of biological engineering, with tury through today; the modern history of a particular focus on synthetic biology biotechnology; and science and disability. http://www.stis.ed.ac.uk/engineeringlife/ He received his doctoral degree in Science home. and Technology Studies from Cornell Uni- Dominic is pursuing a history of DNA versity, where he worked on the history of synthesis in order to broaden the current American military medicine before, dur- historiography of biotechnology, and also ing, and after World War I, as well as the as a way to integrate historical research creation, dissemination, and use of auto- into the study of very contemporary sci- mated external defibrillators in the mid- to ences. This historical work requires col- late 20th century. He received his under- laboration with historians of chemistry, graduate degree in the History of Science, technology and the life sciences and so he Medicine, and Technology from Johns is particularly pleased to have the CHF as Hopkins University. a partner for this workshop. The overall approach requires collaboration with sci- Marvin H. Caruthers entists, sociologists, industry, and philoso- Marvin H. Caruthers phers, and so he is very grateful for your is a Distinguished Pro- participation! fessor of Biochemistry and Chemistry at the Jane Calvert University of Colorado, Jane is a social scientist Boulder. A Guggenheim Fellow, Dr. Caru- based in the Department thers received his B.S. in Chemistry from of Science, Technology Iowa State University, his Ph.D. in Bio- and Innovation Stud- chemistry from Northwestern University, ies at the University of and completed his post-doctoral studies Edinburgh. Her current research project with H. G. Khorana at The University of ‘Engineering Life’, funded by a European Wisconsin and MIT. Research Council Consolidator grant, fo- Professor Caruthers interests include cuses on the ideas, practices, policies and nucleic acids chemistry and biochemistry. promises driving the field of synthetic bi- Approximately 30 years ago, the methodology. Her research focus is the synthetic ologies that are used today for chemically yeast project (Saccharomyces cerevisiae 2.0). synthesizing DNA were developed in his She is also interested in the governance of laboratory and incorporated into so-called emerging technologies, intellectual prop- gene machines for the purpose of syn- erty and open source, and in interdisci- thesizing DNA used by biochemists, bi- plinary collaborations of all sorts. She is a ologists, and molecular biologists for many co-author of the book Synthetic Aesthetics: research applications. More recently his Investigating Synthetic Biology’s Designs on laboratory has developed methods for RNA Nature, published by MIT Press in 2014. chemical synthesis and for the synthesis of 43 DNA / RNA on chips. His laboratory has Roger Eardley-Pryor also pioneered the synthesis of many new Roger is a historian of nucleic acid analogs that have found appli- contemporary science, cations in the nucleic acid diagnostic and technology, and the en- therapeutic areas. vironment. He earned He is the recipient of several academic his PhD in 2014 from and research awards including The Elliott the University of California Santa Barbara Cresson Medal from the Franklin Institute, (UCSB) where he was a National Science The National Academy of Sciences Award Foundation graduate fellow at UCSB’s for Chemistry in Service to Society, The Center for Nanotechnology in Society. Prelog Medal in Recognition of Pioneering Roger is currently a research fellow at the Work on the Chemical Synthesis of DNA, Center for Oral History in the Institute for The Economists Award in Biotechnology Research at the Chemical Heritage Founda- for His Contributions in Automating the tion. Roger’s research explores ways that Synthesis of DNA, and The US National contemporary scientists, culture-makers, Medal of Science for 2006, the nation’s and political actors have imagined, con- highest distinction honoring scientific fronted, or cohered with nature at vari- achievement. He is also the recipient of ous scales, from the atomic to the plan- The National Academy of Science Award etary. His newest project on “Ecotopian in the Chemical Sciences, The American Visioneering” examines scientists who Chemical Society Award for Creative In- imagine a transformative and ecologically vention, and The Frantisek Sorm Medal, sustainable future; who then conduct sci- The Academy of Sciences of the Czech Re- entific and technological research to enact public. and engineer that future; and who widely Dr. Caruthers is an elected member of promote their visions and technologies to The US National Academy of Sciences, The broader audiences—either to the public, American Academy of Arts & Sciences and to investors, or to policy-makers—all in ef- a Corresponding Member of the German fort to create a more ecotopian world. Academy of Science Gottingen. One of the co-founders of Amgen and Applied Biosys- Elihu Gerson tems, Dr. Caruthers remains active in the Elihu M. Gerson is a so- Biotechnology arena – most recently as a ciologist based in San co-founder of Array BioPharma and miRa- Francisco. He has a BA gen Therapeutics. from Queens College, CUNY, and an MA and L. Scott Cole PhD in sociology from the University of Scott is a 3rd year phi- Chicago. His studies the organization of losophy Ph. D student technical work, especially in the life sci- at the University of Cali- ences, where he focuses on patterns of fornia, Davis. His areas alliance among specialties, including col- of focus are philosophy laboration and intellectual integration. In of science, biology and technology. Prior recent years, his research projects have to that, he worked in the corporate world, included a collaborative study of the Mu- mainly for companies that developed and seum of Vertebrate Zoology at UC Berke- marketed technologies for life science re- ley; a study of an extended collaboration search and medical diagnostics including network centered on a unique colony of Applied Biosystems, Agilent Technologies Spotted Hyenas at Berkeley; and observa- and Quest Diagnostics. He has a B.A. in tion of a biochemistry laboratory studying Molecular Biology from UC Berkeley, an chromatin remodeling. He has also studied MS in Microbiology from Columbia Uni- the organization of work in computing, versity, and an MS in Management from and in hospital care of chronic illnesses. MIT’s Sloan School of Management. Analytically, he focuses on mechanisms of innovation in institutions and repertoires, 44 moving from uncertainty, variability and pany, co-authored with W. von Hippel, R. local specificity at daily work sites to reli- G. Stokes, and W. Abelshauser (Cambridge able patterns of conduct at larger time and Univ. Press, 2004); Frontline and Factory: organizational scales. Comparative Perspectives on the Chemical Industry at War, 1914–1924, co-edited with Lijing Jiang R. M. MacLeod (Springer, 2006); and “The Lijing is a Haas Post- Case of the Missing German Quantum doctoral Fellow at the Chemists: On Molecular Models, Mobili- Chemical Heritage zation, and the Paradoxes of Modernizing Foundation. Her schol- Chemistry in Nazi Germany,” Historical arship focuses on how Studies in the Natural Sciences, 43/4 (Sept. certain technological ob- 2013), 391–452. His contribution to the jects or materials for life sciences, such as workshop is based on his current work on the spawning goldfish, aging cells, or diag- the role of chemists in the origins of mod- nostic balloons, shaped the scientific and ern synthetic biology and the technologies social practice around them, mediating the of artificial life. interplays between biology and society. Her major project is a monograph on the Stephanie Lampkin history of making fish species, especially Stephanie Lampkin is the museum collec- the goldfish, into experimental and model tions manager at the Chemical Heritage organisms in life science research institu- Foundation. Stephanie is responsible for tions and aquaculture industry in twenti- the care, preservation, documentation, se- eth-century China. She obtained her PhD curity, and storage of the museum’s object in Biology and Society at the Center for Bi- and fine art collections. She also collabo- ology and Society, Arizona State Universi- rates with other CHF staff members to dig- ty in 2013, and has held research positions itize the museum’s collections. She holds a at Princeton University, Nanyang Techno- PhD in history and a museum studies cer- logical University, and Yale University. tificate from the University of Delaware.

Jeff Johnson Amanda Mahoney Jeffrey Allan Johnson Amanda L. Mahoney, R.N., Ph.D., is a Pub- is Professor of History lic History Fellow at the Chemical Heritage emeritus at Villanova Foundation. A historian of nursing and University. He received clinical practice, her work at CHF focuses his PhD in modern Eu- on the intersections of chemistry and the ropean history and his- life sciences, the history of pharmaceuti- tory of science from Princeton University cals, and the construction of health data. and has also taught at SUNY-Binghamton University and as a guest instructor at the Erin McLeary University of Bielefeld. Currently he is a Erin is CHF’s museum director. Prior to guest scholar in the Research Group on the joining CHF, she served as an exhibit de- History of the Max Planck Society, Max veloper with the National Constitution Planck Institute for History of Science, Center and the Museum of the American working on the history of biochemistry af- Philosophical Society, and as a guest cura- ter the Second World War. His publications tor for the Mütter Museum of the College in the social history of modern chemistry of Physicians of Philadelphia. She received and the chemical industry include The Kai- her PhD in the history and sociology of sci- ser’s Chemists: Science and Modernization in ence from the University of Pennsylvania Imperial Germany (Univ. of North Carolina and has published on the history of Ameri- Press, 1990); German Industry and Global can medical museums, chemistry, and Enterprise. BASF: The History of a Com- color theory.

45 Jody A. Roberts the biosciences, primarily in relation to Jody A. Roberts (PhD, science policy, research funding and labo- Science and Technology ratory science. As part of the Flowers Con- Studies) is director of sortium (at King’s College London) and the CHF’s Institute for Re- Engineering Life project (at the University search and managing di- of Edinburgh) he is currently research- rector of CHF West. CHF’s Institute for Re- ing attempts to automate the practice of search initiates, coordinates, and conducts synthetic biology, the ways that interdis- research at the core of CHF’s mission to ciplinarity and collaborations happen — foster dialogue on science and technology especially between the social and natural in society. In this capacity Roberts over- sciences — and notions of value within re- sees CHF’s Centers for Oral History and search agenda setting, particularly in the Applied History and ensures that research context of ‘grand societal challenges’. at CHF bridges the institution’s unique ability to speak through museum exhibi- Alok Srivastava tions; live, print, and digital programming; Alok is an independent and CHF’s unparalleled collections in the scholar working in so- history of science. The goals of our work ciology, philosophy, and are to develop the methods and tools that history of science in San experiment with the unique capabilities Francisco. He obtained of the science humanities to contribute his Ph.D. in Biochemistry and Biophysics to a more inclusive conversation about from MIT. His Ph.D. research focused on the place of science and technology in our studying the structural aspects of protein lives; to share those tools with our peers; folding as it pertains to engineering pro- and to cultivate and mentor a new genera- teins for stability and function. He has tion of science studies practitioner capable been working in the biotechnology indus- of taking these ideas out into the world. try and was involved in projects developing Since joining CHF—first as a visit- an ultra-sensitive bioassay platform based ing fellow (2005–2007) and then as staff on Bio-Micro-Electro-Mechanical Systems (2007–)—Roberts has experimented with (Bio-MEMs) employing acoustic sensors, ways in which we bring the intellectual and a discovery platform for ultra-specific core of science studies into the operations biomarkers for early detection of cancers of a public-facing institution. Projects based on aberrant Post-Translational Pro- such as From Inception to Reform: An Oral tein Modifications proteins in cancer cells. History of the Toxic Substances Control His current project in industry involves Act and Sensing Change provided early building an online platform for collabora- templates for thinking about how we can tive problem solving to support clinical open new conversations on topics that treatment planning for uncommon cases often seem impenetrable, hidden, or too in cancer. politically charged. More recent and ongo- Dr. Srivastava’s research interests in so- ing projects, such as REACH Ambler, have ciology of science focuses on the processes taken these lessons and continued to ex- of change in scientific capacities of labora- periment with ways in which histories of tories and research communities engaged the present provide platforms for speaking in multi-disciplinary and integrative about possible futures. projects. He is studying these problems . through a series of historical case studies Robert Smith in chemistry, biochemistry, molecular bi- Rob works in the field ology, synthetic biology, integrative medi- of science and technol- cine and related areas. ogy studies. His work explores the social and ethical dimensions of 46 Annex: Workshop Documentation

Questions that inspired the workshop and which were circulated to participants

• How could biologists specify and create • How could a museum collect the history DNA sequences before the chemical ap- of DNA synthesis? proach was an option? What practices did • What are the relations between organ- this involve? isms in receipt of synthesised DNA and • How have biological, chemical, and en- those inheriting DNA through biological gineering knowledge contributed to the reproduction, or receiving it from anoth- development of DNA synthesis and its er organism? expansion into an industry? Not just their • How is synthesis influencing the biologi- knowledge involved? cal sciences? Or the biological sciences • Did the chemical synthesis of DNA teach influencing synthesis? biologists/biochemists anything about bi- • What are the limitations for synthesis? ological phenomena, for example, about • What new social relations does the capac- synthesis processes within organisms? ity for gene and genome synthesis pro- • Who/what were the first companies or duce? organisations to offer synthesis to order, • How are synthesised nucleotides used in or offer synthesis machines? research, be it for scientific or industrial • When is DNA a tool? A product? A puzzle? purposes?

Programme

Tuesday, 28th November. Venue: CHF.

9:30–10:00 Coffee and registration 10:00–10:20 Dominic Berry: Welcome and introduction

Session 1: Whole genomes/organisms (two 20 minute talks and 30 minute discussion) 10:20–10:40 Alok Srivastava & Elihu M. Gerson Synthesis of Viable Genomes and Organisms: Understanding Wholes 10:40–11:00 Jane Calvert Synthetic yeast: a tale of sixteen synthetic chromosomes 11:00–11:30 Questions and discussion

11:20–11:45 Coffee

Session 2: Extending synthesis (two 20 minute talks and 50 minute discussion) 11:45–12:05 L. Scott Cole Selling DNA Synthesis: Applied Biosystems’ DNA Synthesis Business from 1989–1992 12:05–12:25 Marvin H. Carruthers The Chemical Synthesis of DNA, RNA, and Certain Analogs 12:25–13:15 Questions and discussion 47 13:15–14:00 Lunch

14:00–14:20 Erin McLeary, Stephanie Lampkin, Amanda Mahoney The material heritage of DNA synthesis?

Session 3: Epistemics of synthesis 14:20-14:40 Jeff Johnson Factors shaping research in synthetic-chemical biology in the postwar West-German context (1945–1990): Report on a work in progress 14:40-15:00 Robert Smith Visions of value and the making of mega-chunks 15:00-15:30 Questions and discussion

15:30–... Wrap up and final thoughts

Submitted abstracts

Jane Calvert different synthesis and assembly strategies. For Synthetic yeast: a tale of sixteen synthetic example, in Tianjin, China, one of the chromo- chromosomes somes was entirely synthesized by an undergrad- The synthetic yeast project is an international ef- uate class as part of a ‘build-a-genome’ course. fort to comprehensively re-design and construct These different chromosomes also have different the genome of the yeast species Saccharomyces qualities and characteristics, and the scientists cerevisiae wholly from laboratory-synthesised often refer to these to identify their ‘favourite’ DNA. The dual aims of the project are to learn chromosome. In addition, several of the laborato- more about yeast biology and to develop improved ries are starting to design their own novel, bespoke yeast strains for industrial use. Many changes are chromosomes. being made to the genome to further these aims, Some hope that the synthetic yeast project including removing repetitive regions of DNA, marks the start of a new era of whole genome constructing a ‘neochromosome’, and building in ‘writing’ projects, which will involve the synthesis the ability to evolve the yeast on demand. Ques- of the genomes of a range of species, including the tions arise about whether the completed synthetic human. Whether or not this initiative progresses yeast—known as Saccharomyces cerevisiae 2.0—will as planned, I argue that whole genome synthesis be a different species from the wild-type. projects would benefit from increased sociological, Unlike other branches of synthetic biology, historical and philosophical attention. which focus on building discrete genes or genetic circuits, the synthetic yeast project is an example Marvin H. Caruthers of construction at the whole genome scale. It fol- The Chemical Synthesis of DNA, RNA, and Cer- lows in the steps of previous viral and bacterial tain Analogs whole genome synthesis projects, but is approxi- The chemical synthesis of DNA/RNA dates from mately an order of magnitude larger. The size of the mid 1950s in the laboratory of Sir Alexander the project requires an internationally distributed Todd. Shortly thereafter Gobind Khorana pio- effort, involving the coordinated activity of eleven neered the use of synthetic DNA/RNA for solving labs across North America, Europe, China, Singa- various biological problems such as the genetic pore, and Australia. The sixteen chromosomes are code and the use of sequence defined oligonucle- distributed around this international consortium. otides as templates for DNA/RNA polymerases This presentation draws on interviews with and to solve biological problems including the members of the project consortium, and visits to synthesis of genes and studies on how proteins the different laboratories. Although all the syn- recognize DNA/RNA. Following this initial work, thetic chromosomes are designed at the PI’s labo- Bob Letsinger developed an entirely new synthe- ratory in NYU (with the exception of the neochro- sis methodology that was used in the initial DNA mosome), the individual laboratories have pursed sequencing methods from Sanger’s laboratory and 48 for synthesizing the human insulin and human ments in both DNA synthesis instrumentation and growth hormone genes—developments that led reagents enabled the company to achieve a domi- directly to the establishment of the biotechnology nant position in the DNA synthesis market world- industry. A brief review of these methodologies wide. In this talk I will provide a commercial per- and some of the lessons learned about pioneering spective on oligonucleotide synthesis based on my basic research will be discussed. experience as Product Manager for DNA synthesis From 1977–1982 Professor Marvin Caruthers at ABI from 1989 through 1992. This was a time at developed the use of nucleoside phosphoramidites which the need for synthetic oligonucleotides was as stable monomers for the solid phase synthesis growing rapidly, primarily based on rapid growth of DNA and RNA. This ground-breaking chemis- in the use of the Polymerase Chain Reaction (PCR). try was far superior to anything at that time and, I will discuss ABI’s entry into the DNA synthesis even today some 35–40 years later, remains the market, the competitive landscape at the time, how methodology of choice for synthesizing DNA/ the company’s DNA synthesis team was structured RNA. Its chemical accuracy has enabled it to be de- and how it operated, and I’ll provide a sense of ployed from the micromolar scale of DNA oligomer ABI’s corporate culture at the time. preparation for various clinical applications down to microdot, nano-scale chemistry that is used for Jeff Johnson numerous biological, biochemical, diagnostic, and Factors shaping research in synthetic-chemical chemical applications. Currently and in collabo- biology in the postwar West-German context ration with Agilent, Prof. Caruthers has adapted (1945–1990): Report on a work in progress this chemistry to the synthesis of DNA on glass The purpose of the present paper is to examine chips (244,000 DNA segments per chip at 200-300 some of the factors affecting the political, institu- nucleotides in length / segment). For many differ- tional, and scientific context of research in syn- ent research applications, this on-chip process is thetic-chemical biology in postwar West Germany, performed at the level of 6 to 20 billion nucleotide 1945–1990. It is well-known that the West-Germans condensations per day (the equivalent of several were considerably behind their colleagues in other human genomes of 3 billion base pairs). Moreover, western nations (particularly Britain, France, and this work is now at the core of current DNA and the United States) in taking up the challenges and RNA sequencing technologies. Modern biology opportunities posed by the postwar development could not have achieved its explosion of discovery of molecular biology and the various technologies over the last 40 years without the near-flawless leading to genetic engineering. In some ways this phosphorus chemistry that the phosphoramidite is a surprising phenomenon, because at least until methodologies have delivered to science and tech- the 1930s the Germans had been among the world nology. leaders in a field that I will designate as synthetic- Notwithstanding the tremendous success of chemical biology, using the terminology of Emil this basic phosphorus chemistry, Prof. Caruthers Fischer in 1915; unaware of Fischer’s earlier termi- continues to develop the chemistry of key P(III) nology, Ernst-Ludwig Winnacker introduced the species for new purposes. If time permits, the syn- term “synthetic biology” into the German context thesis of a new analog called thiomorpholino DNA in 1983, applying it specifically to the synthesis of will be discussed and certain initial biological re- genes. sults will be presented. Obviously one of the critical factors affecting the German situation was the impact of National L. Scott Cole Socialism, not only its purges of German scientific Selling DNA Synthesis: Applied Biosystems’ institutions but also the destruction brought about DNA Synthesis Business from 1989–1992 by its failed war of conquest. Beyond these factors From its founding in 1981 until its acquisition in were others inherent in the post-Nazi German con- 2008, Applied Biosystems’ Incorporated (ABI, Fos- text of the mid-20th century. In this paper, I would ter City, CA) was the leading supplier of instrument like to examine some of these factors by looking at and reagent platforms for life science research. specific examples of German organic chemists and In 1985, the company introduced the Model 380A biochemists in their institutional contexts, consid- DNA Synthesizer, its first commercial platform ering both the elite Max Planck Institutes (such for phosphoramidite-based DNA synthesis. Over as the MPI for Biochemistry in Munich and the the next several years, a combination of improve- MPI for Medical Research in Heidelberg) as well 49 as university institutes in related fields. I am also or detached from reality. Perhaps the most blunt interested in considering the extent to which the example one can give is to point to the fact that German chemical and pharmaceutical industry in claims about future value are excellent ways to en- the postwar era continued its decades-old tradition rol people into a project. We should then pay ana- of promoting close academic-industrial collabora- lytic attention to claims about the purpose of do- tion. Finally, I would like to examine the political ing DNA synthesis and the ways that they are built context, including German debates over the ethics into websites of objects, people, places, and values. and risks of biotechnology and genetic engineer- In this talk I will take a first pass at doing just ing during the 1980s. When Winnacker introduced that. To do so I will draw on early reflections from the term synthetic biology, the German debate was on-going documentary work and observational just beginning; it culminated in 1990 in the first material at synthetic biology conferences around German Genetic Engineering Law, whose origin the world. I will examine the cultures that such should be seen in the light of the historical and cul- narratives claim to produce, the values that they tural burden of Nazi atrocities. embed and the significance of these things, both for life as we know it and for the social and human SHI Curatorial team sciences as we relate to the natural and physical The material heritage of DNA synthesis? sciences. What is the material heritage of DNA synthesis? In this interactive session, workshop attendees Alok Srivastava & Elihu M. Gerson and CHF museum staff will collectively imagine a Synthesis of Viable Genomes and Organisms: museum of DNA synthesis. What artifacts would Understanding Wholes be displayed in this museum? What stories would This paper explores some issues raised by the those artifacts tell? For what audiences should synthesis of complete functional units – genes, those stories be told? And what would it take to pathways, biochemical complexes and the exten- move from an imagined museum to a collecting sion of this work to the making of autonomous initiative that acquires and preserves the material wholes such as viable genomes and cells. Synthe- heritage of DNA synthesis? sis experiments generate a unique kind of understanding, achieved by de-composing and re- Robert Smith composing functional units. Such efforts directly Visions of value and the making of mega- address the descriptive and interactional complex- chunks ities of biological systems and their constitutive This workshop addresses DNA synthesis as his- mechanisms. toriographically neglected. Today DNA synthesis Synthesis experiments interpret mechanisms seems to be going through somewhat of a resur- by demonstrating that articulated parts, refined gence. For instance, in Britain the UK taxpayer has and reassembled, behave as we expect them to. indirectly contributed more than £150m to syn- Synthesis experiments reveal and mark gaps be- thetic biology projects. Included in this figure is tween the explanations and manipulative results, roughly £17,528,700.00 towards six so-called ‘DNA and help specify the efforts to fill these gaps. foundries’. In the United States the Broad Institute In synthesis experiments, scientists must learn has recently been awarded a five-year, US$32 mil- to deal with incomplete systems that are not (yet) lion contract from the Defense Advanced Research complete or viable. Laboratory procedures act as Projects Agency (DARPA) to design, fabricate, and scaffolds that provide functional support for in- test large DNA sequences at scale. Similarly, and termediate stages of construction. For example, with much bombast, a team with George Church, a database containing the sequence of bases of a Jef Boeke and Andrew Hessel have proposed a full bacterial genome keeps the order and content new grand challenge—the synthesis of large scale of the organism’s genome while it is being chemi- chunks of DNA—accessible for the modest price cally synthesized and biochemically assembled. tag of £500m. This computer file thus functions simultaneously The rhetoric surrounding many of these invest- as a scaffold for the genome under construction, ments is unsurprising to anyone following new and as an important part of the laboratory’s work and emerging forms of knowledge production and organization. technology creation. And yet at the same time, past The laboratory thus acts in place of the cell, sup- work has shown that such claims are not isolated porting and enabling the assembly process by de- 50 veloping and deploying a set of protocols that spec- different groups of procedures. It is useful to un- ify needed resources and context to the incomplete derstand synthesis experiments as explaining system. These protocols also serve as bookkeeping biological systems by carrying out re-composition devices that mark the parts of explanation(s) that experiments corresponding to de-composition ex- are not yet realized as manipulation capacities. periments. A particular kind of understanding is Synthesis thus operates by mapping and track- achieved by these full cycles of de-composition and ing the relationships between de-composition re-composition experiments of functional units procedures and corresponding re-composition and autonomous wholes that directly address the procedures. Making and testing complete func- descriptive and interactional complexities of bio- tional units enforces a reconciliation among the logical systems and their possible mechanisms.