In his recent paper “Synthetic biology and the technicity of biofuels” in the journal Studies in History and Philosophy of Biological and Biomedical Sciences, Mackenzie looks at three startup companies in the biofuels industry–Synthetic Genomics, Amyris, and Joule Unlimited–as case studies of how synthetic biology and biofuels “come into being, change and endure”, asking “how does synthetic biology translate a potential technical object into an actual technical object?”

Joule Unlimited

The ways that these companies design and market their products, both those currently in production as well as future products promised by new technologies, highlight the technical ensembles and supply chains necessary to produce energy, asking different “what if…?” questions about the future. However, while biofuel companies propose a disruption in the ways that we produce fuels, in vats of yeast or ponds of algae, they still rely on many of the networks that support our current infrastructures and industries. Mackenzie writes:

While synthetic biology might come up with revolutionary ways of producing next generation biofuels, these fuels are part of a interlinked large technical systems of aviation, road transport, and shipping that have taken shape over a century or more. In some ways, no matter how revolutionary it is, synthetic biology will be doing very little to change the broad sociotechnical systems of transport…The close fit between next generation biofuels and existing transport socio-technical system means that the ‘revolutionary’ innovation promised by synthetic biology is likely to be in service of changing not much.

Howard et al.--Proceedings of the National Academy of Sciences

There is a wide range in the ways that current biofuel researchers imagine their future products fitting into fuel pipelines and transport infrastructures, from hydrogen gas production that requires adoption of entirely different kinds of transport pipelines, car fuel cells, and fueling stations to “petroleum replica” diesel fuels that can “drop in” to mature petroleum infrastructures with little processing. In the recent paper by researchers at the University of Exeter and the oil company Shell and funded in part by a grant from Shell Research, these petroleum replicas are produced in E. coli starting from processed sugar, placing these molecules not only in current fuel and transport infrastructures, but also agricultural systems needed to produce sugar for the bio-molecular supply chain. In the paper’s conclusion and in news interviews, the researchers make clear the many infrastructures–political, economic, technical, and biological–that are necessary to do this work and will be necessary to scale up production of such a molecule.

It will take a lot more work to truly disrupt the ways that fuel is produced and to move beyond systems that replicate the petroleum industry. In thinking with biofuels and making visible the sources of the carbon molecules and the bond energy of fuel molecules we can ask new kinds of “what if…?” questions and begin to imagine new industrial ecosystems. As Mackenzie closes his article, “[biofuels] bring together many things in relation, not to make something totally new or hitherto unimagined. Just the opposite, they make something familiar—fuel—in ways that remain open to transformation.”

Megan Daalder -- Project Eureka

Megan Daalder‘s Project Eureka is a shape-shifting and multidimensional narrative about life, science, and technology after the end of the world. At her work-in-progress exhibition at the UCLA Art|Science gallery, which opened this week, she invites us to visit Eureka’s future, set in the year 2050. In this future “the ‘Naturals’ have won,” and society aggressively defends an idea of Nature and Natural Selection that is full of conflict, with room only for the naturally genetically fit. In this world, Daalder’s Eureka is an outcast on the run from a society that resists all technological interventions in Nature’s plan. She is the world’s first and last designer baby, engineered to be “futureproof” in a world wracked by climate change.

The specifics of her genome edits and the structure of her society are left open-ended. We’re asked to speculate and fill in many of the gaps in the world hinted at by the exhibition’s two intertwined interviews. On one screen, Eureka talks to my favorite bioethicist, Laurie Zoloth, about Nature and the morality of genetic technologies. As Zoloth discusses purity, ethics, religion, and history, the other screen features an interview with Gizmo Joe, a resident of Slab City, discussing the dangers and hopes that are embedded in all technology. As Zoloth questions which concept of nature we wish to return to and what we define as truly “natural,” Gizmo Joe, at first wary of an engineered human, welcomes Eureka into his desert world, littered with the artifacts of past technologies in various stages of being recycled into future machines.

Project Eureka isn’t meant to simply warn us of a future climate apocalypse or to propose a desired path of progress, but to open up new spaces and times for asking how we can live more effectively together on this planet, with other entities both human and non-human, natural and artificial. Likewise, Eureka’s genetic modifications don’t point the way towards Daalder’s vision of an ideal future human, optimized for any given future scenario. Rather, in her conflicts with a society set on one definition of DNA-inscribed human nature, Eureka shows us that we must transform ourselves in many different ways in order to compose a better future world. In proposing a genetically engineered basis for Eureka’s altruism and kindness–her humanity–Daalder blurs the natural, cultural, and technological in a character that can’t be defined by any one trait or behavior, but is shaped through her relationship to the people she interviews and the world she creates as the project grows and shifts.

Synthetic biology is often referred to as “the field of the future,” the foundation of a fuels, materials, medicines, as well as the way we produce knowledge of biological systems. But while the self-consciously revolutionary language of synthetic biology declares a change of the industrial status quo, the metaphors we rely on are explicit references to the successful revolutions of past industrial technologies. The term synthetic biology echoes the successes of synthetic chemistry, while the guiding concept of standardization in genetic components is modeled on 19th century standardization of interchangeable parts. Industrial metaphors mix further as we climb the abstraction hierarchy; genetic parts are assembled to fit into a cellular chassis, creating logic gates and circuits that can compute biological information, leading to the control of cellular factories, rapidly designed, built, and commercialized on an “Ikea”-like scale.

Bio-computation metaphors from Miyamoto et al. "Synthesizing Biomolecule-Based Boolean Logic Gates"

Fritz Kahn, "Man as Industrial Palace"

These metaphors help us to understand how an industrial revolution might emerge from a biology lab, showing a possible path from ideas to industry. Like the “horseless carriage,” perhaps the analogies of living cells to computers give us a sense of familiarity with a technology whose potential we have not yet fully grasped. Industrial metaphors have long played a role in how we understand biology and the human body, from Fritz Kahn’s 1927 paintings of “Man as Industrial Palace to analogies between brains and computers. By referencing the products and methods of previous industrial revolutions, synthetic biology aims not only to aid understanding but also to demonstrate the future potential of the field. These metaphors draw the projected lines of Moore’s exponential increase as strands of DNA, imagining analogous and expanding industries based on carbon and sunlight rather than silicon and fossil fuels.

How will this revolutionary transition happen? What conditions are necessary to foster such a change? As synthetic biology is largely still a laboratory rather than industrial enterprise, perhaps Thomas Kuhn’s The Structure of Scientific Revolutions, can provide a useful framework for understanding the structure of the promised techno-scientific-industrial revolution of synthetic biology. Based on his analysis of the history of chemistry and physics, Kuhn argues that the evolution of scientific knowledge proceeds by punctuated equilibrium–periods of “normal science” interrupted by scientific revolutions, paradigm shifts that change the nature of the questions being asked and the “puzzles” being solved. Paradigms shift after the accumulated weight of unexpected results becomes too large, when facts that don’t fit the model begin to open new questions and when the “failure of existing rules is the prelude to a search for new ones.”

Some of the failures of modern industry are explicit starting points for synthetic biology projects, like engineered bacteria that can sense or consume industrial pollutants, but no revolution can address all the failures of the paradigms that came before. For scientific revolutions, Kuhn writes, “To be accepted as paradigm, a theory must seem better than its competitors, but it need not, and in fact never does, explain all the facts with which it can be confronted.” What problems can synthetic biology solve and what problems are missed, outside of the paradigmatic umbrella of biotechnology? What new problems might arise with a biology-based industrial revolution?

These are difficult and important questions with no clear answer, questions that we ask ourselves when we talk about risk, implications, and outcomes of new technologies. But perhaps there is a deeper question that emerges when we look at synthetic biology through a Kuhnian lens: by working to solve the problems of current industry, replacing or cleaning up after polluting chemical factories with microscopic cellular factories, are we simply replicating the old paradigm with a biological tint? Are we talking revolution while just solving puzzles?

Industrial metaphors for biological systems are being inverted, but the industrial paradigm remains: “Man as Industrial Palace” becomes “Industrial Palace in a Cell.” How can a biologically driven industry change these metaphors, change the way we make things and the way we do things that takes biology on its own terms, that changes the paradigm through which we see the world?

Within synthetic biology, programs that I’ve been involved with such as Synthetic Biology Leadership Excellence Accelerator Program (LEAP)–sponsored by Synberc’s Practices thrust–are efforts to integrate new questions, metaphors, and paradigms into the research goals and visions of synthetic biologists. Synthetic Aesthetics joins artists and designers with scientists and engineers to consider not just implications of the products of synthetic biology but to reconsider what those products might be—the metaphors that we use to understand and design nature. LEAP has different but complementary goals, bringing together scientists and engineers in academia and industry with experts from policy, ethics, economics, and law and providing a space to creatively consider what it would mean for synthetic biology to work in the public interest.

Both programs encourage those involved with synthetic biology to think beyond existing paradigms, both in science and industry. Conversations like these may help us to push beyond the industrial metaphors that we depend on when we talk about the potential of synthetic biology, providing us with new paradigms that can be truly revolutionary.

I’m fascinated by the biology of soil and the history of “dirtiness”–where dirt and bacteria are allowed to be and where we must clean them away. Mary Douglas defines dirt in her classic book Purity and Danger: An Analysis of Concepts of Pollution and Taboo as “matter out of place”:

[Dirt] is a relative idea. Shoes are not dirty in themselves, but it is dirty to place them on the dining-table; food is not dirty in itself, but it is dirty to leave cooking utensils in the bedroom, or food bespattered on clothing; similarly, bathroom equipment in the drawing room; clothing lying on chairs; out-door things in-doors; upstairs things downstairs; under-clothing appearing where over-clothing should be, and so on.

This is part of why the recent news of an expensive French restaurant in Tokyo serving a dirt-based menu is so surprising and wonderful. Fancy food and soil certainly don’t belong together, but this is no ordinary dirt; the food-grade dirt is specially sourced and lab-tested to ensure cleanliness, heated, strained, and smoothed into chocolate-like sauces, spooned onto elaborate dishes to give an exquisite “earthiness” to the flavor. These symbols of fanciness and good taste, along with the expensive price tag give the dirt a new place at the table. For more about the dirty menu and the history of geophagy (eating dirt) check out this article from Smithsonian.

• Oliver Wright, Guy-Bart Stan and Tom Ellis. Building-in Biosafety for Synthetic Biology. Microbiology, March 2013. Preprint PDF available here.

• Christine Rabinovitch-Deer, John Oliver, Gabriel Rodriguez, and Shota Atsumi. Synthetic BIology and Metabolic Engineering Approaches to Biofuels. Chemical Reviews, March 2013.

• The BIOFAB: International Open Facility Advancing Biotechnology published two papers this month about the precise control of gene expression in E. coli
• Mutalik et al. Precise and Reliable Gene Expression via Standard Transcription and Translation Initiation Elements. Nature Methods, March 2013.
• Mutalik et al. Quantitative Estimation of Activity and Quality for Collections of Functional Genetic Elements. Nature Methods, March 2013.
• An interesting New Scientist article discusses these papers in the context of industrialization of synthetic biology, from “handcrafted” production pathways in yeast to the “Ikea” of synthetic biology production: “Quality control opens path to synthetic biology’s Ikea.”

• Jerome Bonnet, Peter Yin, Monica Ortiz, Pakpoom Subsoontorn, and Drew Endy. Amplifying Genetic Logic Gates. Science, March 2013.

• “Scientists create transistor-like biological device,” Guardian Science News.
• A great piece by Carl Zimmer on Synthetic Biology at Download The Universe: “A Comic Book Guide to Rewiring Life.”

The 29 "living" Caminalcules

In order to assess and teach different methods of building phylogenetic trees, taxonomist Joseph Camin designed a set of adorable imaginary animals in the early 1960′s. The animals, playfully referred to as “Caminalcules” by his graduate students, had a pre-defined evolutionary history that was reflected in the shapes and patterns of Caminalcule phenotypes. The set of 77 Caminalcules includes 29 living species and 48 “fossil” species, allowing a full reconstruction of the evolutionary tree. Students could test out their newly acquired skills of classification on this synthetic data set, comparing their results against the “true” evolutionary history of the answer key. Beyond its utility as a teaching tool, the set of Caminalcules also allowed for the development and testing of new kinds of classification schemes, particularly new numerical methods and algorithms.

In a 1966 article in Scientific American (PDF), entomologist Robert Sokal discusses his work on computational systems that can sort and classify organisms and the ways that he used the Caminalcules to help develop new numerical methods. To Sokal, traditional methods of taxonomy were comparatively more “subjective,” requiring the classifier to identify phenotypic characteristics and organize evolutionary trees by hand and “making taxonomy more of an art than a science.” The emergence of the computer during the 1960′s provided “many possibilities for objective and explicit classification.”

Today the “digital” data held in gene sequences can be compared using algorithmic methods of alignment and clustering, but in the 1966 there weren’t any gene sequences available. Instead, Sokal used numerical and automated methods to compare the “analog” physical characteristics of the organisms using digital programs. One method of automated image processing that Sokal developed to convert variable phenotypic information into numerical data was to simply cover the Caminalcule line drawings with punchcards that had random holes punched out. Each hole would then be assigned a “1″ or a “0″ depending on whether there was a line drawn under that hole. Comparison of these low-resolution digitizations of the different Caminalcules were able to generate trees similar to the original phylogeny.

These punchcard images are a fascinating artifact of early computational biology, anticipating a very different future than what we have today, a future based not on gene sequence but the automation of phenotypic characterization. Indeed, in his Scientific American article Sokal writes:

Most prominent among the devices likely to be useful in taxonomy are optical scanners, which digitize drawings, photographs, microscope preparations and results of biochemical analysis. The veritable flood of information that will flow from these automatic sensors will require computer-based processing and classification, since the human mind is not able to digest these data by traditional means.

Today when we talk about the flood of digital data we’re usually referring to petabytes of genome data coming from sequencing centers and overwhelming our computational capacity to analyze and interpret that information. For Sokal, however, it was “by no means certain whether genes or their effects should form the basis of a classification,” and even today, taxonomists look at a lot more than just gene sequence to classify organisms. Different kinds of phenotypic data might seem like another drop in the already flooded bucket, but biology is more than DNA, and the history of classification shows us that we need much more than sequences to organize and understand life.

Phylogenetic Relationship of the Caminalcules

Stranger Visions, by Heather Dewey-Hagborg

The debate is resurfaced and re-problematized with two recent pieces by artists whose work engages with genetics. Heather Dewey-Hagborg’s piece Stranger Visions is a sometimes creepy look at the genetics of identity and the privacy of the information contained in our DNA. She creates 3D-printed faces based on genetic material isolated from stray hairs, cigarette butts, and chewed gum left behind in New York City streets. The mask-like disembodied faces are computer generated composites from a database of photographs, selected and individualized based on information from just three genetically encoded factors that Dewey-Hagborg amplified and sequenced from the DNA she isolated from the samples: eye color, chromosomal sex, and mitochondrial haplogroup.

Stranger Visions hair samples, by Heather Dewey-Hagborg

As “portraits” generated from only this information, these faces aren’t stable images resembling an actual person, but rather objects that represent the impossibility of separating nature from nurture. Despite the strength of “family resemblance,” determining someone’s facial structure from genes alone is currently impossible, with very few single gene loci consistently corresponding to any distinguishing characteristics and the influence of many developmental and environmental factors. Even determining if someone has attached vs. unattached earlobes, one of the classic classroom examples of simple Mendelian heredity, is actually more complicated than can be explained by the action of a single gene. When multiple genes interact with each other and with external factors to create a spectrum of phenotypes, finding a one-to-one correspondence between sequence and physiognomy becomes statistically unlikely. For Dewey-Hagborg, interpreting the sequence of genes coding for something as straightforward eye color showed just how difficult it is to define someone’s characteristics through DNA sequence alone. Quoted in an article about the piece from Fast Company, Dewey-Harborg says that in some cases the DNA results showed that “There’s an 80% chance that this person has brown eyes and 20% chance that they have green eyes. You have to make that call.”

Gender as determined by chromosomes or ethnicity defined by mitochondrial ancestry is of course much much more biologically and socially complicated than eye color. Sex, gender, race, and ethnicity are demarcated by culturally defined boundaries in spectrums of biological characteristics influenced by countless genes and even more social and environmental factors. There are many layers of assumptions built into the genetic and computer models that were required to design faces that represent someone via their chromosomes and haplgroup. Again, from the Fast Company article:

“In order to generate a face, you need to teach a computer what a face is,” Dewey-Hagborg explains. But how do you tell a computer what something as complicated as a human’s gender or race looks like?…Dewey-Hagborg calls the process “problematic,” and she says she hopes her work provokes more of a discussion around subjectivity in both DNA analysis and computer modeling of faces. “It does involve, essentially, creating a stereotype, and generating faces based on those stereotyped ideas, so that’s something I’m hoping to question with this work.”

Given these challenges, it’s surprising (ok, maybe not that surprising) to see some of the ways that this piece is being interpreted. The headline of the Fast Company article itself claims that “These 3-D Portraits Were Created Using Only A Person’s DNA,” ignoring the many assumptions and stereotypes included in the model and explicitly discussed in the article. Even more surprising is a quote in the Wall Street Journal’s article on the piece from Ellen Jorgensen, the director of Genspace, where Dewey-Hagborg did the genetic work for the piece. Jorgensen says, “It really gets you when you realize someone can pick up a hair on the street and know more about you than a doctor can, conceivably.” It’s a big leap from the ability to sequence genes in a hair to the ability for those sequences to say so much about someone. Despite many notable cases of genetic variations starkly affecting health, for most people, health is usually much more the result of where you were born and your socioeconomic status than the genes you were born with.

While Dewey-Hagborg’s piece highlights some of the difficulties of extrapolating from DNA to individuals, Koby Barhad’s piece All That I Am playfully demonstrates the inseparability of nature and nurture by trying to do the opposite–using “nurture” to recreate Elvis Presley in a mouse.

All That I Am, by Koby Barhad

Like Dewey-Hagborg’s work, Barhad’s speculative project begins with the genetic analysis of one of Elvis’ hairs, purchased from eBay. Sequences associated with behavioral characteristics could theoretically be cloned into a genetically modified mouse, making a chimeric Elvis-mouse. Because genes alone didn’t make Elvis who he really was, Barhad also designed a complex mouse habitat that would somehow reflect different periods in Elvis’ life and relationships, creating an environment for the proper expression of Elvis’ genes. An article in We Make Money Not Art describes each stage of the mouse’s travel through the Elvis habitat:

Some of the main themes that the designer identified as being influential in making Elvis are: his close relationship with his mother (and so the mouse is given a mouse companion), being the victim of bullying when he was a child (in this cage, the mouse is submitted to external stimuli that frightens it), the discovery of his talents, becoming a star (features a distorted mirror that makes the mouse appear bigger), the Graceland period (in every place the mouse pokes nose, it gets a positive reaction in the shape of food or toys and keeps filling the cage to the point making it anxious), the army, the death of mum, the divorce from Priscilla are events that are represented by a cage that functions as an isolation chamber. The last cage embodies the last three years of the life of Elvis, when he worked himself to death, that period is represented by a little treadmill at the top of the cages. The mouse would run, run, run and eventually fall down.

Koby didn’t push the project to the point of having a genetically engineered mouse go though all these cages, that would have been far too cruel for the animal but his project [does] make us wonder if one day it will be possible to enter a new kind of pet shop and ask for a dog, a fish or a cat that no only has the same genetic traits as a pop icon or a historical figure but also behaves like them.

What made Elvis who he was? What does it mean for a mouse to behave like Elvis? The absurdity of the Elvis mouse and the uncanniness of the DNA-inspired faces give us opposite but interlinked extremes of nature and nurture, highlighting much more than concern with DNA privacy and ownership, or even DNA-based marketing. We should be fighting to protect our genetic privacy, but we should also be fighting the idea that our DNA is somehow fundamentally who we are.

As theorized by medieval and early modern intellectuals, wonder was a cognitive passion, as much about knowing as about feeling…The passion of wonder had a mixed reception among late medieval and Renaissance natural inquirers, scorned by some as a token of ignorance and praised by others, following Aristotle, as “the beginning of philosophy.” All, however, agreed that wonder was not simply a private emotional experience but rather, depending on context, a prelude to divine contemplation, a shaming admission of ignorance, a cowardly flight into fear of the unknown, or a plunge into energetic investigation…Since the Enlightenment, however, wonder has become a disreputable passion in workaday science, redolent of the popular, the amateurish, and the childish. Scientists now reserve expressions of wonder fo their personal memoirs, not their professional publications. They may acknowledge wonder as a motivation, but they no longer consider it part of doing science.

Mirabilis jalapa

Wonder, however, has a way of sneaking its way into the scientific record. Take Mirabilis jalapa, a plant from South America with bright, multicolored flowers. The etymology of its genus name is the Latin word for wonderful, amazing, miraculous, or remarkable. Embedded in the scientific name of the flower is the amazement of the taxonomist marveling at the colorful flowers, exclaiming “Oh! How wonderful to behold.”

At the species level there are more than 1000 plants and animals with the species designation mirabilis, from the nursery web spider Pisaura mirabilis to the longjaw mudsucker fish Gillichthys mirabilis to this crazy looking sea slug. Many of these species were named and identified in the mid 19th to early 20th century, when scientific reports were a little more florid than they are today and the remarkable nature of some of these creatures could be remarked on directly, though still scientifically detached. The identification of the mushroom species Boletus mirabilis for example, published in the journal Mycologia in 1912 states, “this remarkable species was found several times in the vicinity of Seattle on the ground in woods. It is one of the most difficult species to preserve, owing to its extremely juicy consistency.”

Other remarkable species get the mirabilis label after some more drawn out taxonomic confusion. In a letter to the Proceedings of the Linnean Society in 1861 (PDF), the Austrian botanist Friedrich Welwitsch reported a most unusual plant in the desert of Southwestern Africa:

[T]he coast rises to a height of about 300 to 400 feet, forming a continuous plateau, extending over six miles inland, as flat as a table. This tabular elevation…[is] clothed with a vegetation which, though scanty, consists of plants of the highest interest; among them a dwarf tree was particularly remarkable, which, with a diameter of stem often of 4 feet, never rose higher above the surface than 1 foot, and which, through its entire duration, that not unfrequently might exceed a century, always retained the two woody leaves which it threw up at the time of germination, and besides these it never puts forth another. The entire plant looks like a round table, a foot high, projecting over the tolerably hard sandy soil; the two opposite leaves (often a fathom long by 2 to 2½ feet broad) extend on the soil to its margin, each of them split up into numerous ribbon-like segments. As I bring some specimens of this wonderful plant to Europe…it will suffice just now to append to the foregoing a short notice of it in the technical language.

At this point Welwitsch continues on to describe the plant’s characteristics entirely in Latin, including giving his suggested genus designation of Tumboa, after the word used by the local population to identify the plant. After it was realized that “tumbo” was a more general word for “plant,” rather than a specific word for this plant in the local language, the amazing specimen was renamed after Welwitsch (another taxonomic trend) and became Welwitschia mirabilis (h/t to one of the remarkable undergrads in my lab who introduced me to this species during the lab’s “plant of the week” discussion).

Welwitschia mirabilis

Proteus mirabilis

Many fewer microbes share the species name mirabilis than multicellular organisms, but one is—in my opinion—particularly remarkable. Proteus mirabilis is a swarming bacteria that can spread in waves over a petri dish and sometimes causes urinary tract infections. The genus was discovered in 1885 by Gustav Hauser during an analysis of the microbes living in a piece of rotting meat. Hauser named the bacteria Proteus after the shape-shifting god in Homer’s Odyssey because of its ability to differentiate into swarming and stationary cell types. Interestingly, the genus includes the miraculous P. mirabilis as well as the extremely similar but less remarkably named P. vulgaris.

When memorizing species names for biology class or working with model organisms in the lab we’re usually focusing on getting all the syllables in Caenorhabditis elegans rather than thinking about the elegance of nematodes (let alone the elegance of the hundreds of other species named C. elegans). Genus and species names tell a story about the identification and classification of organisms as scientists try to squeeze the messiness of nature into the organized drawers of natural history museums and online databases. These taxonomic stories can tell us about the ego and personality of the scientist, the place where the organism was found, or perhaps something about the magic of encountering a new organism.

While the New Scientist article about the implications of the Neandertal genome was pessimistic on the short-term prospect of “resurrecting” Neandertals, George Church himself has more recently made news by suggesting how such a future scenario might work in his recent book Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves. In the book’s introduction, Church (with science writer Ed Regis) writes:

You’d start with a stem cell genome from a human adult and gradually reverse-engineer it into the Neanderthal genome or a reasonably close equivalent. These stem cells can produce tissues and organs. If society becomes comfortable with cloning and sees value in true human diversity, then the whole Neanderthal creature itself could be cloned by a surrogate mother chimp–or by an extremely adventurous human female.

While the news storm has made it seem like this is an active area of research in the Church lab, George has been clear that his statements were meant to spark discussion about the myriad social and ethical aspects of such an endeavor given its possible technical feasibility, not to recruit any surrogate mothers to a study.

Ethical concerns have been paramount in the development of reproductive technologies, mammalian cloning, stem cell biology, genomics, and synthetic biology in recent decades, and the question of Neandertal resurrection would certainly engage with the ethical concerns arising from all of these fields. For now, I want to address just one very small social aspect of Church’s statement, and how it affects the practice of synthetic biology. For Church, the prospect of cloning Neandertals is in large part about diversity. In the Der Spiegel interview, Church contradicts the interviewer when asked whether it would be ethical to create a Neandertal for the sake of curiosity. Church says:

Well, curiosity may be part of it, but it’s not the most important driving force. The main goal is to increase diversity. The one thing that is bad for society is low diversity. This is true for culture or evolution, for species and also for whole societies. If you become a monoculture, you are at great risk of perishing. Therefore the recreation of Neanderthals would be mainly a question of societal risk avoidance.

For such a technological commitment to human diversity, Church’s book tells a very different story about diversity amongst the practitioners of synthetic biology. Of the approximately 160 names mentioned in the book’s index, only 10% are the names of women, and only one of those names is a practicing academic synthetic biologist, involved in the founding of one of Church’s many startup companies. The “extremely adventurous human female” mentioned in the context of Neandertal surrogacy (and easily replaceable by a chimpanzee) therefore represents a significant percentage of all the women mentioned in the whole book.

This observation points at not only the continuing lack of women and minorities in science, engineering, and technology, but at perhaps a deeper problem about the culturally perceived character of the engineer and the growing mythology surrounding well-known synthetic biologists. Craig Venter, a major figure in genomics, both natural and synthetic, and no stranger to the myth-making of scientists, wrote about how he sees himself in response to the 2013 Edge question “What *Should* We Be Worried About”:

As a scientist, an optimist, an atheist and an alpha male I don’t worry. As a scientist I explore and seek understanding of the world (s) around me and in me. As an optimist I wake up each morning with a new start on all my endeavors with hope and excitement. As an atheist I know I only have the time between my birth and my death to accomplish something meaningful. As an alpha male I believe I can and do work to solve problems and change the world.

As we write the history of synthetic biology and the pioneering scientists and engineers who are rewriting the code of life, it is these “alpha males” who are written as the adventurous creators of new life forms and “adventurous females” that are the anonymous vessels for their DNA-based creations. For Venter’s “Synthia,” the chemically synthesized genome came to be seen as “life,” while the host cell whose membrane, cytoplasm, and proteins “booted up” the inert DNA is but the “chassis.” In the potential design of a Neandertal baby, a human being is the “chassis” organism, the “donor cell” for a transplanted genome, the unpredictable host context that can confound synthetic biology designs.

In such scientific imaginings we get futuristic versions of some very retrograde cultural ideas about gender. While I know that these men don’t actually think of the women in their lives and in their labs as simply vessels for DNA (some of my best friends are male synthetic biologists!), I also know that leaving these kinds of statements unexamined can lead to an environment that makes it harder for women working in these labs, harder for women to be chosen as speakers at quantitative synthetic biology conferences, and harder for women to be promoted and advance in their field. Before we discuss the potential of cloned Neandertals to boost human diversity, we must first consider our role in boosting the diversity of our labs, companies, faculty, and conferences with the humans that actually exist.

Most scientists consider crystal healing, with its “energies” and “vibrations” as New Age mumbo jumbo, but there’s another way to think about these crystals that has nothing to do with chakras. Different colors and shapes of crystals are supposed to represent different things, from better health to increased financial security, and wearing a crystal that matches these goals is a way of clearly stating your intentions. Crystals are placebos that you can wear as jewelry, constantly reminding you of your goals, whether they are to be more mindful and keep a clearer head, better monitor your health or your bank account.

So then activity trackers are like crystals, not because of any magical energy that emanates from certain arrangements of silicon atoms, but because they are both physical manifestations of intention. For activity trackers, the intention is obvious: increased physical activity. As we reach the time of year where most New Year’s resolutions are abandoned, these devices and their online rankings and achievement badges can help keep us on track. Psychology studies have shown that having clear goals, rewards rather than punishments, and supportive friends can all help in achieving health-related resolutions, and activity trackers combine all these into a device that clips onto your belt and reminds you to take the stairs.

Tracking your footsteps and calorie intake, monitoring fork movements, tracking mood, and the many many other ways to quantify yourself are about much more than the information you can get from the data itself. The devices, trackers, apps, and spreadsheets are talismans meant to influence health and wealth through numerical mindfulness, externalizing and amplifying intentions. Just like there’s nothing magic to the energy of crystals, there’s nothing magic about the data streams coming from these devices. Their power is in how these data streams and energy flows can convince us to change.

The Slow Fork

I’m going to reserve judgement on the merits of the smartfork, invented by the French company Slow Control and marketed by HAPILABS, but I think it’s interesting to look at this cutlery innovation in the context of fork history, from its origins in Ancient Egypt to the two-in-one spork and beyond. Forks weren’t always the well-designed ergonomic tools for shoveling food into your face that they are today. In the 11th century, a Byzantine princess marrying a Venetian aristocrat scandalized Venice by using a fork to eat at her wedding feast. A member of the local clergy condemned this uptight behavior, saying “God in his wisdom has provided man with natural forks—his fingers. Therefore it is an insult to him to substitute artificial metal forks for them when eating.”

After the princess’s untimely death, forks remained unpopular in Europe, but eventually spread throughout the continent, gaining popularity over the centuries. In “A Feast for Aesculapius: Historical Diets for Asthma and Sexual Pleasure” in the Annual Review of Nutrition, historian Madeleine Pelner Cosman describes one aspect of the slow cultural and religious shift in fork etiquette and its relationship to the sensual experience of food:

Almost all medieval feast foods were conveyed to the mouth by elaborate, and often elegant, finger choreography…However, both pinky fingers were extended, never touching food or gravy or sauce, reserved as spice fingers. Dipped into the salt, sweet basil, cinnamoned sugar, or ground mustard seed, then raised to the tongue, the spice fingers displayed a feaster’s digital finesse while adding another sensual pleasure: touch of food’s texture.

Some modern polite extensions of pinky fingers, serving no physical pur­pose, are cultural remembrances of medieval spice fingers. In fact, a medieval clerical encouragement for use of the fork was to eliminate the pleasure of touch. The fork was generally ignored until the late 16th century as a super­fluous and foppish metallic intrusion between sensual food and willing mouth. Using a fork reduced the “feel” of food. As St. Thomas said, in matters of food and sex, gluttony and lust are concerned with the pleasure of touch.

Given the ceremonial, spiritual, and sensual importance of food-delivery technologies in Europe and around the world, what does the robo-fork say about our moment in time? How will we eat in the future?

Anthropologist Heather Paxson’s excellent new book, The Life of Cheese: Crafting Food and Value in America explores the microbiopolitics of cheese production and the macropolitics of culture, economics, and policy of artisanal foods. Through participant observation in small dairy farms in Vermont, Wisconsin, and California, Paxson highlights the work that goes into making and marketing handcrafted, artisanal cheese, a “post-pastoral” and “post-Pasteurian” product that blurs the boundaries between nature and culture, urban and rural, production and consumption, and “itself exemplifies cultured nature, the product of human skill working in concert with the natural agencies of bacteria, yeasts, and molds to transform a fluid made by ruminant animals.”

Handcrafted cheese brings the symbiotic practices of cheesemaking “back to the future,” reintroducing techniques that have been marginalized and largely eliminated during the modernization of industrial agriculture and food production over the past century. Through artisanal cheese, producers and consumers challenge these industrial imperatives, leading to diverse and exuberant cheeses and cheese-consumption. Historian of science Steven Shapin discusses similar tensions that industrialization of cheese has brought to French cheese cultures in a review of Camembert: A National Myth for the London Review of Books. Laws governing food safety and the economics of industrial efficiency and product consistency transformed the local production of Camembert to a centralized and highly mechanized factory process:

Robots with 20 arms now mimic traditional human actions, assuring hygiene and dependability, and, of course, reducing cost: the skilled women have largely disappeared from present-day Norman factories, the five largest of which turn out about 1.5 million Camemberts a day, employing a workforce of fewer than 500. ‘No cheese here has been touched by human hands,’ the manager of one of these factories boasts.

In handcrafted cheese, human hands are a crucial part of the process, contributing to the slow food goodness of the final product. Paxson relates a very different story of cheese production to that of the robotic Camembert factory:

Rather than follow a preprogrammed procedure, artisan cheesemakers reach into the vat, thrusting fingers into coagulating curd to ascertain when it is ready to be cut and drained from the whey. Artisanal manufacture represents an extension of the craftsperson’s body into the productive process rather than its replacement by computer-programmed machinery.

For other artisan cheese makers, hands aren’t important only for their interaction with the physical properties of the curd, but also for the potential microbial contribution of the human skin. A 2008 New York Times article quotes a Spanish cheesemaker on the importance of her hands to her cheese’s flavor:

“The reason my cheese is so delicious,” said Ms. Amieva, without a trace of modesty, “is my hands.” She turned her meaty, callused palms over for inspection. “The natural bacteria in my skin makes the cheese more flavorful.”

Stirring Cheese Curds--Photo by Rachel Dutton

The connections between the skin and cheese, both in ecologies of production and ecologies of microbes, was the primary inspiration for my project with Sissel Tolaas for Synthetic Aesthetics. Paxson’s earlier work on the microbiopolitics of human and microbial cultures in raw milk cheese (PDF) also had a huge influence on us as we made our own cheeses from microbes cultured from our own skin. In The Life of Cheese, Paxson looks further at how a new awareness of the microbial inhabitants of cheese is contributing to the production and identity of artisanal cheeses.

Cheese SEM from Rachel Dutton and the Harvard Microbial Sciences Initiative

Microbiologists and cheesemakers are increasingly interested in the microbial inhabitants of local environments and the unique communities that shape a place and its cheeses. Microbial terroir emphasizes the importance of the unique biological geography of a place, using the identity of microbes to craft an identity for a brand of cheese. While the microbial similarities of cheeses from different regions are often more striking than their differences (like the similarities between cheese and skin microbes), identifying cheeses through their bacteria is a fascinating way to get to know the microbes in our lives. Microbial knowledge can add to notions of healthfulness, like the probiotic Lactobacillus that curdles milk, or to the romantic image of a cheese, like the Brachybacterium Rachel Dutton found in the rind a Vermont cheese, “an unusual microbe that has been found in Arctic sea ice, on human skin, and in an Etruscan tomb.”

Microbial Terroir--Ben Wolfe

Terroir is of course much more than just microbes. The epigraph to Paxson’s fascinating chapter on place and taste is from Brad Kessler’s Goat Song, and shows how tightly the idea of terroir is tied to artisanal cheesemaking: “Every raw-milk cheese is an artifact of the land; it carries the imprint of the earth from which it came. A cheese–even a fresh chèvre–is never just a thing to put in your mouth. It’s a living piece of geography. A sense of place.” Creating and cultivating a sense of place for American artisanal cheesemakers means not just the microbiology, geography, and climate of the land, but importantly, the ethics of the farm’s practices, from the stewardship and maintenance of the land to the working conditions for farm employees. Paxson shows how the ethics of food and eating become embedded in the taste of good cheeses through the story of her experiences at a craft cheese tasting:

[The cheese makers] went on to describe [the] newly installed methane digester, apparently without worry that we would register suggestive hints of manure in the odor and taste of the cheese. Instead, we were meant to taste the goodness of greenhouse gas mitigation. Something is happening here to taste education…

Why does cheese taste good? It is not merely because cheese is a food rich in fat and salt, nor even that well-made artisanal cheese reflects the taste of clean milk, healty animals, and fresh pastures. The festival’s taste education suggested that consumer enjoyment of a cheese can be heightened by knowing that the methods of its fabrication helped to accomplish other ends as well–in keeping agricultural land out of the hands of developers, or in the organic remediation of industrially damaged land, or in ssutaining the ability of a fourth generation to continue farming as a family. Here, eaters with “good taste” are enjoined to taste the social place of a “good” cheese–or, perhaps, the “goodness” of a place-based cheese.

The ethics and politics of locally produced foods, of organic agriculture, of American farmstead or imported raw-milk cheeses are all symbols of a very privileged kind of eating, but with their own challenges and their own complex cultural contexts. The Life of Cheese shows us that “All commodities have biographies or ‘social lives’ of production. In finished commodities, these backstories are obscure to consumers. In the place of labor and indirect costs, new stories are written for commodity goods through corporate branding and marketing.” Moreover, uncovering the many complex practices of artisanal cheesemakers, both in cultivating microbes and cultivating a sense of place, shows that “‘nature’ as we know it is clearly a product of human activity,” that “industrial ecologies of cheese production are no more or less ‘natural’ than farmstead ecologies; they are differently cultured.” There is no single “right” way to produce food, no single ideal of “natural” food, but The Life of Cheese is one way to better understand that food is never just a thing to put in your mouth.

The microbes are super cute, and it also has one of the best anthropomorphized earthworms I’ve ever seen:

I of course also loved the chapter on beneficial microbes and gut flora:

And toe fungus!

While there’s a lot of silliness that happens, the characters are very serious about microbes:

There’s even a live action adaptation with adorable CGI microbes that cheer “Let’s brew!” that you can watch on YouTube!

Many scientists and philosophers have discussed the role of beauty in science, in particular when judging competing theories in physics. Glenn Parsons reviews these arguments and looks at the role of aesthetics in chemistry and biology– in the representation of molecular structure, and in the form and function of molecules. He cites Francis Crick calling DNA ‘‘the molecule which has style,’’ for the simplicity and elegance of how the structural form of the double helix reflected the replicative function of the molecule.

For many science lovers, the aesthetic value of DNA lies in the modernist design maxim “form follows function,” but in his review “Aesthetics in Synthesis and Synthetic Biology,” Steven Benner argues that DNA, like other products of natural selection, is more of a “hack” than a perfected form:

Again and again, detailed inspections of living systems have taught biologists that Darwinian evolution generally has not delivered elegant solutions, aesthetic solutions, or even simple solutions, to challenges presented by the need to remain alive. Instead, in its underlying detail, biology reflects four billion years of random variation, historical accident, flawed adaptation, and partial optimization. Thus, biology (at least as known to biologists) is better described as a ‘hack’. In its details, life resemble less an aesthetic, and more something expected from generations of computer nerds re-writing code originally written for another purpose, at a different place, and with imperfect skill…

[L]ike so much else in biology, the aesthetic beauty of DNA comes only from artistic renderings of the molecule that make visible a particular that cannot, in fact, be seen at all. The colors in those renderings come from wavelengths of light that are 1000-fold larger than a DNA molecule itself. And as often as not, the molecule is abstracted by, well, things that look like Legos.

To have properly designed DNA, Benner argues for a modified set of 12 bases with improved symmetry and utility. To philosophers of aesthetics like Glenn Parsons, however, utility and function are not necessarily part of the aesthetic value of an object or a work of art, and he argues that the “molecular delights” that a chemist sees are not always in the realm of the aesthetic per se. Despite these technical and philosophical arguments, there can be aesthetic pleasure in the experimental design and the molecular representations that advance our understanding, that let us see the invisible, from the first X-ray crystallography images of DNA sixty years ago to the first electron microscope photographs of DNA published this week.

Scientific images and representations can translate different kinds of sensory information into data that we can visualize, parse, understand, and share. This scientific synesthesia influences how we define scientific information and is influenced by sensory and aesthetic factors, from line drawings or ball-and-stick chemical structures to colorful paintings of protein structures.

We need images and models of the invisible world in order to understand it, and Emily Candela‘s review “Assembling an Aesthetic” looks at the aesthetic and sensory experience of touch and its interaction with protein crystallography. Structural biologists and crystallographers use drawings and computer renderings as well as physical models and more recently immersive 3D virtual environments to explore protein structures. Like work by anthropologist of science Natasha Myers, who has studied the molecular embodiment of protein structures in the practice of crystallography, Candela explores the translation of nanoscale protein data to human-scale physical models to be assembled, touched, and experienced:

Touch takes us into domains that are difficult to access through vision alone – those of material and process…Technologies are also extending tactile possibilities, as in the case of scanning probe microscopy’s ‘process of touching the nanoscale.’ In fact, ‘process’ is a key word, for it is where such an exploration of touch, embroiled as it is in the ‘daily work’ of science, leads. An aesthetics of touch can reveal those moments preceding relative certainty, during testing, when matter is in transition and failure remains an imminent possibility…

Many of the processes brought up in research on models, from their manipulation to ‘dancing’ a protein, are among those facets of scientific research that Maura Flannery, writing on the aesthetics of biology (PDF), comments, ‘are not considered under the ‘Methods’ section’ of most scientific papers, ‘but they might well be among the most important methods that distinguished researchers use in their work’…Such an aesthetic can also have an impact beyond the walls of scientific research institutions. Much, but not all, ‘communication of science’ outside these walls is concerned with conveying knowledge that is in a relatively conclusive state. The aesthetic outlined here, on the contrary, which takes process as its starting point, engages instead with the inconclusive, contingent, messy, and ongoing…It gets at aspects of scientific practice that are difficult to express (especially to non- scientists) with an illustration or photograph – those qualities, movements, moments of contact and material change, which in fact take after the model, as ‘unfolding’.

The aesthetics of assembly and the molecular delights of chemical aesthetics also play a role in the bottom-up synthetic biology of protocells. Michele Forlin, Roberta Lentini, and Sheref Mansy explore “Cellular Imitations” in their review, discussing the subjectivity of the line that divides the living from the nonliving:

There is no satisfactory definition of life. Nevertheless, it is generally agreed that biological parts alone are not alive, but the properties that emerge from their cooperation are collectively referred to as living. Without clear criteria that can be objectively fulfilled for a system to be considered living, the available path forward is simply to build systems that imitate the common features of life. For example, living things generally reproduce, move, adapt to changing environmental conditions, and interact with each other. Of these features of life, reproduction has attracted the most attention, which is understandable since replication and evolution form the foundation of life as we know it. However, a machine, even a machine that is built with natural biological parts, that is programmed to copy DNA and to split into two probably would not be confused with a living system. Perhaps this is because the decision of whether something is alive or not is the result of a subjective comparison between what was previously agreed upon as living with the system in question. The successful mimicking of a single trait when compared against the complexity of a living cell would be perceived as an inadequate representation of cellular life.

Interestingly, the errors and mistakes of evolution–the “hacks” that diminish the aesthetic value of biology for some of the other contributors to the issue–become a crucial part of the aesthetic and and subjective definition of life for the protocell engineers:

Additionally, the programming of repetitive behavior in itself misses another aspect of life, which is error. Cellular function is largely based on stochastic processes and even the fundamental event of genomic replication proceeds with error. A system that mimics a trait of life too well, probably would be perceived more as a machine rather than life.

If the objectivity of machines is not life-like enough for true synthetic life, the human subjectivity involved in deciding when something is alive is not scientific enough for protocell science. Forlin et. al. discuss instead the possibility of constructing “cellular Turing tests,” where “the responsibility of determining whether something is alive or not [is moved] away from us and towards natural cells” (PDF). Scientific objectivity depends on the tools that can interface between the human senses and the object of study, the machines that can translate the natural world into the visualizations, models, and datasets that we experience, aesthetize, and interpret. An exploration of the aesthetic and sensual in science and technology exposes the beautiful fuzzy edges of scientific practice. We can add many layers in between human subjectivity and scientific objects, but there is always something human and beautiful in science.

Our other senses don’t have as clearly defined ranges of perception. We can’t give a smell, a taste, or a texture a number the same way that a color or a tone can be defined by a wavelength, but a fascinating recent paper shows that by mixing many different smelly molecules at equal intensities, our perception of the odor will converge on “olfactory white.”

The researchers created this strangely neutral smell from different mixtures of up to thirty odors, chosen from a set of 86 molecules that represent a wide range of the kinds of things that we can smell. Human “olfactory stimulus space” contains thousands of molecules, from the fragrant and floral to the putrid. We can distinguish and name many smells, but odors don’t map neatly onto a one dimensional spectrum. Sampling the multidimensional stimulus space of odors requires a much more complicated mapping of the smell universe. The figure on the left shows the position of the 86 molecules within two maps of olfactory stimulus space. The first is based on the way that we perceive odors (perceptual space, A) and the second based on the chemical structures of the molecules (physicochemical space, B).

The perceptual map is built with data from Dravnieks’ Atlas of Odor Character Profiles of 144 different molecules. Each smell was compared by 150 professional noses against a list of 146 different odor descriptions like “fruity” “etherish” “decayed” or “seasoning for meat.” This enormous multidimensional dataset represents the way that we experience and name olfactory space. Using principal component analysis this 146 dimensional space can be simplified into the two dimensional projection that represents the “distance” between the smells of the different odors in this space.

Physicochemical olfactory space is both more objective and more dense than the map of perceptual space, built from 1514 descriptions of the chemical structures of 1565 odorant molecules. These descriptions include things like the number of atoms, the presence or absence of specific chemical groups, and the weight and shapes of the molecules. The shape of a molecule isn’t usually enough to predict its odor but there are some correlations that can be made between the 1514-dimensional space and other perceptual maps, based on professional descriptions or even brain activity.

The position of isoamyl acetate (banana oil) vs. skatole (a strong fecal odor at high concentrations) in different representations of olfactory space

Maps of brain, rodent olfactory bulb, or odor receptor activation in response to different odors represent a different kind of olfactory space, one mapped and coded in the structure of the sensory organs themselves. The activity map of the rat olfactory bulb for increasing concentrations of isoamyl acetate (banana smell) shows the regions of cells activating and sending signals to the brain saying “banana!”

I’m curious what these activity maps would look like for “white smell,” although the authors suggest that the perception may not be caused by the wide activation that characterizes the perception of white light or white noise. Whereas white light equally activates the three color receptors of the eye, using electricity to stimulate the olfactory system leads to no sensation of smell at all rather than the “chemical” “fragrant” or “perfumey” scent of white smell.

These maps provide an interesting way to categorize and discuss smells, but the full extent of olfactory space remains unknown, ready for explorers to build more many-dimensioned maps of smell experiences. You can play around with the olfactory stimulus maps at the Sobel Lab website, look at the databases of rodent brain activity maps, and begin smelling the world more critically and enthusiastically today.

Looking through Hans Laube’s patents for Smell-O-Vision and more recent technologies for delivering odors as part of an immersive multimedia experience, I was struck by the simple weirdness of smell as media. We’re used to media that are transmitted through sight and sound, but smells are not just waves and photons, they are volatile molecules, chemicals in the air that are “broadcast” to the nose, transmitted very differently from the images and sound of the movie. Storing, emitting, targeting, and synchronizing smells with precise timepoints in a film requires vials, heaters, motors, fans, and maybe even masks, and the behavior of smells in a large space and how they reach the audience’s noses is much harder to control than the pictures on the screen.

Shortly after the first (and last) release of a Smell-O-Vision movie, Scent of Mystery, where the murderer was revealed by the smell of his pipe tobacco, other engineers experimented with more individualized immersive media experiences. The Sensorama was Morton Heilig’s vision of the “cinema of the future,” showing a film of a ride on a motorbike with a vibrating and tilting seat, fans blowing wind in the viewer’s face, and the aroma of flowers or baking pizza as the rider passes a garden or an Italian restaurant. However, like Smell-O-Vision before it, Sensorama failed to attract funding and is now merely a mechanical curiosity in the early history of virtual reality.

Smell was rarely part of virtual reality apparatuses, but a 1997 patent shows how fragrances could be incorporated into “virtual reality shows” or computer games to create a more fully realized and embodied sensory experience.

A later patent citing the virtual reality system imagines digital release of smells in an immersive device for therapeutic purposes:

These virtual reality systems require encoding scents as digital information, bits that must be converted to the atoms of odor molecules that will travel through the helmet’s tubes. Digitally sensing, encoding, and “compressing” chemical data, from the millions that could be present in the air, to the thousands that we can smell, to the few that are the primary factors that influence a scent is an extremely difficult problem. Technologies that allow computers to sense and interpret smells have primarily focused on their application in industrial food production, medicine, and environmental sensing, but some researchers are using these methods to develop tools for digitally transmitting odor information, to make a “Smell-O-Internet”.

The “resolution” of smell information in these these multi-sensory media experiences has gone from the single smell of rose oil in 1906 to about a dozen smells in 1960′s analog Smell-O-Vision, to approximately 100 “primary” smells that engineers hope can be mixed to make many more complex scents in digital products like iSmell from the early 2000′s.

Even as the technology improves the weirdness of smell remains, and the social reality of odors keeps the technology at the fringes. It might be nice to smell a scene of baking cookies or a photograph of a strawberry, but do we really want to smell the internet?

Synthetic biologists, however, talk about design all the time. We design genetic networks and metabolic pathways and we try to understand the logic of how cells have evolved to develop better “design principles.” We use evolution to help us optimize enzymes and pathways, designing schemes and selections for directed evolution, and we worry about what will happen to the products and technologies built with synthetic biology if they continue to evolve.

Variation, mutation, and evolution of a product that is made by or actually is a living organism has to be carefully managed and controlled in biotechnology and industrial food production, and will play a large role in future synthetic biologies. But what about other kinds of human-designed products? Can concepts from evolution ever apply to the nonliving world?

I’ve been listening to old episodes of the wonderful podcast about design 99% invisible, which did a short episode about a year ago on an evolutionary leap in the design of the toothbrush. They talked with one of the designers who outlined their process of “mutation,” where they prototyped many variants, changing the shape and thickness of the handle and the position and angle of the bristles, and the process of “selection,” testing the variants with consumers and having them choose the one they liked best. The product is shaped by its environment and its “heredity,” alterations happen around the basic format of handle and bristles, and designs are selected based on their ergonomics, function and style. The environment can also be shaped by the product, affecting our overall oral hygiene and by simply requiring different shaped toothbrush holders.

An interesting essay from Next Nature looks at a similar “evolutionary” process in the design of the razor and “natural selection” by buyer behavior and markets. The section on “Evolution, but not as we know it” I find particularly interesting, and I quote it here at length:

The evolution of the razor, by Next Nature

Of course there are also arguments against this evolutionary view on the development of razor technology – so lets get both sides of the coin here. The most common objection is that “people play a role in the process, so it can’t be evolution.”

This reasoning is tempting, however, it also positions people outside of nature – as if we are somehow placed outside of the game of evolution and its rules don’t apply for us. There is no reason to believe this is the case: after all people have evolved just like all other life. The fact that my razors are dependent on people to multiply is also not unprecedented. The same is valid nowadays for many domesticated fruits like bananas as well as a majority of the cattle on our planet. Moreover, we see similar symbiotic relationships in old nature: just think of the flowers that are dependent on bees to spread their seeds.

Another objection might be that my razors cannot be the result of an evolutionary development because they are made of metal and plastic and not a carbon–based biological species. Underneath this argument lies the assumption that evolution only takes place within a certain medium: carbon–based life forms. A variation of this argument states that evolution only takes place if there are genes involved – like with humans, animals and plants. This way of thinking exemplifies a limited understanding of evolution, as it is a mistake to constrain it to a certain medium rather than to understand it as a principle. In fact the genetic system of DNA underlying our species, is itself also a product of evolution – DNA evolved from the simpler RNA system as a successful medium of coding life. There is no reason why evolutionary processes could not transfer itself to other media: Richard Dawkins already proposed ‘memes’ as a building block of cultural evolution, whereas Susan Blackmore suggested ‘temes’ as building blocks for technological evolution.

In the end, the question we should ask ourselves: are the environmental forces of economy and technology, at least equally or perhaps even more important for the shaping of razor technology, than the design decisions made by the ‘inventors’ of the individual models. I am pretty sure this is the case and hence I propose to consider the development of razors as a truly evolutionary process – not metaphorically, but as reality. The species it brought into being we will call: Razorius Gillettus. It is just one of the numerous new species emerging within the techno-economical system – and it is evolving fast.

Anthropomorphizing evolution is inappropriate for many reasons, and we should be careful about “evolutionizing” human designs. Exploring evolution in design shouldn’t imply design in evolution and shouldn’t be used to naturalize planned obsolescence and the excesses of consumer culture. Rather, understanding better the interrelationships between ecology, technology, and human societies–how we co-evolve with our designs and with our environments–will hopefully lead to technologies that are better adapted for the future.

Leslie Vosshall’s Laboratory of Neurogenetics and Behavior at Rockefeller University studies how complex behaviors are influenced by the chemical senses in organisms ranging from mosquitoes to humans. In order to better understand how human odor perception varies, both within individuals at different times and between different people, the lab asked nearly 400 New Yorkers to describe and rate the intensity and pleasantness of 66 different smells, at the same time collecting demographic data (significantly more diverse than the typical study of undergraduate psychology students) as well as data about their eating habits and perfume usage, finding many instances of variability in how people perceive smells. The lab recently published their extensive survey titled “An olfactory demography of a diverse metropolitan population” in the open-access journal BMC Neuroscience. They’ve also made their data freely available (you can download the huge excel file here) for further analysis or data-mining.

Odor Descriptions from "An olfactory demography of a diverse metropolitan population"

This study has been ongoing for several years, and two years ago inspired Nicola Twilley’s wonderful Scratch-and-Sniff Map of New York’s olfactory psychogeography. Rather than mapping what people smell, the odors that they would encounter in different neighborhoods, she mapped how they smell, mapping odor preferences by neighborhood using homemade scratch-and-sniff stickers, sampling some of the variation in our smell universe.

Scratch-and-Sniff Smell Maps by Nicola Twilley

You can learn a lot more about the project from Edible Geography and from a detailed how-to in The Atlantic, as well as this video of a great talk Nicola gave about how we smell:

It’s a lovely project, allowing people to explore the city in an unexpected way, using their fingers and noses to encounter the invisible. At the gallery opening, visitors also created their own crowd-sourced map by smelling the 12 different scratch-and-sniff options, choosing their favorite and placing it on their neighborhood on a blank map. For this version the visitors also were also asked to describe their favorite smell by writing on the sticker. The descriptions are remarkably poetic and the variation is striking. The same smell is described as “New England museum,” “Altoid,” “Relax,” “Sunday June 23, 07:33am,” and most surprisingly, “CAT LITTER.” In the variation between preferences and descriptions, we see some of the way that odor can capture our imagination.

Odor Descriptions from the Scratch-and-Sniff Map

The Urine Wheel for diagnosing metabolic diseases, from Epiphanie Medicorum by Ullrich Pinder in 1506

Many diseases affect metabolism and many changes in metabolism can be detected in the urine. For example, diabetics will excrete sugar in their urine–sometimes enough sugar that it can be fermented into whisky. There are many other diseases that change the smell of a person’s urine, including the very descriptively named Maple Syrup Urine Disease or Sweaty Feet Syndrome, now much more likely to be diagnosed by electronic sensor arrays than actually tasting the urine. I’m fascinated by all the ways that people categorize and arrange information about flavors and odors, as wheels or otherwise, and the ways that those arrangements affect our perception, consumption, and even diagnosis.

This is by far the largest amount of non-biological information synthesized and stored in DNA—a total of 5.27 megabits, way beyond the 7,920 bit record previously held by the Venter Institute’s watermarks in their chemically synthesized genome (written using an undisclosed code for each letter and punctuation mark).

The sequence of Watermark 4 in the Venter Institute's synthetic genome

While news reports about the DNA book often acknowledge this previous DNA message, as well as a 1999 paper encoding the World War II spy message “JUNE 6 INVASION: NORMANDY” in DNA (PDF), they don’t mention the very first synthetic DNA message cited in the paper. In 1988, Joe Davis, an artist collaborating with molecular biologist Dana Boyd in Jon Beckwith’s lab at Harvard Medical School (and currently a research affiliate in George Church’s lab), designed and synthesized an 18 base-pair message encoding the image of the ancient Germanic rune representing life and the female earth. The Microvenus message was then pasted into a vector and transformed into E. coli, creating a living work of art.

Microvenus--The first non-biological message encoded in DNA, by Joe Davis

The Arecibo Message

The coding scheme for Microvenus was inspired by the binary message sent by Carl Sagan and Frank Drake from the Arecibo radio telescope in 1974, an attempt to open up communication with extraterrestrial intelligence (as well as demonstrate the capabilities of the newly remodeled telescope). The image is a 23×73 rectangle (having the dimensions be two prime numbers makes it easier to decode the single stream of binary digits) showing pictures of the telescope, a person, and information about our solar system and our DNA. Microvenus is coded with a similar principle, the lines of the image translated to ones and zeros in a 5×7 grid, converted to DNA with phase-change values rather than numerical values. The DNA bases are arranged by size — C= 1, T=2, A =3, G=4 — and represent the number of bits needed before you switch to the opposite bit. For example, 10101 translates to CCCCC because each digit occurs once before it switches, and 00011 would be AG because there are three 0 before it switches to two ones.

Despite its tendency to mutate and evolve as cells divide, DNA is a remarkably inert and stable chemical on its own, lasting long enough for archeologists to be able to sequence strands of DNA many thousands of years old. In a microbial spore hurtling through space, DNA could theoretically last long enough to be found by an extraterrestrial civilization that could sequence it and decode the message inside. In the late 1970′s, some scientists even hypothesized the inverse possibility—that viruses on Earth could have been sent as messages from extraterrestrials. Attempts to decode the φX174 viral genome sequence into two dimensional images of course didn’t yield any striking alien messages, but did open up the possibility of sending out different kinds of messages of our own.

For Davis, the messages that we send to aliens aren’t just about sending out a friendly description of life, art, and science on Earth, but of better understanding those things ourselves. He writes in his paper describing the Microvenus project:

By sending messages to extraterrestrial intelligence, human beings are importantly engaged in a search for themselves. They must first reveal themselves to themselves before they can reveal themselves to anyone else. This has not only been a central dilemmain the search for extraterrestrial intelligence, but it has also been an essential element of art, history, psychology, and classical philosophy.

Thus, the image encoded in Microvenus also represents some of the anatomical detail left out of the female figure on the Pioneer plaque, omitted out of a fear that a more accurate image might lead the perhaps puritanical NASA bureaucracy to block the addition of the plaque. While Carl Sagan has said that in retrospect this fear may have been unfounded, we ended up sending not just an image of the human form, but a very specific image of what we find “acceptable.” If this is how we communicate with aliens, what does it mean about us?

These are recurring themes in Davis’s work, which constantly jumps from the microscopic to the interstellar at the interface of art, science, and philosophy. Davis draws from and influences both art and science, collaborating with researchers in many fields to show the connection of aesthetics and values with science and technology. Microvenus, he writes, “is a work of art, a poetic image, yet the project to create it originated as a collaborationin both art and science. Now, like the particle/wave duality, neither explanation seems completely adequate.”

Joe Davis is also a fascinating person, and I highly recommend the documentary about his life and work, Heaven and Earth and Joe Davis by Peter Sasowsky. Here’s a short preview:

It’s a fascinating look at the history of what and how we should eat to be healthy, in particular the medieval rules for eating associated with the four humors and creating balance in your body based on your temperament. Medicine has certainly come a long way since bleeding was used as a cure-all treatment, but the notion of balance may be an important one in a time of increasing obesity but also of increasing fad eating, ascetic cleanses, and paleo-dieting. You can watch the video of the lecture above, or download the podcast here.

My nervousness that tweeting about impostor syndrome would make everyone realize that I was actually an unqualified fraud and rescind my invitation to scifoo was quickly relieved as friends urged me to suggest the panel (thanks Debbie, Sara, Andrew, and Bora!). But then I thought that if I did run a session about impostor syndrome then people would really really know I was an impostor, and why should people listen to me talking about my feelings anyway? How am I qualified to talk about this with anyone?

Exactly.

While the schedule for the weekend was coming together in a flurry of post-it notes, a conversation with the wonderful and eminently qualified professors Kate Clancy (check our her terrific post on the session here) and Sally Otto turned into a plan for a session about impostor syndrome and the culture of science. How does the culture of science and the ways that we define expertise influence our feelings of impostorhood? Can we do a better job of supporting each other and in the process do better science?

We put our post-it on the board assuming we’d have a session where those more traditionally associated with feelings of being an impostor—women and graduate students—would have a chance to talk and listen, supporting and motivating each other to speak up and speak out about their experiences and their areas of expertise.

Instead the table filled up not with nervous young people, but with faculty members at the top of their fields, the heads of various research institutes around the world, a former member of parliament, and even a Nobel prize winner. We moved slowly around the circle, everyone getting a chance to introduce themselves and share stories about their feelings of being an impostor. As we shared and listened, a few really interesting and important themes emerged.

First, almost everyone feels like an impostor sometimes. Even (and maybe especially) after gaining enormous recognition for your achievements. The feeling isn’t unique to any one group, and that’s important to remember for both those who might be feeling like an impostor and those in a position to give advice and support to others. You are not alone!

But while almost everyone mentioned feeling like an impostor, it was only women who described times when they had been told by someone that they don’t “look like a scientist,” only women who were actually being called out as impostors, regardless of their knowledge and experience. Impostor syndrome can happen when the image you have in your head of the kind of person who deserves to be recognized doesn’t match with the kind of person you are. When the kind of person you are doesn’t match with the culturally dominant image, then it’s not always just the voice in your head telling you that you don’t belong. With internal feelings of being an impostor magnified by external forces, both explicit and implicit, overt and subtle, you can end up with a very damaging feedback loop. While women shared stories of their knowledge and experience being pushed aside and ignored, leading them to question their talents, several men discussed the opposite problem—people assuming they have expertise in areas far outside their training and leading them to overestimate their ability to contribute to any conversation.

At the same time, many at the session shared stories that emphasized how it can be useful to sometimes actually be an impostor, to jump into a completely different field, to build bridges between disciplines when you have no official business being there. Around the table people shared stories of new and exciting research emerging from occasionally being in over your head and not letting the voices inside or outside stop you from creating something new and interesting. This theme came up again and again, from people who had founded new disciplines, started new companies, or promoted new ways of doing or communicating science. Being a purposeful impostor doesn’t mean storming into arguments and claiming expertise from authority rather than knowledge, but something more akin to the notion of the public amateur, a person who is not afraid to learn and to create in public, to allow the process of learning something new be part of the process of creating something different.

By opening up about our uncertainties, perhaps that something different will be not just new science (or technology or art) but also a new and more diverse community, a more open and welcoming culture of science. In either case we will all have be willing to go outside of our comfort zones, willing to ask new questions, but also willing to question what it means to be an insider vs. an impostor and to help support those that may not fit into the image we have in our mind.

What is the future of synthetic biology? How do we get there? The recent Six Parties Symposium on Synthetic Biology brought together scientists, engineers, policy makers, and social scientists from the US, the UK, and China to think about the future. Panels focused on the grand challenges that we face, the potential for synthetic biology to address some of these challenges, and the tools—technical and otherwise—necessary to see this potential through to real world applications.

Many of the presentations included timelines on vastly different scales: graphs of rising global temperatures in the past hundred years and graphs of carbon dioxide levels extrapolated out to 12,000 AD; graphs of the exponentially increasing computer processing power in the past fifty years, the exponentially decreasing cost of sequencing and synthesizing DNA in the past ten, and the rapidly increasing number of students participating in iGEM over the past five. Connecting these different timelines, harnessing growing communities and improving technologies to address complex and large-scale environmental problems is the focus of a different kind of timeline—the technology “roadmaps” that set out goals and timeframes for problem solving and industry development in synthetic biology.

But to advance the goals of synthetic biology, first we have to decide on what synthetic biology is, what the goals are, and what is necessary to actually reach those goals. Synthetic biology is a combination of engineering and biology, interpreted and defined in many ways but often in contrast to traditional biology fields. One of the many such definitions of synthetic biology discussed at the symposium was that synthetic biology reverses the genotype to phenotype link; while research in genetics and molecular biology aims to understand how a cell’s genotype leads to an observed phenotype, synthetic biology begins with a desired phenotype and seeks to design the corresponding genotype. The complexity of biological systems and the context-dependence and stochasticity inherent in how phenotypes emerge from genotypes complicate efforts to design functional synthetic networks, but also provide a useful metaphor for thinking about the futures of synthetic biology.

Like the connections between genotype and phenotype, the connections between the roadmaps and the futures that they aim to predict are complex, context-dependent and involve much more than just efficiency and technical feasibility. Indeed, the tools that synthetic biology has focused on in the past decade have always been both technical and social—principles like standardization are encouraged to enable streamlined engineering but also to promote collaboration and open-source development. The symposium, with talks from people working in academia, industry, IP law, environmental advocacy, law enforcement, and government foregrounded many of the issues that complicate the path from roadmaps to futures, including the politics of science funding, the economics of fossil fuels, the reward structures for academic researchers, the educational programs available for interdisciplinary training, risk assessment, regulations, media representations and public perceptions.

Given the complexity of factors influencing the funding of and research in synthetic biology, it’s no surprise that there are almost as many proposed futures as there are definitions and technical standards for the field (like opinions, everyone has one). As Nikolas Rose warned during a panel on social issues involved in synthetic biology, “Too many roadmaps means you don’t know where you’re going.” How can we keep from getting lost? How do we get a future that we want? Who gets to decide?

Perhaps the diversity of goals and the diversity of approaches can be a strength rather than a weakness. Synthetic biology alone can’t solve any of our grand challenges, and synthetic biology can’t develop in a vacuum, isolated from all non-technical factors. The range of voices and perspectives at the symposium reflect the kind of community necessary to understand problems and to craft sustainable solutions.