EmergingTechs Nanotechnology, Synthetic Biology, and Geoengineering in the Governance Eye

The second annual Governance of Emerging Technologies conference held in Phoenix AZ May 27-29, 2014 discussed a variety of governance (regulation), legal, and ethical aspects of three areas of emerging technology: nanotechnology, synthetic biology, and geoengineering (climate management).

The prevailing attitude in nanotechnology is much like that in artificial intelligence, “no new news” and some degree of weariness after having experienced a few hype-bust cycles, coupled with the invisibility frontier. The invisibility frontier is when an exciting emerging technology becomes so pervasive and widely-deployed that it becomes invisible. There are numerous nanotechnology implementations in a range of fields including materials, computing, structures, nanoparticles, and new methods, similar to the way artificial intelligence deployments are also widely in use but ‘invisible’ in fraud detection, ATM machine operation, data management algorithms, and traffic coordination.

Perhaps the biggest moment of clarity was that different groups of people with different value systems, cultures, and ideals are coming together with more frequency than historically to solve problems. The locus of international interaction is no longer primarily geopolitics, but shifting to be much more one of collaboration between smaller groups in specific contexts who are inventing models for sharing knowledge that simultaneously reconfigure and extend it to different perspectives and value systems.

Fundamental Advances in DNA Nanotechnology: Probes, Synthesis, Photonics, and 3D Printing

The focus of the 11th annual conference on the Foundations of Nanoscience (FNANO) held April 14-17, 2014 in Snowbird UT was self-assembled architectures and devices. The conference continues to be important in providing a comprehensive look at fundamental enabling technologies across a range of nanoscience fields and the eventual advent of molecular electronics.

The majority of the conference discussed self-assembled architectures and devices in the context of DNA nanotechnology (using DNA as a structural building block in nanomaterials construction). DNA is the material of choice for constructing nanoscale objects. It is a useful construction material because the interactions between complementary base pairs are understood, and can be designed and built to create frames and scaffolds that hold other molecules and create structures on their own.

The main technique in DNA nanotechnology is inducing self-assembly, where advances in different methods were discussed such as lithography, 3D printing, electro-chemicals, electronics, and photonics (controlled light interactions with matter).

The scale and required replicability of nanomaterials engenders a strong focus on tool development to determine and assess the progress and quality of self-assembly and other operations. New research was presented in tools related to working with DNA such as probes, detectors, samplers, nanopores, and nanochannels (i.e. waldoes). In silico modeling and prediction remains a crucial step, for example improving the prediction of DNA and RNA folding helps in targeting RNA interference.

Synthetic biology, biomedicine, energy, and basic materials continue to be the important application areas for DNA nanotechnology.

Synbio Reformulates the Traditional Scientific Method

Synthetic biology continues to be one of the most wide-spread trends reshaping the conduct of science.

Lauded as the potential ‘transistor of the 21st century’ given its transformative possibilities, synthetic biology is the design and construction of biological devices and systems. It is highly multi-disciplinary, linking biology, engineering, functional design, and computation.

One of the key application areas is metabolic engineering, working with cells to greatly expand their usual production of substances that can then be used for energy, agricultural, and pharmaceutical purposes.

Since the nature of synthetic biology is pro-actively creating de novo biological systems, organisms, and capacities (the opposite of the esprit of the passive characterization of phenomena for which the original scientific method was developed), synbio is reformulating the traditional scientific method.

While it is true that optimizing genetic and regulatory processes within cells can be partially construed under the scientific method, the overall scope of activity and methods are much broader.

Innovating de novo organisms and functionality requires a significantly different scientific methodology than that supported by the traditional scientific method. This includes computational modeling and simulation, engineering practices, feedback loops, automated bio-printing, and a re-conceptualization of science as an endeavor of characterizing and creating.

Biodesign: a Prevalent Cultural Trope

A new science or technology field really starts to capture the imagination and become mainstream when it seeps into art and culture. This is increasingly evident with bioart, bioprinting, and synthetic biology.

In bioart (using biological materials to make art), there have already been several phases starting with bacteria drawings in petri dishes and more recently culminating in DNA manipulation, live cells growing into cultured shapes in galleries, and the Algae Opera (an opera singer’s CO2 producing algae in real-time for audience consumption).

Bioprinting is an emerging field which marries the 3D printing revolution with biohacking and DIYlabs in the 3D printing of designed human materials for aesthetic and functional purposes.  

Synthetic biology (the design and construction of biological devices and systems) is being featured in art shows alongside industry conferences and in film festivals, including in its own Bio-Fiction, an international synthetic biology science, art, and film festival series.

Not only are we making art with biology as an artistic material, culture is being made in new ways through biology. 

The theme of biodesign is becoming prevalent as a cultural trope through the rapid expansion of designed biology into the arts, culture, collective human consciousness, and science and technology. These ideas are becoming quite normal, which can only mean that their demise through kitschification and cliché could be coming soon in a subsequent era of anti-bioart, post-bioprinting, post-synbio!

Future of Life Sciences: Top 10 List

The next wave of the biotechnology revolution is underway and promises to reshape the world in ways even more transformative than the agricultural, industrial, and information revolutions that preceded it.

It is not unimaginable that at some point, all biological processes, human and otherwise, could be understood and managed directly.

Here is a top ten list of key areas of contemporary advance in life sciences:

1. Synthetic Biology and Biotechnology 
2. Regenerative Medicine and 3D Printing 
3. Genomics, “Omics,” and Preventive Medicine 
4. Neuroscience 
5. Nanotechnology 
6. Big Health Data and Information Visualization 
7. Quantified Self (QS), Wearable Computing, and the Internet-of-Things (IOT) 
8. DIYscience, Citizen Science, Participatory Health, and Collective Intelligence 
9. Aging, Rejuvenation, Health Extension, and Robotics 
10. Space 

More information: Slideshare talk from the Max Planck Institute

Innovation in Epistemology

Rather than being a dusty old concept in philosophy, epistemology is a source of philosophical advance, and is perhaps shifting in some even more vibrant ways per the contemporary science and technology era of big data, information visualization, synthetic biology, biohacking, DIYscience, and the quantified self.

Epistemology (the study of knowledge) is one of the three main branches of philosophy, together with metaphysics (nature of reality), and aesthetics (nature of beauty). The study of knowledge remains one of the most dense and unresolved areas in philosophy. Some of the usual concerns of epistemology are: What is knowledge? How can knowledge be acquired? To what extent can any subject or entity be known? What are the limits of knowledge?

There are two main traditional theories as to how knowledge is obtained: either through the senses and perception (empiricism; e.g.; Locke’s “All ideas come from sensation”) or through reason (rationalism; e.g.; Descartes’ “I think therefore I am”).

There has been much movement in epistemology from the basic structure of this empiricism-rationalism debate. Both empiricism and rationalism seek common foundations upon which all other ideas are built (foundationalism). Foundationalism is problematic in several ways, two of the most basic are ‘what are these underlying foundations?’ and ‘how do these foundations connect to upstream ideas?’ Traditional/analytic philosophers propose coherentism as an alternative to foundationalism. Coherentism is the notion of it being more important that ideas make sense together and flow from one to the next than that they have immutable discernible foundations.

Continental philosophy too has a response to foundationalism and other aspects of the empiricst/rationalist debate. Gadamer enlarges the notion of epistemology, suggesting that discovering facts is just one of many edification activities; that man’s focus is self-betterment, a higher level than knowledge acquisition. Likewise Heidegger thinks that the higher-order engagement of man is beyond knowing facts and rather in understanding. Further that the circular structure of interpretation (the hermeneutic circle: acquiring new information and updating thoughts) is what makes knowledge possible. Rorty also calls for a larger, more holistic notion of epistemology that includes both conceptualization and the demonstration of practice.

Other new epistemologies also extend, reformulate and reinvigorate our understanding of epistemology and can be brought to bear on contemporary science and technology. Some of these alt.epistemologies are from the areas of social, feminist, queer, decolonial, and Eastern philosophy.

Programmable RNA and other recent advances in synthetic biology

There were 50-100 attendees at the Cell Press-sponsored Synthetic Biology conference at the University of California, San Francisco held on December 14, 2011. There was the usual acknowledgment of the field’s status (early-stage), potential impact (considerable), and articulation of what is needed (easy-to-use tools, reliable at-scale design and manufacturing processes, and standardized interoperable parts libraries) that has been typical at group gatherings (e.g.; SB 5.0) for the last few years. Also the point about a better marketing approach to attract scientists and public support to the field, something more enticing than the admittedly deadpan…

We pipette colorless liquids from one tube to another … we’re trying to cure cancer and change the world.

What was different was the degree of sophistication in the approaches, the easy multi-disciplinarity that researchers are bringing to the field, a more comprehensive understanding of the constituent materials (for example, the 5’ DNA does a lot of things: degradation, elongation, binding, etc. in a dynamic system where different processes come online to change resource use per osmolarity, temperature, etc.), and the contemplation of process portability across model organisms, for example from yeast to mammalian cells. The conference structure focused on the overall status and issues of the industry in a panel with leading scientists, and had talks regarding foundational technologies and applications.

Key points made by synthetic biology visionary Drew Endy (Stanford)

• Biology is the best manufacturing partner we’ll find, it has taken over the earth; biology is interesting as both a type of inquiry (we don’t understand everything yet) and as a building material
• Design experts (e.g.; from RSID, the New School, etc.) should be brought into biological design
• Bio-manufacturing is big, but storing data in cells could be bigger
• Metrology advances are needed, in units, reference standards, etc.; for example when shipping a gene expression module to colleagues in Shenzhen, what units should be employed?
• 4-D space-time programming languages is an important new area, only six people worldwide are thinking about this so far
• We need to do regenerative medicine without scaffolds, we know biological cells can differentiate into 3-D, how can we engineer this to happen?
• Synthetic biology needs to expand beyond the few workhorse chemicals used all the time like theophylline and tetracycline
• An important application area is drug design since small molecules, the main current paradigm used in drug development, are limited by their surface area, where they can travel to in the body, and other internal properties

Key conference themes

RNA as a programmable material
Programmable materials are an important input to synthetic biology as they may allow ongoing control over the dynamic processes of living cells. RNA is exemplar as a programmable substrate since it can be used to sense the presence of small molecules in cells and control gene expression by influencing which proteins are made and many other cellular activities [1]. In the keynote talk, Gerald Joyce (Scripps) discussed the specifics of exploiting RNA with a technique analogous to PCR (polymerase chain reaction), where an exponential number of copies of DNA are made to trigger desired cellular behaviors. In this case, an exponential number of copies of certain ligands (building-block molecules that bind with other molecules to trigger reactions in cells) are made that a certain enzyme-making RNA binds to for carrying out a desired cellular function [2].

Not only can RNA be used on a unitary basis to direct cellular actions, it can also be used as a component in constructing gene networks that serve as sophisticated molecular control devices like switches and circuits. Christina Smolke (Stanford) presented research using RNA to build synthetic controllers, for example a ribozyme-based device that can be used to detect metabolites non-invasively, a ribosome binding site-based device that can degrade harmful chemicals into neutral products, and a splicing-based device that can be used to target cell death [3]. A potential application was discussed using a synthetic RNA device to regulate cell signaling and T-cell proliferation in mammalian cells [4]. Alan Arkin (UC Berkeley and LBNL) suggested desirable ways to increase the complexity of synthetically generated devices, for example, assembling complexity from the constituent properties of the materials that is modular or context-free in deployment, and by having diverse RNA control elements on a single transcript [5]. This could also make devices more replicable.

Manipulating organelles
After the theme of RNA as a programmable material and synthetic genetic network regulatory element, another de facto theme was the capability to manipulate organelles.

David Savage (UC Berkeley) presented work regarding carboxysomes (protein-enclosed bacterial organelles). Synthetic organelles could be constructed that would be useful for a variety of cellular activities, including improving on current biological processes like RuBisCO leakage (an enzyme involved in the first major step of carbon fixation). Synthetic organelles could be developed based on previous work characterizing carboxysomes with shell and cargo fluorescent tagging [6], and recent work improving the stability and well-formedness of shells through shell-protein modification, particularly by adding a novel protein, CsoS1D, discovered by Cheryl Kerfeld’s lab (UC Berkeley and LBNL) [7,8].

Wallace Marshall (UCSF) discussed the importance of understanding and controlling organelle size, shape, and composition, the trade-offs between lipid and starch storage and controlled metabolism, for example. Tuning flagellar length could be important in the understanding and remedy of ciliary diseases [9], and experimental research suggested in one case that the quantity of LF4 (long flagella) protein being injected could be the key fulcrum of the control system. Organelle-tuning could have a broad range of useful applications, for example tuning up and down the ability of vacuoles to tolerate toxic compounds.

Applying synthetic biology to drug design
Michelle Chang (UC Berkeley) pointed out how the toxicity of fluorine makes it useful in drugs, and perhaps synthetic biology techniques could improve its effectiveness. A naturally-occurring fluorine-specific enzyme (FIK) was examined that demonstrated dramatic improvement in recognizing molecules [10]. Leor Weinberger (Gladstone Institute and UCSF) discussed synthetic viral circuits called therapeutic interfering particles (TIPs) that have been shown to reduce HIV/AIDS infection rates. The TIPs replicate conditionally in the presence of the pathogen and spread between individuals [11].

Developing foundational technologies
Hana El-Samad (UCSF) discussed the benefits of using hybrid biological and computer-based systems, where software algorithms were used to control a gene expression circuit’s behavior in real-time through a light-responsive module [12].

John Dueber (UC Berkeley) discussed the benefits of controlling the volume of enzymes expressed in cells, optimizing flux through cells. A desirable tool for this is combinatorial libraries to manage expression in multi-gene pathways. Further, when there are flux limitations in the pathway that cannot be managed with gene expression, there has been some interesting work building synthetic scaffolds to co-locate pathway enzymes around the areas of interest [13].

Nathan Hillson (LBNL) presented ways to automate and speed up the engineering cycle (design-build-test) with a component repository, selected components, and assembled components. Software design automation for assembly tools were discussed such as the JBEI-ICE repository platform and the GLAMM design tool.


References

1. Liu CC, Arkin AP. The case for RNA. Science. 2010 Nov 26;330(6008):1185-6.
2. Lam BJ, Joyce GF. An isothermal system that couples ligand-dependent catalysis to ligand-independent exponential amplification. J Am Chem Soc. 2011 Mar 9;133(9):3191-7.
3. Liang JC, Bloom RJ, Smolke CD. Engineering biological systems with synthetic RNA molecules. Mol Cell. 2011 Sep 16;43(6):915-26.
4. Chen YY, Jensen MC, Smolke CD. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc Natl Acad Sci U S A. 2010 May 11;107(19):8531-6.
5. Lucks JB, Qi L, Mutalik VK, Wang D, Arkin AP. Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc Natl Acad Sci U S A. 2011 May 24;108(21):8617-22.
6. Savage DF, Afonso B, Chen AH, Silver PA. Spatially ordered dynamics of the bacterial carbon fixation machinery. Science. 2010 Mar 5;327(5970):1258-61.
7. Roberts EW, Cai F, Kerfeld CA, Cannon GC, Heinhorst S. Isolation and Characterization of the Prochlorococcus Carboxysome Reveals the Presence of the Novel Shell Protein CsoS1D. J Bacteriol. 2011 Dec 9.
8. Klein MG, Zwart P, Bagby SC, Cai F, Chisholm SW, Heinhorst S, Cannon GC, Kerfeld CA. Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport. J Mol Biol. 2009 Sep 18;392(2):319-33.
9. Wemmer KA, Marshall WF. Flagellar length control in chlamydomonas--paradigm for organelle size regulation. Int Rev Cytol. 2007;260:175-212.
10. Weeks AM, Coyle SM, Jinek M, Doudna JA, Chang MC. Structural and biochemical studies of a fluoroacetyl-CoA-specific thioesterase reveal a molecular basis for fluorine selectivity. Biochemistry. 2010 Nov 2;49(43):9269-79.
11. Metzger VT, Lloyd-Smith JO, Weinberger LS. Autonomous targeting of infectious superspreaders using engineered transmissible therapies. PLoS Comput Biol. 2011 Mar;7(3):e1002015.
12. Milias-Argeitis A, Summers S, Stewart-Ornstein J, Zuleta I, Pincus D, El-Samad H, Khammash M, Lygeros J. In silico feedback for in vivo regulation of a gene expression circuit. Nat Biotechnol. 2011 Nov 6;29(12):1114-6.
13. Whitaker WR, Dueber JE. Metabolic pathway flux enhancement by synthetic protein scaffolding. Methods Enzymol. 2011;497:447-68.

Synbio revolution: biology is the engineering medium

Synthetic Biology 5.0: The Fifth International Meeting on Synthetic Biology, was held at Stanford University June 15-17, 2011. There were 700 registered attendees, 400 posters, and 100 people at peak on the live ustream video broadcast. Synthetic biology (synbio) is the design and construction of new biological entities such as enzymes, genetic circuits, and cells or the redesign of existing biological systems. Engineering principles are applied to harness the fundamental components of biology; biology is an engineering medium.

The status of the synbio field was discussed, how

• it is possible to synthesize an enzyme but not design a protein
• it is possible to synthesize a chromosome but not predictably engineer a circuit
• it is not known how to engineer on a whole genome basis
• it is not known how to interface with inorganic material (e.g.; man-made substances)

One of the biggest areas of current activity in synbio is metabolic engineering, optimizing genetic and regulatory processes within cells to increase the cells' production of certain substances, for example biofuel generation. Techniques range from directly deleting and/or overexpressing the genes that encode for metabolic enzymes to targeting the regulatory networks in a cell to efficiently engineer the metabolism.

Theme #1: Biology is finite
The overarching theme that emerged from the conference is that

biology is detailed, systemic, dynamic, and complicated, but in the end finite

The question then becomes ‘how long will it take’ to do certain things. Synthetic biologists have buckled in for the long-term, focusing on the biology revolution being to this century what the computer revolution was to the past century. To be more precise (and congruent with engineering), it may not be that all biology is in the end finitely discoverable and explainable, but rather that even in systems ecologies, manipulations can be conducted effectively within bands wide enough to reach goals and limit risk. An example of a classic problem illustrating the trade-offs of synbio is whether it would be better to engineer wheat that impedes rust or a virus that eats the rust on the wheat.

Theme #2: 3 main approaches to synbio: extend E. coli capacity, biomimicry, de novo synthesis
A recurring theme at synbio conferences is the diversity of approaches. There are three main types, first is extending engineering capacity in the building blocks of nature that are already synbio workhorses such as E. coli and yeast. Second is canvassing nature for additional functionality, including cataloging the natural world and the entire human metabalome, peptidome, virome, bloodome, etc. Third is de novo engineering from scratch to build necessary functionality in minimal cells/minimal genomes, including the possibility of supplementing nature-provided parts with newly created amino acids and nucleotide base pairs. An example that considers the trade-offs between approaches is engineering up from minimal cells versus engineering down from organisms that already have some of the needed functionality, for example up from E. coli or down from rhizobia, soil bacteria that have nitrogen fixation (biosynthesis) capability.

Grand challenges
There was an attempt to define some of the grand challenges in synbio, which can be categorized as building block, biology characterization, and systems engineering challenges.

Building block challenge

• Synthesize the full genome of a bacterium
• Design and manufacture a minimal cell
• Design bacteria that hunt and kill tumors
• Enhance the photosynthesis process in plants
• Expand model organism culturing capability from E. coli and yeast to the vast number of microbes

Biology characterization challenges

• Understand the key interactions of band gap material in a cell
• Understand the multigenic epistasis of thousands of genes in heterologous systems
• Understand contact from a cellular basis
• Figure out how to create programmatic control of complex development steps (for example, body plan)
• Define how many changes are necessary to create a new species

Systems engineering challenges

• Define designs and specifications (that can be predictably and reliably verified and constructed)
• Improve challenges in the synthesis, design, analysis of existing systems
• Engineer for the open systems of the real world, beyond closed-environment bioreactors
• Improve tools for computer-based circuit, genome, and chromosome design
• Develop theoretical frameworks to scale synbio to bigger questions; envision the future beyond putting a lot of small pieces of DNA together more quickly and cheaply
• Develop effective means to design, generate, and test recombinant organisms in the environment (for example, injestable bacteria in humans like an organism that cures cancer or probiotic bacteria for Crohn’s disease)

Synbio update: reference standards, protein fusions, and bioscaffolds

One of the core tools developed and used by synthetic biologists is the Registry of Standard Biological Parts which has over 5,000 available parts (paper). A contemporary research focus is on improving methods for working with the standardized parts. Three recent innovations are described below.

1. In vivo reference standards
One advance is in establishing in vivo reference standards for the different biological parts. For example, the absolute activity of different promoters (gene transcription regulators) varies across experimental conditions and measurement instruments. Variation in promoter activity was reduced 50% by using a selected promoter as an in vivo reference standard against which other promoters were measured (paper).

2. Construction of protein fusions
Another advance is in allowing the construction of protein fusions. This is not feasible in the current assembly standard due to an unfavorable scar sequence that encodes an in-frame stop codon. Restriction enzymes BglII and BamHI are employed in a new assembly standard that replaces the scar sequence with a generally innocuous glycine-serine peptide linker (paper).

3. Rapid circuit generation with BioScaffolds
A third advance is in the creation of a new part, a BioScaffold, that can be used in the rapid generation of synthetic biological circuits. The BioScaffold can be inserted into cloning vectors and excised from them to leave a gap into which other DNA elements can be placed. Targeted circuit modification simplifies and speeds up the iterative design-build-test process through the direct reuse of existing circuits (paper).

Human morphology-changing technologies

To date, most technology has been human-created. It can be grouped into two categories, technologies that are not likely to have an immediate direct impact on human morphology, and those that might.

Technologies that would likely not change human morphology
There could be the rapid advent of significantly more dramatic technologies than have been experienced to date. While these new technologies could change some aspects of life, human biological drives could remain unchanged, and therefore the structure and dynamics of human societal organization, interaction, and goal pursuit could also remain unchanged. Some examples of these advances could include the realization of molecular nanotechnology, quantum computing, cold fusion, and immortality. Even with several of these revolutionary technologies implemented, the seemingly different world would not actually be structurally different if humanity is still ordered around the same familiar biologically-driven goals.

Technologies that might change human morphology
The other group of technologies is those which could possibly have a near-term impact on the structure and form of what it means to be human, for example, cognitive augmentation, genomic therapies, and synthetic biology. The area with the greatest possible change is improving human mental capability. There have been several significant advances in a variety of neurology-related fields in the last few years that if ultimately realized, could potentially alter human morphology. Even the resolution of all mental pathologies such as Parkinson’s disease, depression, stroke rehabilitation, and addiction would constitute morphological change at a basic level. Augmenting cognition and deliberately managing biophysical states would constitute morphological change at other levels.

Synbio in space

Many interesting applications of synthetic biology in space missions were discussed at the Synthetic Biology workshop held October 30-31, 2010 at NASA Ames in conjunction with the National Academies Keck Futures Initiative. Scientists from a variety of backgrounds came together to brainstorm solutions in an integrative approach. The most impressive aspect was how different areas of synthetic biology have been progressing enough to discuss ideas and techniques that could be applied to space missions in a robust way.

Environment enhancement
One of the most important areas that synthetic biology may be able to help with is in making space environments more manageable and habitable by humans. The regolith, the powdery blanket covering the moon and Mars, may likely need to be ameliorated into harder less dusty surfaces.

Biomining
Synthetic biology could be helpful in creating microbes to faster weather regolith/rock for an order of magnitude quicker release of bioessential elements such as Magnesium, Calcium, Potassium, and Iron. (related publications)

Biomaterials and self-building habitats
Synthetic biology could help to create microbes for use in building structures, both as scaffolds and by growing on scaffolds. Bacterially-generated alternatives to Portland cement (bricks made from bacteria, sand, calcium chloride, and urea) are currently being investigated, along with other plant-development inspired architectures.

New gene function
While the discovery of new mammalian genes has become saturated, the majority of newly sequenced ocean-based microbes continue to have novel gene functions. Some of these may be quite useful in space environments, for example, D. radiodurans, which can withstand significant radiation and rebuild its DNA when damaged.

Space economics – the Basalt Economy
The economics of space suggest that synthetic biological solutions might be developed more readily for space challenges, and later deployed on Earth as the technologies mature. The main constraint for space is developing in-situ solutions that are cheaper than lifting materials from Earth, as opposed to creating competitive products for Earth-based supply chains (e.g.; synthetic biofuel).

Tools
Whole human genome and metabiome sequencing, genome synthesis and assembly, and genetic design and proofing software (bioCAD) as shown in Figure 1 are all improving. A vast industry similar to that of semiconductor design and manufacture could likely develop for synthetic biology.

Figure 1: Example of SLIC/Gibson/CPEC gene sequence assembly (Source)

Blood tests 2.0: finger-stick and microneedle array

The farther future could include smartpatches - non-invasive, invisible, continuously-worn health self-monitoring skin patches. In the nearer future, a killer app for synthetic biology and other new chemistry and biology 2.0 methods could be the ability to create one's own vitamin supplements, and possibly innovate low-cost, non-prescription based finger-stick blood tests, and saliva and urine panels for self-testing.

Barrier to Citizen Science
A significant barrier to the wide-scale adoption of citizen science in the context of health self-management, intervention exploration, and preventive medicine implementation is the high cost, inconvenience and discomfort involved in obtaining traditional lab tests. While many tests may be ordered in a direct-to-consumer fashion through DirectLabs, the Life Extension Foundation, and other websites, it still costs ~$100 per test.

The challenge is to identify the requisite chemistry and processes involved and see if it may be possible to make simple consumer-friendly finger-stick blood test cartridges, similar to the glucose and HDL measurement kits sold at drug stores, which self-experimenters may perform at home or at community biolabs. Continuous monitoring via microneedle arrays would be useful for self-tracking glucose levels and other markers. For example, there could be consumer-targeted versions of the devices being developed by Orsense.

Figure 1. Non-invasive glucose monitoring device from Orsense

Community labs and high-end home labs may include the (CLIA-waived) Cholestech LDX machine (~$2,000 for the machine + ~$5-10 per measurement cassette) which can assess eight different lipid profiles.

Figure 2. Cholestech LDX finger-stick lipid measurement device

There is an urgent opportunity to expand the range of finger-stick measurement tests. Below is a Wish List of basic tests for one-off or comprehensive panel delivery.

Traditional Blood markers:

• Homocysteine
• Vitamin B-12
• Folate
• Vitamin D
• Creatinine
• eGFR
• Cortisol
• Calcium
• Iron
• Aldosterone

Hormones

• Estrogen
• Progesterone
• Testosterone
• Estradiol

Genomics – The Global Opportunity

Genomics is particularly interesting as a candidate area for possibly making the most difference the most quickly to the most people worldwide by contributing to developments in energy, food and public health.

A full understanding of genomics, the instruction set for life, could mean a more comprehensive ability to manipulate both the world around us and the world within us. Biology evolved to be just good enough to survive and genomics provides the critical next-generation toolkit for its greater exploitation. With the possibility of a complete understanding of biology and the ability to engineer life to be optimum, traditional limits can be overcome, moving from the gene therapies of today (replacing or silencing one gene) to working with whole genomes and possibly creating new ones.

The global challenge and opportunity is for humanity to move safely and expediently into the genomic era of biological manipulation.

The agricultural applications of genomics have been underway for some time in the form of genetically-modified crops. Energy applications of genomics are in development using synthetic biology to generate fossil fuel replacements and are estimated to be ready for commercial launch in 2011. The public health application of genomics is especially promising, using genomics to further understand and eradicate disease. Genetic information is already starting to be medically actionable and is likely to become increasingly useful over time. Its two main current uses are in pharmacogenomics, personalized therapeutics, categorizing drug responders and non-responders for tailored treatment, and in routing higher-risk individuals to earlier screenings for chronic diseases such as prostate cancer and breast cancer. It is estimated that each individual is in the upper 5% risk tier for at least one chronic disease and that $100,000 per person per condition could be saved as a result of earlier detection. By 2010, according to a World Health Organization (WHO) report, cancer will surpass heart disease as the world’s greatest killer, and in fact, developing countries could be at the highest risk due to smoking and high-fat diets.

As our molecular understanding of disease progresses and genomic technologies continue to decrease in cost and become increasingly medically relevant, the use of genomics could become quite widespread. Physicians could start to see the precise, additive information conferred by genomics as a means of improving the care now delivered, finding themselves initially encouraged and eventually regulated into incorporating genomics in care regimens. Pharmaceutical companies are already using genomics as a means of improving efficacy in drug discovery and delivery, providing much-needed assistance to their ailing cost structures. Individuals worldwide could have unprecedented access to their health information which could prompt a much greater level of responsibility-taking and health self-management.

Synthetic biology enables green petroleum

The good news about the number of worldwide vehicles, approximately 1 billion at present and expected to double in the next few decades, is the number of fossil fuel alternatives feverishly underway, many of which have established pilot projects and are expected to launch in selected commercial markets in 2011.

Synbio enables green petroleum

The current killer app of synthetic biology, the programming and engineering of biology, is green petroleum.

Several companies are developing improved versions of fossil fuels which can be easily substituted into the existing worldwide fuel infrastructure for autos, planes, etc. at approximately the same cost of fossil fuels (oil is presently $80 per barrel). Pilot plants are underway and commercial introduction is expected in 2011. Sapphire Energy and Synthetic Genomics are working with algal fuel, ramping the highly efficient natural process of algae creating petroleum through photosynthesis.

Other companies such as Amyris Biotechnologies are using synthetic biology to generate ethanol, and LS9 is synthesizing carbohydrates into petroleum with designer microbes. In the farther future, late-generation biofuels are contentious but already being envisioned by companies like Craig Venter’s Synthetic Genomics, employing carbon dioxide (CO2) as a feedstock for bacteria to convert into methane using molecular hydrogen as the energy source.

Green petroleum vs. electric vehicles
There may be less of a competition between transportation fuel alternatives and more of a market suitability analysis governing which choices arise in which areas. Large markets like the U.S. are already showing signs of both, or all, alternatives arising. Markets and countries with other parameters such as smaller size, increased government involvement and more stringent emissions regulations my make a strategic commitment towards certain choices, for example an interesting train and EV-sharing program announced in Denmark.

International electric vehicle leader Better Place notes that the ‘Goldilocks’ markets for greenfield electric vehicle networks are countries that are not too big to risk the introduction of such a disruptive solution and not too small such that economies of scale would not work. The poster child market for the company is Israel, with has networks of charging stations already installed in Tel Aviv and plans to build another 100 in Jerusalem for the mass availability of electric cars in 2011.

Bio-design automation and synbio tools

The ability to write DNA could have an even greater impact than the ability to read it. Synthetic biologists are developing standardized methodologies and tools to engineer biology into new and improved forms, and presented their progress at the first-of-its-kind Bio-Design Automation workshop (agenda, proceedings) in San Francisco, CA on July 27, 2009, co-located with the computing industry’s annual Design Automation Conference. As with many areas of technological advancement, the requisite focus is on tools, tools, tools! (A PDF of this article is available here.)


Experimental evidence has helped to solidify the mindset that biology is an engineering substrate like any other and the work is now centered on creating standardized tools that are useful and reliable in an experimental setting. The metaphor is very much that of computing: just as most contemporary software developers work at high levels of abstraction and need not concern themselves with the 1s and 0s of machine language, in the future, synthetic biology programmers would not need to work directly with the Ac, Cs, Gs and Ts of DNA or understand the architecture of promoters, terminators, open reading frames and such. However, with synthetic biology being in its early stages, the groundwork to define and assemble these abstraction layers is currently at task.

Status of DNA synthesis
At present, the DNA synthesis process is relatively unautomated, unstandardized and expensive ($0.50-$1.00 per base pair (bp)); it would cost $1.5-3 billion to synthesize a full human genome. Synthesized DNA, which can be ordered from numerous contract labs such as DNA 2.0 in Menlo Park, CA and Tech Dragon in Hong Kong, has been following Moore’s Law (actually faster than Moore’s Law Carlson Curves doubling at 2x/yr vs. 1.5x/yr), but is still slow compared to what is needed. Right now short oligos, oligonucleotide sequences up to 200 bp, can be reliably synthesized but a low-cost repeatable basis for genes and genomes extending into the millions of bp is needed. Further, design capability lags synthesis capability, being about 400-800-fold less capable and allowing only 10,000-20,000 bp systems to be fully forward-engineered at present.

So far, practitioners have organized the design and construction of DNA into four hierarchical tiers: DNA, parts, devices and systems. The status is that the first two tiers, DNA and parts (simple modules such as toggle switches and oscillators), are starting to be consistently identified, characterized and produced. This is allowing more of an upstream focus on the next two tiers, complex devices and systems, and the methodologies that are needed to assemble components together into large-scale structures, for example those containing 10 million bp of DNA.

Standardizing the manipulation of biology
A variety of applied research techniques for standardizing, simulating, predicting, modulating and controlling biology with computational chemistry, quantitative modeling, languages and software tools are under development and were presented at the workshop.

Models and algorithms
In the models and algorithms session, there were some examples of the use of biochemical reactions for computation and optimization, performing arithmetic computation essentially the same way a digital computer would. Basic mathematical models such as the CME (Chemical Master Equation) and SSA (Stochastic Simulation Algorithm) were applied and extended to model, predict and optimize pathways and describe and design networks of reactions.

Experimental biology
The experimental biology session considered some potential applications of synthetic biology, first the automated design of synthetic ribosome binding sites to make protein production faster or slower (finding that the translation rate can be predicted if the Gibbs free energy (delta G) can be predicted). Second, an in-cell disease protection mechanism was presented where synthetic genetic controllers were used to prevent the lysis normally occurring in the lysis-lysogeny switch turned on in the disease process (lysogeny is the no-harm state and lysis is the death state).

Tools and parts
In the tools and parts session, several software-based frameworks and design tools were presented, many of which are listed in the software tools section below.

Languages and standardization
The languages and standardization session had discussions of language standardization projects such as the BioStream language, PoBol (Provisional BioBrick Language) and the BioBrick Open Language (BOL).

Software tools: a SynBio CrunchUp
Several rigorous computer-aided design and validation software tools and platforms are emerging for applied synthetic biology, many of which are freely available and open-source.

• Clotho: An interoperable design framework supporting symbol, data model and data structure standardization; a toolset designed in a platform-based paradigm to consolidate existing synthetic biology tools into one working, integrated toolbox
• SynBioSS - Synthetic Biology Software Suite: A computer-aided synthetic biology tool for the design of synthetic gene regulatory networks; computational synthetic biology
• RBS Calculator: A biological engineering tool that predicts the translation initiation rate of a protein in bacteria; it may be used in Reverse Engineering or Forward Engineering modes
• SeEd - Sequence Editor (work in progress): A tool for designing coding sequence alterations, a system conceptually built around constraints instead of sequences
• Cellucidate: A web-based workspace for investigating the causal and dynamic properties of biological systems; a framework for modeling modular DNA parts for the predictable design of synthetic systems
• iBioSim: A design automation software for analyzing biochemical reaction network models including genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems
• GenoCAD: An experimental tool for building and verifying complex genetic constructs derived from a library of standard genetic parts
• TinkerCell: A computer-aided design software for synthetic biology

Future of BioCAD
One of the most encouraging aspects in the current evolution of synthetic biology is the integrations the field is forging with other disciplines, particularly electronics design and manufacture, DNA nanotechnology and bioinformatics.

Scientists are meticulously applying engineering principles to synthetic biology and realize that novel innovations are also required since there are issues specific to engineering biological systems. Some of these technical issues include device characterization, impedance, matching, rules of composition, noise, cellular context, environmental conditions, rational design vs. directed evolution, persistence, mutations, crosstalk, cell death, chemical diffusion, motility and incomplete biological models.

As it happened in computing, and is happening now in biology, the broader benefit of humanity having the ability to develop and standardize abstraction layers in any field can be envisioned.

Clearly there will be ongoing efforts to more granularly manipulate and create all manner of biology and matter. Some of the subsequent areas where standards and abstraction hierarchies could be useful, though not immediate, are the next generations of computing and communications, molecular nanotechnology (atomically precise matter construction from the bottom up), climate, weather and atmosphere management, planet terraforming and space colony construction.

(Image credits: www.3dscience.com, www.biodesignautomation.org)

Synthetic biology – what is next?

Synthetic biology is the engineering of biology, re-designing existing biological systems and designing new ones, for a myriad of purposes. The most obvious killer apps are the improved synthesis of drugs and other medicines and the synthetic generation of biofuels.

Right now the most exciting aspect of synthetic biology –suggesting that the field is getting some traction – is that three key community constituents are getting more heavily involved: traditional academic researchers (SB 4.0 conference videos and agenda), undergraduates and high school students through the annual iGEM (international genetically engineered machines) competition (1200 students from 112 teams are expected at this fall’s iGEM Jamboree at MIT, and a growing group of non-institutionally affiliated enthusiasts, diybio’ers, the 2000s version of the Homebrew Computer Club, for both wetlab (an interesting recent example) and computer modeling, simulation and data management projects.

Venture capitalists are slowly starting to realize that synthetic biology could be a huge growth industry and could be the next generation of biotechnology. Amyris is probably the best-known synthetic biology company, estimating to launch its biofuel (ethanol) business publicly in Brazil and the US in 2011.

The long road to automation
Other waves in the history of biotechnology have shown that life sciences problems tend to be much more complex, take much longer than expected to solve and ultimately underdeliver results. There is no reason to think that synthetic biology would be any different, but it is obviously not futile to work on the challenges. When the synbio community analogizes their status to the heterogeneous screws and bolts of the construction industry circa 1864, they are not kidding.

The DNA synthesis process is astonishingly unautomated, unstandardized and expensive ($0.50-$1.00 per base pair) at present (it would be $15-30 billion to synthesize the full genome of a human (ignoring ethical, legal, etc. issues)).

Synthetic biology is a new field and the demand for synthesized DNA is still small; the 2,000 or so iGEM community members are the biggest market. Ginkgo Bioworks is working to deliver robotic synthesized DNA assembly and other startups would be likely to spring up in this area. Ginkgo has also helped to expand and improve one of the main synbio tools, the Registry of Standard Biological Parts.

Status of cancer detection

The Canary Foundation’s annual symposium held May 4-6, 2009 indicated progress in two dimensions of a systemic approach to cancer detection: blood biomarker identification and molecular imaging analysis.

Systems approach to cancer detection
A systems approach is required for effective cancer detection as assays show that many proteins, miRNAs, gene variants and other biomarkers found in cancer are also present in healthy organisms. The two current methods are one, looking comprehensively at the full suite of genes and proteins, checking for over-expression, under-expression, mutation, quantity, proximity and other factors in a tapestry of biological interactions and two, seeking to identify biomarkers that are truly unique to cancer, for example resulting from post-translational modifications like glycosylation and phosphorylation. Establishing mathematical simulation models has also been an important step in identifying baseline normal variation, treatment windows and cost trade-offs.

Blood biomarker analysis
There are several innovative approaches to blood biomarker analysis including blood-based protein-assays (identifying and quantifying novel proteins related to cancer), methylation analysis (looking at abnormal methylation as a cancer biomarker) and miRNA biomarker studies (distinguishing miRNAs which originated from tumors). Creating antibodies and assays for better discovery is also advancing particularly protein detection approaches using zero, one and two antibodies.

Molecular Imaging
The techniques for imaging have been improving to molecular level resolution. It is becoming possible to dial-in to any set of 3D coordinates in the body with high-frequency, increase the temperature and destroy only that area of tissue. Three molecular imaging technologies appear especially promising: targeted microbubble ultrasound imaging (where targeted proteins attach to cancer cells and microbubbles are attached to the proteins which make the cancerous cells visible via ultrasound; a 10-20x cheaper technology than the CT scan alternative), Raman spectroscopy (adding light-based imaging to endoscopes) and a new imaging strategy using photoacoustics (light in/sound out).

Tools: Cancer Genome Atlas and nextgen sequencing
As with other high-growth science and technology areas, tools and research findings evolve in lockstep. The next generation of tools for cancer detection includes a vast cataloging of baseline and abnormal data and a more detailed level of assaying and sequencing. In the U.S., the NIH’s Cancer Genome Atlas is completing a pilot phase and being expanded to include 50 tumor types (vs. the pilot phase’s three types: glioblastoma, ovarian and lung) and abnormalities in 25,000 tumors. The project performs a whole genomic scan of cancer tumors, analyzing mutations, methylation, coordination, pathways, copy number, miRNAs and expression. A key tool is sequencing technology itself which is starting to broaden out from basic genomic scanning to targeted sequencing, whole RNA sequencing, methylome sequencing, histone modification sequencing, DNA methylation by arrays and RNA analysis by arrays. The next level would be including another layer of detail, areas such as acetylation and phosphorylation.

Future paradigm shifts: prevention, omnisequencing, nanoscience and synthetic biology
Only small percentages of annual cancer research budgets are spent on detection vs. treatment, but it is possible that the focus will be further upstreamed to prevention and health maintenance as more is understood about the disease mechanisms of cancer. Life sciences technology is not just moving at Moore’s Law paces but there are probably also some paradigm shifts coming.

The three most suggestive areas for coming life science discontinuities are genomic sequencing, nanoscience and synthetic biology.

Genomic sequencing contemplates the routine scanning of each individual and tumor at multiple levels: genomic, proteomic, methylomic, etc. Nanoscience is the ability to design, construct and render mobile a large variety of molecular [biological] devices. Synthetic biology is designing new or modifying existing biological pathways in order to produce systems with superior or different properties, exercised by both traditional practitioners (recent conferences: Advances in Synthetic Biology, Synthetic Biology 4.0) and diybio’ers.

Ultimate possibilities for life and technology

Thinking really long term, what would it be like if all matter, including life, could be designed and built to specification with nanotechnology and synthetic biology? Form factor could become ephemeral and purpose-driven. An intelligence could embody as a human, as a fleet of starships, as a crane, as a school of nanoparticles, or remain digital.

Some interesting issues could come up, say from having multiple persistent copies of one intelligence. What would the social, legal, economic etiquette and governing laws be? Or would these words even make sense anymore? The notion of the distinct individual may become obsolete.

Transhumanism will be an interesting and certainly divisive step, when groups or all humans have radically enhanced capabilities as compared with today. Posthumanism, the moment of speciation, may be quite a shock.

What about utility functions? In a digital format, traditional biological functions make a lot less sense. And what about emotion? Is there a relevant adaptation for the digital substrate or is emotion just another biology-based information system?

What is intelligence and is it reflected differently in a digital medium without the sensory input context of the physical world? Maybe intelligence is nothing more than manipulating patterns of information.

Finally, what are the ultimate possibilities for life and technology once joined? What if any would the activity be? Would the focus be on aesthetics? Analytics?

Roadmap for Synthetic Biology

The most pressing issue in Synthetic Biology is building the groundwork to eventually advance to large-scale commercialization. How can the field’s growth from fringe to core be accelerated? A strategic plan for the Synthetic Biology ecosystem addressing academic, commercial, geopolitical and policy issues would help.

Academically, how many new bioengineering departments per year could be added? Open source course materials are available. Undergraduate and graduate bioengineering program templates including financing guidance, an industry association, faculty databases and implementation mechanisms are needed. Current academic conferences and journals could be expanded to reflect industry growth. There could be regional hands-on workshops for different levels of trained professionals and interested high-school students, similar to Math Jamborees.

Regarding enabling tools, there is a need for research and development, access ease, standardization and scale-up. Existing tools such as the PartsRegistry, OpenWetWare and Gingko Bioworks need to be taken to the next level. Academic and corporate research programs and incubators could develop a strategic roadmap for tools. An IEEE committee could be devoted to Synthetic Biology.

Commercially, there could be specific programs to involve the financing community. Venture Capital-backed SynBio Incubators could be initiated with conferences, programs, technology transfer and onsite startup incubation. Non-academic conferences, marketing and outreach programs, contests, prizes and X Prize grand challenge competitions could reside at incubators.

Safety protocols for practitioners and public discourse is a critical area for the success of Synthetic Biology. Asilomar and the Geneva Conventions could be helpful analogs for policy development.

Gene Encyclopedia of all Life

A tremendous resource would be an open gene database of all of the genes present in eukaryotic, archaeal and bacterial life. There are several open genomic databases now but the information is organized around genomes and organisms rather than specific genes and gene function.

A gene database of all life is in the same vein as E.O. Wilson’s Encyclopedia of Life, but at the next level of detail. The Encyclopedia of Life hopes to provide a webpage with scientific information for every known species on Earth. The gene database would provide a webpage and scientific details for each gene present in life and include other information such as a cross reference to all of the different species in which the gene is expressed.

Merge the Entrez Genome Project and the PartsRegistry
The foundations and perhaps the vision and obviousness of a gene database of all life exist but not its targeted pursuit as a funded research priority. Existing genomics databases such as the U.S. NCBI’s Entrez Genome Project database could be extended and merged into one database that is more explicitly searchable by gene function, possibly joining forces with the PartsRegistry from synthetic biology which provides a homepage, datasheet and genomic sequence by gene or biological function.

NCBI’s Entrez Genome Project database genomic catalog of all life

Unifying the work of E.O. Wilson, Craig Venter, Penny Boston and Drew Endy
An interesting project would be the unification of the Encyclopedia of Life, genomics-by-organism databases and parts registry-by-gene databases together with the aggressive pursuit of cataloguing and sequencing newly discovered organisms and genes. A gene encyclopedia could rapidly extend human knowledge and facilitate the era of personalized medicine as these novel genes could have extensive application in human therapies and pharmaceuticals, energy, climate management, agriculture and other areas.

Tremendous novelty and diversity remains unstudied with species (E.O. Wilson), with organisms in the sea (Craig Venter), and with extremophile life in caves (Penny Boston); 70-90% novel organisms, most of which have not had any gene identification and sequencing, functional assessment and cataloging.

A data resource like a gene encyclopedia could also uplevel the research focus to analytics. It will be interesting to see if an era of fully fungible genes across life arises, how easy it is to transplant function and how function expresses differently in different life forms.