Synthetic Biology and the Bacteria That Make Jet Fuel
When Life Becomes Substrate
Life as Platform
Ten years ago in a London lab, E. coli learned to breathe propane. Not as a party trick. Not as a proof of concept. As a job. The bacterium that usually gives us food poisoning was now giving us fuel, following instructions written in a language that sits somewhere between Genesis and GitHub. The researchers celebrated. The bacteria kept breathing. Neither seemed to notice they were rewriting the contract between life and labor.
Synthetic biology (the design and construction of new biological parts, systems, and organisms) has matured into something both deeply creative and unsettlingly industrial. What began as a research curiosity two decades ago is now a cornerstone of the bioeconomy. Companies are using yeast to brew spider silk. Algae to generate plastics. Bacteria to clean up oil spills. Modified cells to make medicines at speeds unimaginable a decade ago. Biology has shifted from observation to engineering.
From Cultures to Codebases
The defining characteristic of modern synthetic biology is its shift from benchwork to programming. Platforms like Ginkgo Bioworks’ “Foundry” and Twist Bioscience’s gene synthesis engines now allow researchers to design genetic pathways the way developers design software. DNA sequences are uploaded, compiled, and tested in automated biofoundries. The discourse has shifted accordingly. Organisms are now described not as grown but as debugged. Their genomes are treated as codebases subject to version control and optimization.
Take Solugen, a startup in Houston. The company’s Bioforge platform combines designed enzymes, metal catalysis, and AI optimization to produce hydrogen peroxide and organic acids. Twelve thousand metric tons per year. Zero hazardous waste. In June 2024, the U.S. Department of Energy awarded Solugen a $214 million loan guarantee to scale production even further. The government is betting on programmable biochemistry.
Meanwhile, Ginkgo Bioworks has partnered with research centers to deploy flexible laboratory automation for biofuels. The modified microbes are being optimized using AI tools that propose and test thousands of genetic variants per week. Biology has become programmable infrastructure. Instead of metal and silicon, we build with genes and enzymes. That changes everything about how we think of life itself.
Nature, Version-Controlled
Nature, version-controlled. That’s what Stanford Medicine called their CRISPR-GPT system, which is like calling a nuclear reactor “a slightly toasty heating element.” When evolution becomes a design parameter, “natural” becomes a toggle switch between options that were never meant to be options. A cell optimized by machine learning isn’t alive in the way we’ve understood life for 3.8 billion years. It’s a living document with track changes visible, accepting updates during automated optimization runs. The bacteria don’t care about these philosophical distinctions. They’re too busy wondering why their new features keep crashing during critical functions.
The distinction between natural and artificial blurs further when extinction itself becomes a variable. Colossal Biosciences raised $200 million at a $10.2 billion valuation to engineer a proxy for the woolly mammoth by splicing mammoth DNA into Asian elephant genomes. In March 2025, researchers created gene-edited “woolly mice” with mammoth-like fur. The company projects mammoth-elephant hybrid calves by 2028.
De-extinction is no longer science fiction. It’s venture-backed conservation. Critics argue this introduces a new hierarchy: species are worth saving only if they can generate return on investment.
We’ve developed the technical capacity to make life editable far faster than we can grapple with the consequences.
The Commercial Frontier
Synthetic biology’s promise lies in its versatility. Consider three developments.
First: Biology as factory. The U.S. Department of Energy has bet heavily on this vision, funding “programmable fermentation” to decarbonize industrial chemistry. The emissions reductions compared to petroleum-based production reach 85%. Companies like Solugen have already displaced thousands of tons of traditional chemical manufacturing. The government is essentially subsidizing the replacement of refineries with fermentation tanks, which sounds environmentally responsible until you remember we’re outsourcing chemical production to organisms we’ve taught to follow instructions without asking questions.
Second: Biology as janitor. Researchers are programming bacteria to metabolize plastics into safe compounds. Think of it as teaching microbes to eat our waste, which is either brilliant problem-solving or a confession that we’ve made so much trash we need to engineer life forms specifically to clean up after us. Critics warn of “ecological leakage,” the polite term for what happens when your plastic-eating organisms decide they prefer something else. Something we’d rather keep uneaten. Large-scale deployment remains years away, assuming the bacteria respect containment and don’t renegotiate their employment terms.
Third: Biology as healer. Cell therapy platforms are becoming increasingly modular. Researchers are developing “chassis” systems: standardized immune cell templates that can be rapidly customized for different diseases. Companies like Cellistic have introduced immune-cloaked stem cell lines as universal platforms for therapy development. The goal is making personalized medicine economically viable beyond wealthy early adopters. Biology packaged in standardized units, now available with volume discounts.
Each represents a different vision of biology: factory, tool, and healer. Together, they mark the transition from discovery to design.
Biosecurity and the New Risk Landscape
Engineering life comes with consequences. That’s biosecurity’s polite way of saying “we might accidentally create something that eats us.” The Johns Hopkins Center for Health Security studies these possibilities through their AIxBio initiative. They examine how the same computational tools that optimize enzyme pathways could be repurposed to design pathogens or evade immune systems. Their solution? “Biosecurity by design”: embedding safety constraints into genetic design tools themselves.
It’s like putting a password on the nuclear launch codes after you’ve already distributed them to every middle manager in the company. The tools that can design bacteria to eat plastic are the same tools that can design bacteria to eat something else. Something we might rather keep uneaten. DARPA’s solution is genetic kill switches: molecular “off buttons” for modified organisms. The problem with kill switches, of course, is that they assume the engineered organism respects authority.
Governments are beginning to act. DARPA’s Safe Genes program continues to develop genetic kill switches and anti-CRISPR proteins. The European Union is developing its Biotech Act, expected in 2026, with requirements for screening who can order synthetic DNA and ensuring independent safety oversight. Regulators are scrambling to ensure that programmable life doesn’t become ungovernable.
Every tool to reshape nature also reshapes who holds power. The technical capacity to edit life, bioengineer Drew Endy points out, races ahead of our ability to govern it fairly. That’s not a bug in the system. That’s the system working exactly as designed.
Who Owns Life?
The question of ownership in synthetic biology is simple: who owns life when you can download it? The answer, predictably, is whoever has the better patent lawyer. Current intellectual property law treats modified organisms like software—patentable, licensable, and subject to version control. The genetic sequences often come from open databases or traditional knowledge, which is the biological equivalent of finding a brilliant open-source project and selling it as your own proprietary product. Indonesia, for instance, signed the WIPO Treaty on Genetic Resources in July 2024. In October 2024, it enacted comprehensive patent law amendments specifically to protect biological data sovereignty. These frameworks reflect growing concerns about biopiracy: the extraction and commercialization of genetic resources without compensation to source communities or nations.
At the same time, synthetic biologists are advocating for open-source models. The FreeGenes initiative at the University of California, Berkeley, has synthesized and distributed 10,000 genes under an Open Material Transfer Agreement. They’re freely available to academic, industrial, and hobbyist users. Working in partnership with Twist Bioscience for DNA synthesis, FreeGenes has distributed major toolkits including essential genes from E. coli and Bacillus subtilis, as well as the entire JCVI-Syn3a minimal genome. Their reasoning is philosophical as much as practical: if life is programmable, access to its code should be universal.
Still, the industry’s dominant players (Ginkgo Bioworks and others) continue to build proprietary platforms that create dependencies and lock-in effects. Amyris, once a synthetic biology darling, filed for Chapter 11 bankruptcy in August 2023 before emerging in May 2024. It’s a reminder of how volatile the commercialization of biology can be. Biology follows the same trajectory as software: innovation coupled with enclosure. Open-source advocates fight to preserve commons against proprietary consolidation.
Ethics Beyond “Playing God”
For decades, critics of genetic engineering worried about “playing god.” That concern feels almost quaint now, like worrying that telephones will eliminate the need for face-to-face conversation. The question in 2025 isn’t whether humans should design life. It’s which venture capitalist gets to patent the design.
Ruha Benjamin, a Princeton sociologist who studies the intersection of race, justice, and technology, points out that control over biology reflects and reinforces control over people. Gene-editing technologies don’t just reproduce existing inequalities. They do it with the efficiency of a startup disrupting an inefficient market. The poor won’t just have less access to healthcare. They’ll have less access to humanity itself, as “natural” becomes a luxury good like organic produce or private schools.
This shift in moral framing (from creation to stewardship) may prove the field’s defining challenge. Coding life means debugging society, whether we’re ready or not.
The Beautiful and the Uncanny
There’s a strange poetry to constructed life. At the Biodesign Lab at Delft University of Technology, researcher Jiwei Zhou has developed a “cyano-chromic interface” using cyanobacteria (Synechocystis sp.) that change color in response to their environment. The work combines living microorganisms with electrochromic materials. It surfaces the photosynthetic activity of bacteria as visible color shifts: living materials that express their metabolic states visually. The research envisions applications like air-purifying curtains covered in green polka dots that shift and breathe.
These projects demonstrate that synthetic biology isn’t just an industrial revolution. It’s an epistemological one. It forces us to reconsider what counts as “alive,” what counts as “made,” and whether the distinction matters anymore.
Extinction, Profit, and the Price of Resurrection
Colossal Biosciences wants to bring back the woolly mammoth, which sounds impressive until you realize their $10.2 billion valuation isn’t based on resurrecting extinct species. It’s based on developing the tools to commodify life itself. The mammoth is just the mascot. The woolly equivalent of a gecko selling car insurance.
The company has established a $50 million foundation for conservation, which is like an oil company funding a climate change documentary. The model remains fundamentally dependent on private capital, which means conservation becomes contingent on market logic. A species without economic potential doesn’t merit revival. The dodo never stood a chance in this economy. It lacked the brand recognition of a mammoth and couldn’t be monetized into a theme park attraction.
When Life Becomes Substrate
Synthetic biology sits at the crossroads of salvation and hubris, which is just another way of saying it’s technology. Its practitioners are building tools that could clean the oceans, feed billions, and decarbonize industry. They’re also building tools that could make life itself a subscription service with terms and conditions nobody reads.
When biology becomes substrate, we stop being inhabitants and become architects of a world we didn’t ask to build. That power demands humility, which is in short supply in an industry that describes organisms as “platforms” and ecosystems as “markets.” The bacteria in our petri dishes don’t know this yet. They’re too busy following instructions, which is exactly what makes them both the perfect workers and the perfect metaphor for our relationship with technology itself. We’re all just following code written by someone else, pretending we’re the ones in control.
Research Notes: Synthetic Biology and Programmable Life
Started with a simple question: Is biology really becoming “programmable” the way software is, or is that just Silicon Valley metaphor creep?