synthetic biology

{{Further|Timeline of biotechnology}}

1910: First identifiable use of the term synthetic biology in Stéphane Leduc's publication Théorie physico-chimique de la vie et générations spontanées.{{Cite book|url=https://openlibrary.org/books/OL23348076M/Th%C3%A9orie_physico-chimique_de_la_vie_et_g%C3%A9n%C3%A9rations_spontan%C3%A9es|title=Théorie physico-chimique de la vie et générations spontanées. | vauthors = Le Duc S |date=October 26, 1910|publisher=A. Poinat|ol=23348076M|via=The Open Library}} He also noted this term in another publication, La Biologie Synthétique in 1912.{{cite book |url=http://www.peiresc.org/bstitre.htm |title=La biologie synthétique, étude de biophysique |vauthors=Leduc S |date=1912 |veditors=Poinat A |access-date=2011-01-23 |archive-date=2016-09-27 |archive-url=https://web.archive.org/web/20160927053618/http://www.peiresc.org/bstitre.htm |url-status=dead }}

1944: Canadian-American scientist Oswald Avery shows that DNA is the material of which genes and chromosomes are made. This becomes the bedrock on which all subsequent genetic research is built.{{Cite book |last=Carey |first=Nessa |title=Hacking the Code of Life |publisher=Icon Books |year=2019 |isbn=978-178578-497-2 |location=London |pages=Page=12 |language=English}}

1953: Francis Crick and James Watson publish the structure of the DNA in Nature.

1961: Jacob and Monod postulate cellular regulation by molecular networks from their study of the lac operon in E. coli and envisioned the ability to assemble new systems from molecular components.Jacob, F.ß. & Monod, J. On the regulation of gene activity. Cold Spring Harb. Symp. Quant. Biol. 26, 193–211 (1961).

1973: First molecular cloning and amplification of DNA in a plasmid is published in P.N.A.S. by Cohen, Boyer et al. constituting the dawn of synthetic biology.{{cite journal | vauthors = Cohen SN, Chang AC, Boyer HW, Helling RB | title = Construction of biologically functional bacterial plasmids in vitro | journal = Proc. Natl. Acad. Sci. USA | volume = 70 | issue = 11 | pages = 3240–3244 | date = 1973 | pmid = 4594039 | doi = 10.1073/pnas.70.11.3240 | bibcode = 1973PNAS...70.3240C | pmc = 427208 | doi-access = free }}

1978: Arber, Nathans and Smith win the Nobel Prize in Physiology or Medicine for the discovery of restriction enzymes, leading Szybalski to offer an editorial comment in the journal Gene:

{{blockquote|The work on restriction nucleases not only permits us easily to construct recombinant DNA molecules and to analyze individual genes, but also has led us into the new era of synthetic biology where not only existing genes are described and analyzed but also new gene arrangements can be constructed and evaluated.{{cite journal | vauthors = Szybalski W, Skalka A | title = Nobel prizes and restriction enzymes | journal = Gene | volume = 4 | issue = 3 | pages = 181–2 | date = November 1978 | pmid = 744485 | doi = 10.1016/0378-1119(78)90016-1 }}}}

1988: First DNA amplification by the polymerase chain reaction (PCR) using a thermostable DNA polymerase is published in Science by Mullis et al.{{cite journal | vauthors = Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA | title = Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase | journal = Science | volume = 239 | issue = 4839 | pages = 487–491 | date = 1988 | pmid = 2448875 | doi = 10.1126/science.239.4839.487 }} This obviated adding new DNA polymerase after each PCR cycle, thus greatly simplifying DNA mutagenesis and assembly.

2000: Two papers in Nature report synthetic biological circuits, a genetic toggle switch and a biological clock, by combining genes within E. coli cells.{{cite journal | vauthors = Elowitz MB, Leibler S | title = A synthetic oscillatory network of transcriptional regulators | journal = Nature | volume = 403 | issue = 6767 | pages = 335–8 | date = January 2000 | pmid = 10659856 | doi = 10.1038/35002125 | bibcode = 2000Natur.403..335E | s2cid = 41632754 }}{{cite journal | vauthors = Gardner TS, Cantor CR, Collins JJ | title = Construction of a genetic toggle switch in Escherichia coli | journal = Nature | volume = 403 | issue = 6767 | pages = 339–42 | date = January 2000 | pmid = 10659857 | doi = 10.1038/35002131 | bibcode = 2000Natur.403..339G | s2cid = 345059 }}

2003: The most widely used standardized DNA parts, BioBrick plasmids, are invented by Tom Knight.{{Cite report | vauthors = Knight T |year=2003|title=Idempotent Vector Design for Standard Assembly of Biobricks | publisher = MIT Artificial Intelligence Laboratory |hdl=1721.1/21168}} These parts will become central to the International Genetically Engineered Machine (iGEM) competition founded at MIT in the following year.

File:Synthetic Biology Open Language (SBOL) standard visual symbols.svg (SBOL) standard visual symbols for use with BioBricks Standard]]

2003: Researchers engineer an artemisinin precursor pathway in E. coli.{{cite journal | vauthors = Martin VJ, Pitera DJ, Withers ST, Newman JD, Keasling JD | title = Engineering a mevalonate pathway in Escherichia coli for production of terpenoids | journal = Nature Biotechnology | volume = 21 | issue = 7 | pages = 796–802 | date = July 2003 | pmid = 12778056 | doi = 10.1038/nbt833 | s2cid = 17214504 }}

2004: First international conference for synthetic biology, Synthetic Biology 1.0 (SB1.0) is held at MIT.

2005: Researchers develop a light-sensing circuit in E. coli.{{cite journal | vauthors = Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voigt CA | display-authors = 6 | title = Synthetic biology: engineering Escherichia coli to see light | journal = Nature | volume = 438 | issue = 7067 | pages = 441–442 | date = November 2005 | pmid = 16306980 | doi = 10.1038/nature04405 | s2cid = 4428475 | bibcode = 2005Natur.438..441L }} Another group designs circuits capable of multicellular pattern formation.{{cite journal | vauthors = Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R | title = A synthetic multicellular system for programmed pattern formation | journal = Nature | volume = 434 | issue = 7037 | pages = 1130–4 | date = April 2005 | pmid = 15858574 | doi = 10.1038/nature03461 | bibcode = 2005Natur.434.1130B | s2cid = 4370309 | url = https://resolver.caltech.edu/CaltechAUTHORS:20150319-084633535 | url-access = subscription }}

2006: Researchers engineer a synthetic circuit that promotes bacterial invasion of tumour cells.{{cite journal | vauthors = Anderson JC, Clarke EJ, Arkin AP, Voigt CA | title = Environmentally controlled invasion of cancer cells by engineered bacteria | journal = Journal of Molecular Biology | volume = 355 | issue = 4 | pages = 619–627 | date = January 2006 | pmid = 16330045 | doi = 10.1016/j.jmb.2005.10.076 }}

2010: Researchers publish in Science the first synthetic bacterial genome, called M. mycoides JCVI-syn1.0.{{Cite news|url=https://www.telegraph.co.uk/news/science/science-news/7747779/American-scientist-who-created-artificial-life-denies-playing-God.html |archive-url=https://ghostarchive.org/archive/20220112/https://www.telegraph.co.uk/news/science/science-news/7747779/American-scientist-who-created-artificial-life-denies-playing-God.html |archive-date=2022-01-12 |url-access=subscription |url-status=live|title=American scientist who created artificial life denies 'playing God'|date=May 2010|website=The Telegraph}}{{cbignore}} The genome is made from chemically-synthesized DNA using yeast recombination.

2011: Functional synthetic chromosome arms are engineered in yeast.{{cite journal | vauthors = Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, Boeke JD | display-authors = 6 | title = Synthetic chromosome arms function in yeast and generate phenotypic diversity by design | journal = Nature | volume = 477 | issue = 7365 | pages = 471–476 | date = September 2011 | pmid = 21918511 | pmc = 3774833 | doi = 10.1038/nature10403 | bibcode = 2011Natur.477..471D }}

2012: Charpentier and Doudna labs publish in Science the programming of CRISPR-Cas9 bacterial immunity for targeting DNA cleavage.{{cite journal | vauthors = Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E | title = A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity | journal = Science | volume = 337 | issue = 6096 | pages = 816–821 | date = 2012 | pmid = 22745249 | doi = 10.1126/science.1225829 | pmc = 6286148 | bibcode = 2012Sci...337..816J }} This technology greatly simplified and expanded eukaryotic gene editing.

2019: Scientists at ETH Zurich report the creation of the first bacterial genome, named Caulobacter ethensis-2.0, made entirely by a computer, although a related viable form of C. ethensis-2.0 does not yet exist.{{cite news |author=ETH Zurich |title=First bacterial genome created entirely with a computer |url=https://www.eurekalert.org/pub_releases/2019-04/ez-fbg032819.php |date=1 April 2019 |work=EurekAlert! |access-date=2 April 2019 |author-link=ETH Zurich |archive-date=8 October 2019 |archive-url=https://web.archive.org/web/20191008040536/https://www.eurekalert.org/pub_releases/2019-04/ez-fbg032819.php |url-status=dead }}{{cite journal | vauthors = Venetz JE, Del Medico L, Wölfle A, Schächle P, Bucher Y, Appert D, Tschan F, Flores-Tinoco CE, van Kooten M, Guennoun R, Deutsch S, Christen M, Christen B | display-authors = 6 | title = Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 116 | issue = 16 | pages = 8070–8079 | date = April 2019 | pmid = 30936302 | pmc = 6475421 | doi = 10.1073/pnas.1818259116 | bibcode = 2019PNAS..116.8070V | doi-access = free }}

2019: Researchers report the production of a new synthetic (possibly artificial) form of viable life, a variant of the bacteria Escherichia coli, by reducing the natural number of 64 codons in the bacterial genome to 59 codons instead, in order to encode 20 amino acids.{{cite news | vauthors = Zimmer C |author-link=Carl Zimmer |title=Scientists Created Bacteria With a Synthetic Genome. Is This Artificial Life? – In a milestone for synthetic biology, colonies of E. coli thrive with DNA constructed from scratch by humans, not nature. |url=https://www.nytimes.com/2019/05/15/science/synthetic-genome-bacteria.html |date=15 May 2019 |work=The New York Times |access-date=16 May 2019 }}{{cite journal | vauthors = Fredens J, Wang K, de la Torre D, Funke LF, Robertson WE, Christova Y, Chia T, Schmied WH, Dunkelmann DL, Beránek V, Uttamapinant C, Llamazares AG, Elliott TS, Chin JW | display-authors = 6 | title = Total synthesis of Escherichia coli with a recoded genome | journal = Nature | volume = 569 | issue = 7757 | pages = 514–518 | date = May 2019 | pmid = 31092918 | pmc = 7039709 | doi = 10.1038/s41586-019-1192-5 | bibcode = 2019Natur.569..514F }}

2020: Scientists created the first xenobot, a programmable synthetic organism derived from frog cells and designed by AI.{{cite news | vauthors = Sokol J |date=2020-04-03 |title=Meet the Xenobots: Virtual Creatures Brought to Life |url=https://www.nytimes.com/2020/04/03/science/xenobots-robots-frogs-xenopus.html |work=The New York Times}}

Demis Hassabis and John M. Jumper presented an AI model called AlphaFold2. With its help, they have been able to predict the structure of virtually all the 200 million proteins that researchers have identified. Since their breakthrough, AlphaFold2 has been used by more than two million people from 190 countries. Among a myriad of scientific applications, researchers can now better understand antibiotic resistance and create images of enzymes that can decompose plastic.Noble Prize Press 2024 see:[https://www.nobelprize.org/prizes/chemistry/2024/press-release/]

{{cite journal | doi=10.1038/s41586-021-03819-2 | title=Highly accurate protein structure prediction with AlphaFold | date=2021 | last1=Jumper | first1=John | last2=Evans | first2=Richard | last3=Pritzel | first3=Alexander | last4=Green | first4=Tim | last5=Figurnov | first5=Michael | last6=Ronneberger | first6=Olaf | last7=Tunyasuvunakool | first7=Kathryn | last8=Bates | first8=Russ | last9=Žídek | first9=Augustin | last10=Potapenko | first10=Anna | last11=Bridgland | first11=Alex | last12=Meyer | first12=Clemens | last13=Kohl | first13=Simon A. A. | last14=Ballard | first14=Andrew J. | last15=Cowie | first15=Andrew | last16=Romera-Paredes | first16=Bernardino | last17=Nikolov | first17=Stanislav | last18=Jain | first18=Rishub | last19=Adler | first19=Jonas | last20=Back | first20=Trevor | last21=Petersen | first21=Stig | last22=Reiman | first22=David | last23=Clancy | first23=Ellen | last24=Zielinski | first24=Michal | last25=Steinegger | first25=Martin | last26=Pacholska | first26=Michalina | last27=Berghammer | first27=Tamas | last28=Bodenstein | first28=Sebastian | last29=Silver | first29=David | last30=Vinyals | first30=Oriol | journal=Nature | volume=596 | issue=7873 | pages=583–589 | pmid=34265844 | pmc=8371605 | bibcode=2021Natur.596..583J | display-authors=1 }}

2021: Scientists reported that xenobots are able to self-replicate by gathering loose cells in the environment and then forming new xenobots.{{cite journal | vauthors = Kriegman S, Blackiston D, Levin M, Bongard J | title = Kinematic self-replication in reconfigurable organisms | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 118 | issue = 49 | date = December 2021 | pmid = 34845026 | pmc = 8670470 | doi = 10.1073/pnas.2112672118 | bibcode = 2021PNAS..11812672K | doi-access = free }}

2023: Advancements in RNA therapeutics, including vaccines, RNA circuits, and genetic modifications, have improved safety and efficiency in synthetic biology. RNA-based therapeutics are considered safer than DNA-based systems as they do not integrate into the host genome, reducing the risk of unintended genetic alterations. Additionally, RNA-based systems, constructed from RNA devices and circuits, act more rapidly than DNA-based counterparts since they do not require transcription. These advancements have expanded the potential applications of RNA in gene therapy, personalized medicine, and vaccine development.{{Cite journal

| last1 = Pfeifer

| first1 = Blaine A.

| last2 = Beitelshees

| first2 = Marie

| last3 = Hill

| first3 = Andrew

| last4 = Bassett

| first4 = Justin

| last5 = Jones

| first5 = Charles H.

| title = Harnessing synthetic biology for advancing RNA therapeutics and vaccine design

| journal = npj Systems Biology and Applications

| volume = 9

| issue = 1

| date = 30 November 2023

| page = 60

| doi = 10.1038/s41540-023-00323-3

| pmid = 38036580

| pmc = 10689799

}}

It is a field whose scope is expanding in terms of systems integration, engineered organisms, and practical findings.

Engineers view biology as technology (in other words, a given system includes biotechnology or its biological engineering).{{cite journal | volume = 6 | vauthors = Zeng J | title = On the concept of systems bio-engineering | journal = Coomunication on Transgenic Animals, June 1994, CAS, PRC }} Synthetic biology includes the broad redefinition and expansion of biotechnology, with the ultimate goal of being able to design and build engineered live biological systems that process information, manipulate chemicals, fabricate materials and structures, produce energy, provide food, and maintain and enhance human health, as well as advance fundamental knowledge of biological systems {{Crossreference|(see Biomedical engineering)}} and our environment.{{cite journal | volume = 6 | vauthors = Chopra P, Kamma A | title = Engineering life through Synthetic Biology | journal = In Silico Biology }}

Researchers and companies working in synthetic biology are using nature's power to solve issues in agriculture, manufacturing, and medicine.

Due to more powerful genetic engineering capabilities and decreased DNA synthesis and sequencing costs, the field of synthetic biology is rapidly growing. In 2016, more than 350 companies across 40 countries were actively engaged in synthetic biology applications; all these companies had an estimated net worth of $3.9 billion in the global market.{{cite journal |vauthors=Flores Bueso Y, Tangney M |date=May 2017 |title=Synthetic Biology in the Driving Seat of the Bioeconomy |journal=Trends in Biotechnology |volume=35 |issue=5 |pages=373–378 |doi=10.1016/j.tibtech.2017.02.002 |pmid=28249675}} Synthetic biology currently has no generally accepted definition. Here are a few examples:

It is the science of emerging genetic and physical engineering to produce new (and, therefore, synthetic) life forms. To develop organisms with novel or enhanced characteristics, this emerging field of study combines biology, engineering, and related disciplines' knowledge and techniques to design chemically synthesised DNA.{{cite journal |vauthors=Hunter D |date=October 2013 |title=How to object to radically new technologies on the basis of justice: the case of synthetic biology |journal=Bioethics |volume=27 |issue=8 |pages=426–434 |doi=10.1111/bioe.12049 |pmid=24010854 |s2cid=23895514}}{{cite journal |vauthors=Gutmann A |year=2011 |title=The ethics of synthetic biology: guiding principles for emerging technologies |journal=The Hastings Center Report |volume=41 |issue=4 |pages=17–22 |doi=10.1002/j.1552-146x.2011.tb00118.x |pmid=21845917 |s2cid=20662786}}

Biomolecular engineering includes approaches that aim to create a toolkit of functional units that can be introduced to present new technological functions in living cells. Genetic engineering includes approaches to construct synthetic chromosomes or minimal organisms like Mycoplasma laboratorium.

Biomolecular design refers to the general idea of de novo design and additive combination of biomolecular components. Each of these approaches shares a similar task: to develop a more synthetic entity at a higher level of complexity by inventively manipulating a simpler part at the preceding level.{{cite journal | vauthors = Channon K, Bromley EH, Woolfson DN | title = Synthetic biology through biomolecular design and engineering | journal = Current Opinion in Structural Biology | volume = 18 | issue = 4 | pages = 491–498 | date = August 2008 | pmid = 18644449 | doi = 10.1016/j.sbi.2008.06.006 }}{{cite journal | vauthors = Duran-Nebreda S, Pla J, Vidiella B, Piñero J, Conde-Pueyo N, Solé R | title = Synthetic Lateral Inhibition in Periodic Pattern Forming Microbial Colonies | journal = ACS Synthetic Biology | volume = 10 | issue = 2 | pages = 277–285 | date = February 2021 | pmid = 33449631 | pmc = 8486170 | doi = 10.1021/acssynbio.0c00318 | s2cid = 231624252 }} Optimizing these exogenous pathways in unnatural systems takes iterative fine-tuning of the individual biomolecular components to select the highest concentrations of the desired product.{{Cite web| vauthors = van Warmerdam T |date=December 25, 2021|title=Exploring biotechnological advancements in the exogenous biological production of industrial small molecules and pharmaceuticals|url=https://www.yourbiohelper.com/research|website=YourBioHelper.com}}

On the other hand, "re-writers" are synthetic biologists interested in testing the irreducibility of biological systems. Due to the complexity of natural biological systems, it would be simpler to rebuild the natural systems of interest from the ground up; to provide engineered surrogates that are easier to comprehend, control and manipulate.{{cite journal | vauthors = Stone M | title = Life Redesigned to Suit the Engineering Crowd | journal = Microbe | volume = 1 | issue = 12 | pages = 566–570 | date = 2006 | s2cid = 7171812 | url = https://pdfs.semanticscholar.org/8d45/e0f37a0fb6c1a3c659c71ee9c52619b18364.pdf | archive-url = https://web.archive.org/web/20180612142707/https://pdfs.semanticscholar.org/8d45/e0f37a0fb6c1a3c659c71ee9c52619b18364.pdf | url-status = dead | archive-date = 2018-06-12 }} Re-writers draw inspiration from refactoring, a process sometimes used to improve computer software.

Bioengineering, synthetic genomics, protocell synthetic biology, unconventional molecular biology, and in silico techniques are the five categories of synthetic biology.{{Cite journal |last=Deplazes |first=Anna |date=May 2009 |title=Piecing together a puzzle: An exposition of synthetic biology |journal=EMBO Reports |language=en |volume=10 |issue=5 |pages=428–432 |doi=10.1038/embor.2009.76 |issn=1469-221X |pmc=2680885 |pmid=19415076}}

It is necessary to review the distinctions and analogies between the categories of synthetic biology for its social and ethical assessment, to distinguish between issues affecting the whole field and particular to a specific one.

The subfield of bioengineering concentrates on creating novel metabolic and regulatory pathways, and is currently the one that likely draws the attention of most researchers and funding. It is primarily motivated by the desire to establish biotechnology as a legitimate engineering discipline. When referring to this area of synthetic biology, the word "bioengineering" should not be confused with "traditional genetic engineering", which involves introducing a single transgene into the intended organism. Bioengineers adapted synthetic biology to provide a substantially more integrated perspective on how to alter organisms or metabolic systems.

A typical example of single-gene genetic engineering is the insertion of the human insulin gene into bacteria to create transgenic proteins. The creation of whole new signalling pathways, containing numerous genes and regulatory components (such as an oscillator circuit to initiate the periodic production of green fluorescent protein (GFP) in mammalian cells), is known as bioengineering as part of synthetic biology.

By utilising simplified and abstracted metabolic and regulatory modules as well as other standardized parts that may be freely combined to create new pathways or creatures, bioengineering aims to create innovative biological systems. In addition to creating infinite opportunities for novel applications, this strategy is anticipated to make bioengineering more predictable and controllable than traditional biotechnology.

The formation of animals with a chemically manufactured (minimal) genome is another facet of synthetic biology that is highlighted by synthetic genomics. This area of synthetic biology has been made possible by ongoing advancements in DNA synthesis technology, which now makes it feasible to produce DNA molecules with thousands of base pairs at a reasonable cost. The goal is to combine these molecules into complete genomes and transplant them into living cells, replacing the host cell's genome and reprogramming its metabolism to perform different functions.

Scientists have previously demonstrated the potential of this approach by creating infectious viruses by synthesising the genomes of multiple viruses. These significant advances in science and technology triggered the initial public concerns concerning the risks associated with this technology.

A simple genome might also work as a "chassis genome" that could be enlarged quickly by gene inclusion created for particular tasks. Such "chassis creatures" would be more suited for the insertion of new functions than wild organisms since they would have fewer biological pathways that could potentially conflict with the new functionalities in addition to having specific insertion sites. Synthetic genomics strives to create creatures with novel "architectures," much like the bioengineering method. It adopts an integrative or holistic perspective of the organism. In this case, the objective is the creation of chassis genomes based on necessary genes and other required DNA sequences rather than the design of metabolic or regulatory pathways based on abstract criteria.

The in vitro generation of synthetic cells is the protocell branch of synthetic biology. Lipid vesicles, which have all the necessary components to function as a complete system, can be used to create these artificial cells. In the end, these synthetic cells should meet the requirements for being deemed alive, namely the capacity for self-replication, self-maintenance, and evolution. The protocell technique has this as its end aim, however there are other intermediary steps that fall short of meeting all the criteria for a living cell. In order to carry out a specific function, these lipid vesicles contain cell extracts or more specific sets of biological macromolecules and complex structures, such as enzymes, nucleic acids, or ribosomes. For instance, liposomes may carry out particular polymerase chain reactions or synthesise a particular protein.

Protocell synthetic biology takes artificial life one step closer to reality by eventually synthesizing not only the genome but also every component of the cell in vitro, as opposed to the synthetic genomics approach, which relies on coercing a natural cell to carry out the instructions encoded by the introduced synthetic genome. Synthetic biologists in this field view their work as basic study into the conditions necessary for life to exist and its origin more than in any of the other techniques. The protocell technique, however, also lends itself well to applications; similar to other synthetic biology byproducts, protocells could be employed for the manufacture of biopolymers and medicines.

The objective of the "unnatural molecular biology" strategy is to create new varieties of life that are based on a different kind of molecular biology, such as new types of nucleic acids or a new genetic code. The creation of new types of nucleotides that can be built into unique nucleic acids could be accomplished by changing certain DNA or RNA constituents, such as the bases or the backbone sugars.

The normal genetic code is being altered by inserting quadruplet codons or changing some codons to encode new amino acids, which would subsequently permit the use of non-natural amino acids with unique features in protein production. It is a scientific and technological problem to adjust the enzymatic machinery of the cell for both approaches.

A new sort of life would be formed by organisms with a genome built on synthetic nucleic acids or on a totally new coding system for synthetic amino acids. This new style of life would have some benefits but also some new dangers. On release into the environment, there would be no horizontal gene transfer or outcrossing of genes with natural species. Furthermore, these kinds of synthetic organisms might be created to require non-natural materials for protein or nucleic acid synthesis, rendering them unable to thrive in the wild if they accidentally escaped.

On the other hand, if these organisms ultimately were able to survive outside of controlled space, they might have a particular benefit over natural organisms because they would be resistant to predatory living organisms or natural viruses, that could lead to an unmanaged spread of the synthetic organisms.

Synthetic biology in silico and the various strategies are interconnected. The development of complex designs, whether they are metabolic pathways, fundamental cellular processes, or chassis genomes, is one of the major difficulties faced by the four synthetic-biology methods outlined above. Because of this, synthetic biology has a robust in silico branch, similar to systems biology, that aims to create computational models for the design of common biological components or synthetic circuits, which are essentially simulations of synthetic organisms.

The practical application of simulations and models through bioengineering or other fields of synthetic biology is the long-term goal of in silico synthetic biology. Many of the computational simulations of synthetic organisms up to this point possess little to no direct analogy to living things. Due to this, in silico synthetic biology is regarded as a separate group in this article.

It is sensible to integrate the five areas under the umbrella of synthetic biology as one unified area of study. Even though they focus on various facets of life, such as metabolic regulation, essential elements, or biochemical makeup, these five strategies all work toward the same end: creating new types of living organisms. Additionally, the varied methodologies begin with numerous methodological approaches, which leads to the diversity of synthetic biology approaches.

Synthetic biology is an interdisciplinary field that draws from and is inspired by many different scientific disciplines, not one single field or technique. Synthetic biologists all have the same underlying objective of designing and producing new forms of life, despite the fact that they may employ various methodologies, techniques, and research instruments. Any evaluation of synthetic biology, whether it examines ethical, legal, or safety considerations, must take into account the fact that while some questions, risks, and issues are unique to each technique, in other circumstances, synthetic biology as a whole must be taken into consideration.

Synthetic biology has traditionally been divided into four different engineering approaches: top down, parallel, orthogonal and bottom up.{{Citation |last=Acevedo-Rocha |first=Carlos G. |title=The Synthetic Nature of Biology |date=2016 |url=https://doi.org/10.1007/978-3-319-21088-9_2 |work=Ambivalences of Creating Life: Societal and Philosophical Dimensions of Synthetic Biology |series=Ethics of Science and Technology Assessment |volume=45 |pages=9–53 |editor-last=Hagen |editor-first=Kristin |place=Cham |publisher=Springer International Publishing |language=en |doi=10.1007/978-3-319-21088-9_2 |isbn=978-3-319-21088-9 |pmc=7123144 |access-date=2023-01-23 |editor2-last=Engelhard |editor2-first=Margret |editor3-last=Toepfer |editor3-first=Georg}}

To replicate emergent behaviours from natural biology and build artificial life, unnatural chemicals are used. The other looks for interchangeable components from biological systems to put together and create systems that do not work naturally. In either case, a synthetic objective compels researchers to venture into new area in order to engage and resolve issues that cannot be readily resolved by analysis. Due to this, new paradigms are driven to arise in ways that analysis cannot easily do. In addition to equipments that oscillate, creep, and play tic-tac-toe, synthetic biology has produced diagnostic instruments that enhance the treatment of patients with infectious diseases.{{cite journal |vauthors=Benner SA, Sismour AM |date=July 2005 |title=Synthetic biology |journal=Nature Reviews. Genetics |volume=6 |issue=7 |pages=533–543 |doi=10.1038/nrg1637 |pmc=7097405 |pmid=15995697}}

It involves using metabolic and genetic engineering techniques to impart new functions to living cells.{{Cite journal |last=Schwille |first=Petra |date=2011-09-02 |title=Bottom-Up Synthetic Biology: Engineering in a Tinkerer's World |url=https://www.science.org/doi/10.1126/science.1211701 |journal=Science |language=en |volume=333 |issue=6047 |pages=1252–1254 |doi=10.1126/science.1211701 |pmid=21885774 |bibcode=2011Sci...333.1252S |s2cid=43354332 |issn=0036-8075|url-access=subscription }} By comparing universal genes and eliminating non-essential ones to create a basic genome, this method seeks to lessen the complexity of existing cells. These initiatives are founded on the hypothesis of a single genesis for cellular life, the so-called Last Universal Common Ancestor, which supports the presence of a universal minimal genome that gave rise to all living things. Recent studies, however, raise the possibility that the eukaryotic and prokaryotic cells that make up the tree of life may have evolved from a group of primordial cells rather than from a single cell. As a result, even while the Holy Grail-like pursuit of the "minimum genome" has grown elusive, cutting out a number of non-essential functions impairs an organism's fitness and leads to "fragile" genomes.

This approach involves creating new biological systems in vitro by bringing together 'non-living' biomolecular components,{{cite journal |vauthors=Schwille P |date=September 2011 |title=Bottom-up synthetic biology: engineering in a tinkerer's world |journal=Science |volume=333 |issue=6047 |pages=1252–4 |bibcode=2011Sci...333.1252S |doi=10.1126/science.1211701 |pmid=21885774 |s2cid=43354332}} often with the aim of constructing an artificial cell.

Reproduction, replication, and assembly are three crucial self-organizational principles that are taken into account in order to accomplish this. Cells, which are made up of a container and a metabolism, are considered "hardware" in the definition of reproduction, whereas replication occurs when a system duplicates a perfect copy of itself, as in the case of DNA, which is considered "software." When vesicles or containers (such as Oparin's coacervates) formed of tiny droplets of molecules that are organic like lipids or liposomes, membrane-like structures comprising phospholipids, aggregate, assembly occur.

The study of protocells exists along with other in vitro synthetic biology initiatives that seek to produce minimal cells, metabolic pathways, or "never-born proteins" as well as to mimic physiological functions including cell division and growth. Recently a cell-free system capable of self-sustaining using CO2 was engineered by bottom-up integrating metabolism with gene expression.{{Cite journal |last1=Giaveri |first1=Simone |last2=Bohra |first2=Nitin |last3=Diehl |first3=Christoph |last4=Yang |first4=Hao Yuan |last5=Ballinger |first5=Martine |last6=Paczia |first6=Nicole |last7=Glatter |first7=Timo |last8=Erb |first8=Tobias J. |date=2024-07-12 |title=Integrated translation and metabolism in a partially self-synthesizing biochemical network |url=https://www.science.org/doi/abs/10.1126/science.adn3856 |journal=Science |volume=385 |issue=6705 |pages=174–178 |doi=10.1126/science.adn3856|pmid=38991083 |bibcode=2024Sci...385..174G }} This research, which is primarily essential, deserves proper recognition as synthetic biology research.

Parallel engineering is also known as bioengineering. The basic genetic code is the foundation for parallel engineering research, which uses conventional biomolecules like nucleic acids and the 20 amino acids to construct biological systems. For a variety of applications in biocomputing, bioenergy, biofuels, bioremediation, optogenetics, and medicine, it involves the standardisation of DNA components, engineering of switches, biosensors, genetic circuits, logic gates, and cellular communication operators. For directing the expression of two or more genes and/or proteins, the majority of these applications often rely on the use of one or more vectors (or plasmids). Small, circular, double-strand DNA units known as plasmids, which are primarily found in prokaryotic but can also occasionally be detected in eukaryotic cells, may replicate autonomously of chromosomal DNA.

It is also known as perpendicular engineering. This strategy, also referred to as "chemical synthetic biology," principally seeks to alter or enlarge the genetic codes of living systems utilising artificial DNA bases and/or amino acids. This subfield is also connected to xenobiology, a newly developed field that combines systems chemistry, synthetic biology, exobiology, and research into the origins of life. In recent decades, researchers have created compounds that are structurally similar to the DNA canonical bases to see if those "alien" or xeno (XNA) molecules may be employed as genetic information carriers. Similar to this, noncanonical moieties have taken the place of the DNA sugar (deoxyribose). In order to express information other than the 20 conventional amino acids of proteins, the genetic code can be altered or enlarged. One method involves incorporating a specified unnatural, noncanonical, or xeno amino acid (XAA) into one or more proteins at one or more precise places using orthogonal enzymes and a transfer RNA adaptor from an other organism. By using "directed evolution," which entails repeated cycles of gene mutagenesis (genotypic diversity production), screening or selection (of a specific phenotypic trait), and amplification of a better variant for the following iterative round, orthogonal enzymes are produced Numerous XAAs have been effectively incorporated into proteins in more complex creatures like worms and flies as well as in bacteria, yeast, and human cell lines. As a result of canonical DNA sequence changes, directed evolution also enables the development of orthogonal ribosomes, which make it easier to incorporate XAAs into proteins or create "mirror life," or biological systems that contain biomolecules made up of enantiomers with different chiral orientations.

Several novel enabling technologies were critical to the success of synthetic biology. Concepts include standardization of biological parts and hierarchical abstraction to permit using those parts in synthetic systems.{{cite journal | vauthors = Baker D, Church G, Collins J, Endy D, Jacobson J, Keasling J, Modrich P, Smolke C, Weiss R | display-authors = 6 | title = Engineering life: building a fab for biology | journal = Scientific American | volume = 294 | issue = 6 | pages = 44–51 | date = June 2006 | pmid = 16711359 | doi = 10.1038/scientificamerican0606-44 | bibcode = 2006SciAm.294f..44B }} DNA serves as the guide for how biological processes should function, like the score to a complex symphony of life. Our ability to comprehend and design biological systems has undergone significant modifications as a result of developments in the previous few decades in both reading (sequencing) and writing (synthesis) DNA sequences. These developments have produced ground-breaking techniques for designing, assembling, and modifying DNA-encoded genes, materials, circuits, and metabolic pathways, enabling an ever-increasing amount of control over biological systems and even entire organisms.{{cite journal | vauthors = Hughes RA, Ellington AD | title = Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology | journal = Cold Spring Harbor Perspectives in Biology | volume = 9 | issue = 1 | pages = a023812 | date = January 2017 | pmid = 28049645 | pmc = 5204324 | doi = 10.1101/cshperspect.a023812 }}

Basic technologies include reading and writing DNA (sequencing and fabrication). Measurements under multiple conditions are needed for accurate modeling and computer-aided design (CAD).

{{Main|Artificial gene synthesis|Synthetic genomics}}Driven by dramatic decreases in costs of oligonucleotide ("oligos") synthesis and the advent of PCR, the sizes of DNA constructions from oligos have increased to the genomic level.{{cite journal | vauthors = Kosuri S, Church GM | title = Large-scale de novo DNA synthesis: technologies and applications | journal = Nature Methods | volume = 11 | issue = 5 | pages = 499–507 | date = May 2014 | pmid = 24781323 | doi = 10.1038/nmeth.2918 | pmc = 7098426 }} In 2000, researchers reported synthesis of the 9.6 kbp (kilo bp) Hepatitis C virus genome from chemically synthesized 60 to 80-mers.{{cite journal | vauthors = Blight KJ, Kolykhalov AA, Rice CM | title = Efficient initiation of HCV RNA replication in cell culture | journal = Science | volume = 290 | issue = 5498 | pages = 1972–4 | date = December 2000 | pmid = 11110665 | doi = 10.1126/science.290.5498.1972 | bibcode = 2000Sci...290.1972B }} In 2002, researchers at Stony Brook University succeeded in synthesizing the 7741 bp poliovirus genome from its published sequence, producing the second synthetic genome, spanning two years.{{cite journal | vauthors = Couzin J | title = Virology. Active poliovirus baked from scratch | journal = Science | volume = 297 | issue = 5579 | pages = 174–5 | date = July 2002 | pmid = 12114601 | doi = 10.1126/science.297.5579.174b | s2cid = 83531627 }} In 2003, the 5386 bp genome of the bacteriophage Phi X 174 was assembled in about two weeks.{{cite journal | vauthors = Smith HO, Hutchison CA, Pfannkoch C, Venter JC | title = Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 100 | issue = 26 | pages = 15440–5 | date = December 2003 | pmid = 14657399 | pmc = 307586 | doi = 10.1073/pnas.2237126100 | bibcode = 2003PNAS..10015440S | doi-access = free }} In 2006, the same team, at the J. Craig Venter Institute, constructed and patented a synthetic genome of a novel minimal bacterium, Mycoplasma laboratorium and were working on getting it functioning in a living cell.{{cite news|url=https://www.nytimes.com/2007/06/29/science/29cells.html|title=Scientists Transplant Genome of Bacteria| vauthors = Wade N |date=2007-06-29|work=The New York Times|access-date=2007-12-28|issn=0362-4331}}{{cite journal | vauthors = Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA, Smith HO | title = Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome | journal = Science | volume = 319 | issue = 5867 | pages = 1215–20 | date = February 2008 | pmid = 18218864 | doi = 10.1126/science.1151721 | bibcode = 2008Sci...319.1215G | s2cid = 8190996 }}{{cite journal| vauthors = Ball P |date=2016|title=Man Made: A History of Synthetic Life|url=https://www.sciencehistory.org/distillations/magazine/man-made-a-history-of-synthetic-life|journal=Distillations|volume=2|issue=1|pages=15–23|access-date=22 March 2018}}

In 2007, it was reported that several companies were offering synthesis of genetic sequences up to 2000 base pairs (bp) long, for a price of about $1 per bp and a turnaround time of less than two weeks.{{cite news| issn = 0362-4331| vauthors = Pollack A | title = How Do You Like Your Genes? Biofabs Take Orders | work = The New York Times | access-date = 2007-12-28| date = 2007-09-12 | url = https://www.nytimes.com/2007/09/12/technology/techspecial/12gene.html?pagewanted=2&_r=1}} Oligonucleotides harvested from a photolithographic- or inkjet-manufactured DNA chip combined with PCR and DNA mismatch error-correction allows inexpensive large-scale changes of codons in genetic systems to improve gene expression or incorporate novel amino-acids (see George M. Church's and Anthony Forster's synthetic cell projects.{{Cite web|url=http://arep.med.harvard.edu/SBP|title=Synthetic Biology Projects|website=arep.med.harvard.edu|access-date=2018-02-17}}{{cite journal | vauthors = Forster AC, Church GM | title = Towards synthesis of a minimal cell | journal = Molecular Systems Biology | volume = 2 | issue = 1 | pages = 45 | date = 2006-08-22 | pmid = 16924266 | pmc = 1681520 | doi = 10.1038/msb4100090 }}). This favors a synthesis-from-scratch approach.

Additionally, the CRISPR/Cas system has emerged as a promising technique for gene editing. It was described as "the most important innovation in the synthetic biology space in nearly 30 years".{{cite news| vauthors = Basulto D |title=Everything you need to know about why CRISPR is such a hot technology|url=https://www.washingtonpost.com/news/innovations/wp/2015/11/04/everything-you-need-to-know-about-why-crispr-is-such-a-hot-technology/|access-date=5 December 2015|newspaper=Washington Post|date=November 4, 2015}} While other methods take months or years to edit gene sequences, CRISPR speeds that time up to weeks. Due to its ease of use and accessibility, however, it has raised ethical concerns, especially surrounding its use in biohacking.{{cite news |vauthors=Kahn J |title=The Crispr Quandary |url=https://www.nytimes.com/2015/11/15/magazine/the-crispr-quandary.html?_r=0 |access-date=5 December 2015 |work=The New York Times|date=November 9, 2015}}{{cite journal |vauthors=Ledford H |title=CRISPR, the disruptor |journal=Nature |date=June 3, 2015 |pmid=26040877 |doi=10.1038/522020a |volume=522 |issue=7554 |pages=20–4|bibcode=2015Natur.522...20L |doi-access=free}}{{cite magazine |vauthors=Higginbotham S |title=Top VC Says Gene Editing Is Riskier Than Artificial Intelligence |url=http://fortune.com/2015/12/04/khosla-crispr-ai/ |access-date=5 December 2015 |magazine=Fortune |date=4 December 2015}}

DNA sequencing determines the order of nucleotide bases in a DNA molecule. Synthetic biologists use DNA sequencing in their work in several ways. First, large-scale genome sequencing efforts continue to provide information on naturally occurring organisms. This information provides a rich substrate from which synthetic biologists can construct parts and devices. Second, sequencing can verify that the fabricated system is as intended. Third, fast, cheap, and reliable sequencing can facilitate rapid detection and identification of synthetic systems and organisms.{{cite journal| author = Rollie| date = 2012 |title = Designing biological systems: Systems Engineering meets Synthetic Biology| journal = Chemical Engineering Science| volume = 69 | pages = 1–29| doi=10.1016/j.ces.2011.10.068| issue=1| bibcode = 2012ChEnS..69....1R |display-authors=etal}}

This is the ability of a system or component to operate without reference to its context.{{cite journal | vauthors = Khalil AS, Collins JJ | title = Synthetic biology: applications come of age | journal = Nature Reviews. Genetics | volume = 11 | issue = 5 | pages = 367–379 | date = May 2010 | pmid = 20395970 | pmc = 2896386 | doi = 10.1038/nrg2775 }}

The most used{{Cite book|title=Synthetic Biology – A Primer| vauthors = Freemont PS, Kitney TI |date=2012|publisher=World Scientific|isbn=978-1-84816-863-3|doi=10.1142/p837}}{{rp|22–23}} standardized DNA parts are BioBrick plasmids, invented by Tom Knight in 2003. Biobricks are stored at the Registry of Standard Biological Parts in Cambridge, Massachusetts. The BioBrick standard has been used by tens of thousands of students worldwide in the international Genetically Engineered Machine (iGEM) competition. BioBrick Assembly Standard 10 promotes modularity by allowing BioBrick coding sequences to be spliced out and exchanged using restriction enzymes EcoRI or XbaI (BioBrick prefix) and SpeI and PstI (BioBrick suffix).{{rp|22–23}}

Sequence overlap between two genetic elements (genes or coding sequences), called overlapping genes, can prevent their individual manipulation.{{cite journal | vauthors = Wright BW, Molloy MP, Jaschke PR | title = Overlapping genes in natural and engineered genomes | journal = Nature Reviews. Genetics | volume = 23 | issue = 3 | pages = 154–168 | date = March 2022 | pmid = 34611352 | pmc = 8490965 | doi = 10.1038/s41576-021-00417-w }} To increase genome modularity, the practice of genome refactoring or improving "the internal structure of an existing system for future use, while simultaneously maintaining external system function"{{cite journal | vauthors = Chan LY, Kosuri S, Endy D | title = Refactoring bacteriophage T7 | journal = Molecular Systems Biology | volume = 1 | pages = 2005.0018 | date = 2005 | pmid = 16729053 | pmc = 1681472 | doi = 10.1038/msb4100025 }} has been adopted across synthetic biology disciplines. Some notable examples of refactoring including the nitrogen fixation cluster{{cite journal | vauthors = Temme K, Zhao D, Voigt CA | title = Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 109 | issue = 18 | pages = 7085–7090 | date = May 2012 | pmid = 22509035 | pmc = 3345007 | doi = 10.1073/pnas.1120788109 | doi-access = free | bibcode = 2012PNAS..109.7085T }} and type III secretion system{{cite journal | vauthors = Song M, Sukovich DJ, Ciccarelli L, Mayr J, Fernandez-Rodriguez J, Mirsky EA, Tucker AC, Gordon DB, Marlovits TC, Voigt CA | display-authors = 6 | title = Control of type III protein secretion using a minimal genetic system | journal = Nature Communications | volume = 8 | issue = 1 | pages = 14737 | date = May 2017 | pmid = 28485369 | pmc = 5436071 | doi = 10.1038/ncomms14737 | bibcode = 2017NatCo...814737S }} along with bacteriophages T7 and ΦX174.{{cite journal | vauthors = Jaschke PR, Lieberman EK, Rodriguez J, Sierra A, Endy D | title = A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast | journal = Virology | volume = 434 | issue = 2 | pages = 278–284 | date = December 2012 | pmid = 23079106 | doi = 10.1016/j.virol.2012.09.020 | doi-access = free }}

While DNA is most important for information storage, a large fraction of the cell's activities are carried out by proteins. Tools can send proteins to specific regions of the cell and to link different proteins together. The interaction strength between protein partners should be tunable between a lifetime of seconds (desirable for dynamic signaling events) up to an irreversible interaction (desirable for device stability or resilient to harsh conditions). Interactions such as coiled coils,{{cite journal | vauthors = Woolfson DN, Bartlett GJ, Bruning M, Thomson AR | title = New currency for old rope: from coiled-coil assemblies to α-helical barrels | journal = Current Opinion in Structural Biology | volume = 22 | issue = 4 | pages = 432–41 | date = August 2012 | pmid = 22445228 | doi = 10.1016/j.sbi.2012.03.002 }} SH3 domain-peptide binding{{cite journal | vauthors = Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KL, Keasling JD | title = Synthetic protein scaffolds provide modular control over metabolic flux | journal = Nature Biotechnology | volume = 27 | issue = 8 | pages = 753–9 | date = August 2009 | pmid = 19648908 | doi = 10.1038/nbt.1557 | s2cid = 2756476 }} or SpyTag/SpyCatcher{{cite journal | vauthors = Reddington SC, Howarth M | title = Secrets of a covalent interaction for biomaterials and biotechnology: SpyTag and SpyCatcher | journal = Current Opinion in Chemical Biology | volume = 29 | pages = 94–9 | date = December 2015 | pmid = 26517567 | doi = 10.1016/j.cbpa.2015.10.002 | doi-access = free | url = https://ora.ox.ac.uk/objects/uuid:9efe6e76-bc90-4f29-9332-babd367d9890/files/mef554acb3de40f147d002be164e6739d }} offer such control. In addition, it is necessary to regulate protein-protein interactions in cells, such as with light (using light-oxygen-voltage-sensing domains) or cell-permeable small molecules by chemically induced dimerization.{{cite journal | vauthors = Bayle JH, Grimley JS, Stankunas K, Gestwicki JE, Wandless TJ, Crabtree GR | title = Rapamycin analogs with differential binding specificity permit orthogonal control of protein activity | journal = Chemistry & Biology | volume = 13 | issue = 1 | pages = 99–107 | date = January 2006 | pmid = 16426976 | doi = 10.1016/j.chembiol.2005.10.017 | doi-access = free }}

In a living cell, molecular motifs are embedded in a bigger network with upstream and downstream components. These components may alter the signaling capability of the modeling module. In the case of ultrasensitive modules, the sensitivity contribution of a module can differ from the sensitivity that the module sustains in isolation.{{cite journal | vauthors = Altszyler E, Ventura A, Colman-Lerner A, Chernomoretz A | title = Impact of upstream and downstream constraints on a signaling module's ultrasensitivity | journal = Physical Biology | volume = 11 | issue = 6 | pages = 066003 | date = October 2014 | pmid = 25313165 | pmc = 4233326 | doi = 10.1088/1478-3975/11/6/066003 | bibcode = 2014PhBio..11f6003A }}{{cite journal | vauthors = Altszyler E, Ventura AC, Colman-Lerner A, Chernomoretz A | title = Ultrasensitivity in signaling cascades revisited: Linking local and global ultrasensitivity estimations | journal = PLOS ONE | volume = 12 | issue = 6 | pages = e0180083 | year = 2017 | pmid = 28662096 | pmc = 5491127 | doi = 10.1371/journal.pone.0180083 | bibcode = 2017PLoSO..1280083A | arxiv = 1608.08007 | doi-access = free }}

Models inform the design of engineered biological systems by better predicting system behavior prior to fabrication. Synthetic biology benefits from better models of how biological molecules bind substrates and catalyze reactions, how DNA encodes the information needed to specify the cell and how multi-component integrated systems behave. Multiscale models of gene regulatory networks focus on synthetic biology applications. Simulations can model all biomolecular interactions in transcription, translation, regulation and induction of gene regulatory networks.{{cite journal | vauthors = Carbonell-Ballestero M, Duran-Nebreda S, Montañez R, Solé R, Macía J, Rodríguez-Caso C | title = A bottom-up characterization of transfer functions for synthetic biology designs: lessons from enzymology | journal = Nucleic Acids Research | volume = 42 | issue = 22 | pages = 14060–14069 | date = December 2014 | pmid = 25404136 | pmc = 4267673 | doi = 10.1093/nar/gku964 }}

{{cite journal | vauthors = Kaznessis YN | title = Models for synthetic biology | journal = BMC Systems Biology | volume = 1 | issue = 1 | pages = 47 | date = November 2007 | pmid = 17986347 | pmc = 2194732 | doi = 10.1186/1752-0509-1-47 | doi-access = free }}

{{cite conference |vauthors=Tuza ZA, Singhal V, Kim J, Murray RM | title = An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular "breadboard" system. |book-title=52nd IEEE Conference on Decision and Control |date=December 2013 |doi=10.1109/CDC.2013.6760079}}{{cite journal | vauthors = LaFleur TL, Hossain A, Salis HM | title = Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria | journal = Nature Communications | volume = 13 | issue = 1 | pages = 5159 | date = September 2022 | pmid = 36056029 | doi = 10.1038/s41467-022-32829-5 | pmc = 9440211 | bibcode = 2022NatCo..13.5159L }}

Only extensive modelling can enable the exploration of dynamic gene expression in a form suitable for research and design due to the numerous involved species and the intricacy of their relationships. Dynamic simulations of the entire biomolecular interconnection involved in regulation, transport, transcription, induction, and translation enable the molecular level detailing of designs. As opposed to modelling artificial networks a posteriori, this is contrasted.{{Cite journal |last=Kaznessis |first=Yiannis N |date=2007 |title=Models for synthetic biology |journal=BMC Systems Biology |language=en |volume=1 |issue=1 |pages=47 |doi=10.1186/1752-0509-1-47 |issn=1752-0509 |pmc=2194732 |pmid=17986347 |doi-access=free }}

Microfluidics, in particular droplet microfluidics, is an emerging tool used to construct new components, and to analyze and characterize them.{{cite journal | vauthors = Elani Y | title = Construction of membrane-bound artificial cells using microfluidics: a new frontier in bottom-up synthetic biology | journal = Biochemical Society Transactions | volume = 44 | issue = 3 | pages = 723–30 | date = June 2016 | pmid = 27284034 | pmc = 4900754 | doi = 10.1042/BST20160052 }}{{cite journal | vauthors = Gach PC, Iwai K, Kim PW, Hillson NJ, Singh AK | title = Droplet microfluidics for synthetic biology | journal = Lab on a Chip | volume = 17 | issue = 20 | pages = 3388–3400 | date = October 2017 | pmid = 28820204 | doi = 10.1039/C7LC00576H | osti = 1421856 | s2cid = 206094816 | url = https://escholarship.org/content/qt6cr3k0v5/qt6cr3k0v5.pdf?t=oz5hqt }} It is widely employed in screening assays.{{cite journal | vauthors = Vinuselvi P, Park S, Kim M, Park JM, Kim T, Lee SK | title = Microfluidic technologies for synthetic biology | journal = International Journal of Molecular Sciences | volume = 12 | issue = 6 | pages = 3576–93 | date = 2011-06-03 | pmid = 21747695 | pmc = 3131579 | doi = 10.3390/ijms12063576 | doi-access = free }}

Studies have considered the components of the DNA transcription mechanism. One desire of scientists creating synthetic biological circuits is to be able to control the transcription of synthetic DNA in unicellular organisms (prokaryotes) and in multicellular organisms (eukaryotes). One study tested the adjustability of synthetic transcription factors (sTFs) in areas of transcription output and cooperative ability among multiple transcription factor complexes.{{cite journal | vauthors = Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ | title = A synthetic biology framework for programming eukaryotic transcription functions | journal = Cell | volume = 150 | issue = 3 | pages = 647–58 | date = August 2012 | pmid = 22863014 | pmc = 3653585 | doi = 10.1016/j.cell.2012.05.045 }} Researchers were able to mutate functional regions called zinc fingers, the DNA specific component of sTFs, to decrease their affinity for specific operator DNA sequence sites, and thus decrease the associated site-specific activity of the sTF (usually transcriptional regulation). They further used the zinc fingers as components of complex-forming sTFs, which are the eukaryotic translation mechanisms.

Synthetic biology initiatives frequently aim to redesign organisms so that they can create a material, such as a drug or fuel, or acquire a new function, such as the ability to sense something in the environment. Examples of what researchers are creating using synthetic biology include:

• Utilizing microorganisms for bioremediation to remove contaminants from our water, soil, and air.
• Production of complex natural products that are usually extracted from plants but cannot be obtained in sufficient amounts, e.g. drugs of natural origin, such as artemisinin and paclitaxel.
• Beta-carotene, a substance typically associated with carrots that prevents vitamin A deficiency, is produced by rice that has been modified. Every year, between 250,000 and 500,000 children lose their vision due to vitamin A deficiency, which also significantly raises their chance of dying from infectious infections.
• As a sustainable and environmentally benign alternative to the fresh roses that perfumers use to create expensive smells, yeast has been created to produce rose oil.{{Cite web |title=Synthetic Biology |url=https://www.genome.gov/about-genomics/policy-issues/Synthetic-Biology |access-date=2023-01-23 |website=Genome.gov |language=en}}

A biosensor refers to an engineered organism, usually a bacterium, that is capable of reporting some ambient phenomenon such as the presence of heavy metals or toxins. One such system is the Lux operon of Aliivibrio fischeri,{{cite journal | vauthors = de Almeida PE, van Rappard JR, Wu JC | title = In vivo bioluminescence for tracking cell fate and function | journal = American Journal of Physiology. Heart and Circulatory Physiology | volume = 301 | issue = 3 | pages = H663–71 | date = September 2011 | pmid = 21666118 | pmc = 3191083 | doi = 10.1152/ajpheart.00337.2011 }} which codes for the enzyme that is the source of bacterial bioluminescence, and can be placed after a respondent promoter to express the luminescence genes in response to a specific environmental stimulus.{{cite journal | vauthors = Close DM, Xu T, Sayler GS, Ripp S | title = In vivo bioluminescent imaging (BLI): noninvasive visualization and interrogation of biological processes in living animals | journal = Sensors | volume = 11 | issue = 1 | pages = 180–206 | date = 2011 | pmid = 22346573 | pmc = 3274065 | doi = 10.3390/s110100180 | doi-access = free }} One such sensor created, consisted of a bioluminescent bacterial coating on a photosensitive computer chip to detect certain petroleum pollutants. When the bacteria sense the pollutant, they luminesce.{{cite journal| vauthors = Gibbs WW |date=1997 |title=Critters on a Chip |url=http://www.sciam.com/article.cfm?id=critters-on-a-chip |journal=Scientific American|access-date=2 Mar 2009}} Another example of a similar mechanism is the detection of landmines by an engineered E.coli reporter strain capable of detecting TNT and its main degradation product DNT, and consequently producing a green fluorescent protein (GFP).{{cite journal | vauthors = Belkin S, Yagur-Kroll S, Kabessa Y, Korouma V, Septon T, Anati Y, Zohar-Perez C, Rabinovitz Z, Nussinovitch A, Agranat AJ | display-authors = 6 | title = Remote detection of buried landmines using a bacterial sensor | journal = Nature Biotechnology | volume = 35 | issue = 4 | pages = 308–310 | date = April 2017 | pmid = 28398330 | doi = 10.1038/nbt.3791 | s2cid = 3645230 }}

Modified organisms can sense environmental signals and send output signals that can be detected and serve diagnostic purposes. Microbe cohorts have been used.{{cite journal | vauthors = Danino T, Prindle A, Kwong GA, Skalak M, Li H, Allen K, Hasty J, Bhatia SN | title = Programmable probiotics for detection of cancer in urine | journal = Science Translational Medicine | volume = 7 | issue = 289 | pages = 289ra84 | date = May 2015 | pmid = 26019220 | pmc = 4511399 | doi = 10.1126/scitranslmed.aaa3519 }}

Biosensors could also be used to detect pathogenic signatures—such as of SARS-CoV-2—and can be wearable.{{cite news |title=Face masks that can diagnose COVID-19 |url=https://medicalxpress.com/news/2021-06-masks-covid-.html |access-date=11 July 2021 |work=medicalxpress.com |language=en}}{{cite journal | vauthors = Nguyen PQ, Soenksen LR, Donghia NM, Angenent-Mari NM, de Puig H, Huang A, Lee R, Slomovic S, Galbersanini T, Lansberry G, Sallum HM, Zhao EM, Niemi JB, Collins JJ | display-authors = 6 | title = Wearable materials with embedded synthetic biology sensors for biomolecule detection | journal = Nature Biotechnology | volume = 39 | issue = 11 | pages = 1366–1374 | date = November 2021 | pmid = 34183860 | doi = 10.1038/s41587-021-00950-3 | s2cid = 235673261 | doi-access = free | hdl = 1721.1/131278 | hdl-access = free }}

For the purpose of detecting and reacting to various and temporary environmental factors, cells have developed a wide range of regulatory circuits, ranging from transcriptional to post-translational. These circuits are made up of transducer modules that filter the signals and activate a biological response, as well as carefully designed sensitive sections that attach analytes and regulate signal-detection thresholds. Modularity and selectivity are programmed to biosensor circuits at the transcriptional, translational, and post-translational levels, to achieve the delicate balancing of the two basic sensing modules.{{Cite journal |last1=Khalil |first1=Ahmad S. |last2=Collins |first2=James J. |date=May 2010 |title=Synthetic biology: applications come of age |journal=Nature Reviews Genetics |language=en |volume=11 |issue=5 |pages=367–379 |doi=10.1038/nrg2775 |pmid=20395970 |pmc=2896386 |issn=1471-0064}}

{{Excerpt | 1=Cellular agriculture }}

File:Assembly of fibrous muscle, fat, and vascular tissues to cultured steak.webp method to produce steak-like cultured meat.{{cite news |title=Japanese scientists produce first 3D-bioprinted, marbled Wagyu beef |url=https://newatlas.com/science/world-first-lab-grown-wagyu-beef-japan/ |access-date=21 September 2021 |work=New Atlas |date=25 August 2021}}{{cite journal |vauthors=Kang DH, Louis F, Liu H, Shimoda H, Nishiyama Y, Nozawa H, Kakitani M, Takagi D, Kasa D, Nagamori E, Irie S, Kitano S, Matsusaki M |display-authors=6 |title=Engineered whole cut meat-like tissue by the assembly of cell fibers using tendon-gel integrated bioprinting |journal=Nature Communications |volume=12 |issue=1 |pages=5059 |date=August 2021 |pmid=34429413 |pmc=8385070 |doi=10.1038/s41467-021-25236-9 |bibcode=2021NatCo..12.5059K}}]]

However, not all synthetic nutrition products are animal food products – for instance, as of 2021, there are also products of synthetic coffee that are reported to be close to commercialization.{{cite news | vauthors = Lavars N |title=Lab-grown coffee cuts out the beans and deforestation |url=https://newatlas.com/science/lab-grown-coffee-beans-deforestation/ |access-date=18 October 2021 |work=New Atlas |date=20 September 2021}}{{cite news |title=Eco-friendly, lab-grown coffee is on the way, but it comes with a catch |url=https://www.theguardian.com/environment/2021/oct/16/lab-grown-coffee-eco-friendly |access-date=26 October 2021 |work=The Guardian |date=16 October 2021 |language=en}}{{cite web |title=Sustainable coffee grown in Finland | work = VTT News | date = 15 September 2021 |url=https://www.vttresearch.com/en/news-and-ideas/sustainable-coffee-grown-finland-land-drinks-most-coffee-capita-produces-its-first |access-date=18 October 2021 |language=en}} Similar fields of research and production based on synthetic biology that can be used for the production of food and drink are:

• Genetically engineered microbial food cultures (e.g. for solar-energy-based protein powder){{cite news |title=Growing food with air and solar power: More efficient than planting crops |url=https://phys.org/news/2021-06-food-air-solar-power-efficient.html |access-date=11 July 2021 |work=phys.org |language=en}}{{cite journal | vauthors = Leger D, Matassa S, Noor E, Shepon A, Milo R, Bar-Even A | title = Photovoltaic-driven microbial protein production can use land and sunlight more efficiently than conventional crops | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 118 | issue = 26 | pages = e2015025118 | date = June 2021 | pmid = 34155098 | pmc = 8255800 | doi = 10.1073/pnas.2015025118 | bibcode = 2021PNAS..11815025L | s2cid = 235595143 | doi-access = free }}
• Cell-free artificial synthesis (e.g. synthetic starch;{{cite news |title=World-first artificial synthesis of starch from CO2 outperforms nature |url=https://newatlas.com/science/artificial-synthesis-starch-from-co2/ |access-date=18 October 2021 |work=New Atlas |date=28 September 2021}}{{cite journal | vauthors = Cai T, Sun H, Qiao J, Zhu L, Zhang F, Zhang J, Tang Z, Wei X, Yang J, Yuan Q, Wang W, Yang X, Chu H, Wang Q, You C, Ma H, Sun Y, Li Y, Li C, Jiang H, Wang Q, Ma Y | display-authors = 6 | title = Cell-free chemoenzymatic starch synthesis from carbon dioxide | language = EN | journal = Science | volume = 373 | issue = 6562 | pages = 1523–1527 | date = September 2021 | pmid = 34554807 | doi = 10.1126/science.abh4049 | s2cid = 237615280 | bibcode = 2021Sci...373.1523C | doi-access = free }} {{Crossreference|see Biobased economy#Agriculture}})

Photosynthetic microbial cells have been used as a step to synthetic production of spider silk.{{cite news |title=Spider silk made by photosynthetic bacteria |url=https://phys.org/news/2020-07-spider-silk-photosynthetic-bacteria.html |access-date=16 August 2020 |work=phys.org |language=en |archive-date=7 August 2020 |archive-url=https://web.archive.org/web/20200807092649/https://phys.org/news/2020-07-spider-silk-photosynthetic-bacteria.html |url-status=live }}{{cite journal | vauthors = Foong CP, Higuchi-Takeuchi M, Malay AD, Oktaviani NA, Thagun C, Numata K | title = A marine photosynthetic microbial cell factory as a platform for spider silk production | journal = Communications Biology | volume = 3 | issue = 1 | pages = 357 | date = July 2020 | pmid = 32641733 | pmc = 7343832 | doi = 10.1038/s42003-020-1099-6 | publisher = Springer Science and Business Media LLC }}

A biological computer refers to an engineered biological system that can perform computer-like operations, which is a dominant paradigm in synthetic biology. Researchers built and characterized a variety of logic gates in a number of organisms,{{cite journal | vauthors = Singh V | title = Recent advances and opportunities in synthetic logic gates engineering in living cells | journal = Systems and Synthetic Biology | volume = 8 | issue = 4 | pages = 271–82 | date = December 2014 | pmid = 26396651 | pmc = 4571725 | doi = 10.1007/s11693-014-9154-6 }} and demonstrated both analog and digital computation in living cells. They demonstrated that bacteria can be engineered to perform both analog and/or digital computation.{{cite journal | vauthors = Purcell O, Lu TK | title = Synthetic analog and digital circuits for cellular computation and memory | journal = Current Opinion in Biotechnology | volume = 29 | pages = 146–55 | date = October 2014 | pmid = 24794536 | pmc = 4237220 | doi = 10.1016/j.copbio.2014.04.009 | series = Cell and Pathway Engineering }}{{cite journal | vauthors = Daniel R, Rubens JR, Sarpeshkar R, Lu TK | title = Synthetic analog computation in living cells | journal = Nature | volume = 497 | issue = 7451 | pages = 619–23 | date = May 2013 | pmid = 23676681 | doi = 10.1038/nature12148 | bibcode = 2013Natur.497..619D | s2cid = 4358570 }} In 2007, in human cells, research demonstrated a universal logic evaluator that operates in mammalian cells.{{cite journal | vauthors = Rinaudo K, Bleris L, Maddamsetti R, Subramanian S, Weiss R, Benenson Y | title = A universal RNAi-based logic evaluator that operates in mammalian cells | journal = Nature Biotechnology | volume = 25 | issue = 7 | pages = 795–801 | date = July 2007 | pmid = 17515909 | doi = 10.1038/nbt1307 | s2cid = 280451 }} Subsequently, researchers utilized this paradigm to demonstrate a proof-of-concept therapy that uses biological digital computation to detect and kill human cancer cells in 2011.{{cite journal | vauthors = Xie Z, Wroblewska L, Prochazka L, Weiss R, Benenson Y | title = Multi-input RNAi-based logic circuit for identification of specific cancer cells | journal = Science | volume = 333 | issue = 6047 | pages = 1307–11 | date = September 2011 | pmid = 21885784 | doi = 10.1126/science.1205527 | bibcode = 2011Sci...333.1307X | s2cid = 13743291 | url = https://semanticscholar.org/paper/372e175668b5323d79950b58f12b36f6974a81ef }} In 2016, another group of researchers demonstrated that principles of computer engineering can be used to automate digital circuit design in bacterial cells.{{cite journal | vauthors = Nielsen AA, Der BS, Shin J, Vaidyanathan P, Paralanov V, Strychalski EA, Ross D, Densmore D, Voigt CA | title = Genetic circuit design automation | journal = Science | volume = 352 | issue = 6281 | pages = aac7341 | date = April 2016 | pmid = 27034378 | doi = 10.1126/science.aac7341 | doi-access = free }} In 2017, researchers demonstrated the 'Boolean logic and arithmetic through DNA excision' (BLADE) system to engineer digital computation in human cells.{{cite journal | vauthors = Weinberg BH, Pham NT, Caraballo LD, Lozanoski T, Engel A, Bhatia S, Wong WW | title = Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells | journal = Nature Biotechnology | volume = 35 | issue = 5 | pages = 453–462 | date = May 2017 | pmid = 28346402 | pmc = 5423837 | doi = 10.1038/nbt.3805 }} In 2019, researchers implemented a perceptron in biological systems opening the way for machine learning in these systems.{{cite journal | vauthors = Pandi A, Koch M, Voyvodic PL, Soudier P, Bonnet J, Kushwaha M, Faulon JL | title = Metabolic perceptrons for neural computing in biological systems | journal = Nature Communications | volume = 10 | issue = 1 | date = August 2019 | page = 3880 | pmid = 31462649 | pmc = 6713752 | doi = 10.1038/s41467-019-11889-0 | bibcode = 2019NatCo..10.3880P }}

{{Main|Transformation (genetics)}}Cells use interacting genes and proteins, which are called gene circuits, to implement diverse function, such as responding to environmental signals, decision making and communication. Three key components are involved: DNA, RNA and Synthetic biologist designed gene circuits that can control gene expression from several levels including transcriptional, post-transcriptional and translational levels.

Traditional metabolic engineering has been bolstered by the introduction of combinations of foreign genes and optimization by directed evolution. This includes engineering E. coli and yeast for commercial production of a precursor of the antimalarial drug, Artemisinin.{{cite journal | vauthors = Westfall PJ, Pitera DJ, Lenihan JR, Eng D, Woolard FX, Regentin R, Horning T, Tsuruta H, Melis DJ, Owens A, Fickes S, Diola D, Benjamin KR, Keasling JD, Leavell MD, McPhee DJ, Renninger NS, Newman JD, Paddon CJ | title = Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 109 | issue = 3 | pages = E111–8 | date = January 2012 | pmid = 22247290 | pmc = 3271868 | doi = 10.1073/pnas.1110740109 | bibcode = 2012PNAS..109E.111W | doi-access = free }}

Entire organisms have yet to be created from scratch, although living cells can be transformed with new DNA. Several ways allow constructing synthetic DNA components and even entire synthetic genomes, but once the desired genetic code is obtained, it is integrated into a living cell that is expected to manifest the desired new capabilities or phenotypes while growing and thriving.{{cite news |url=https://www.independent.co.uk/news/science/eureka-scientists-unveil-giant-leap-towards-synthetic-life-9219644.html |url-status=live |archive-url=https://ghostarchive.org/archive/20220526/https://www.independent.co.uk/news/science/eureka-scientists-unveil-giant-leap-towards-synthetic-life-9219644.html |archive-date=2022-05-26 |url-access=subscription |title=Eureka! Scientists unveil giant leap towards synthetic life| vauthors = Connor S |date=28 March 2014|work=The Independent|access-date=2015-08-06}} Cell transformation is used to create biological circuits, which can be manipulated to yield desired outputs.

By integrating synthetic biology with materials science, it would be possible to use cells as microscopic molecular foundries to produce materials whose properties were genetically encoded. Re-engineering has produced Curli fibers, the amyloid component of extracellular material of biofilms, as a platform for programmable nanomaterial. These nanofibers were genetically constructed for specific functions, including adhesion to substrates, nanoparticle templating and protein immobilization.{{cite journal|vauthors=Nguyen PQ, Botyanszki Z, Tay PK, Joshi NS|date=September 2014|title=Programmable biofilm-based materials from engineered curli nanofibres|journal=Nature Communications|volume=5|pages=4945|bibcode=2014NatCo...5.4945N|doi=10.1038/ncomms5945|pmid=25229329|doi-access=free}}

File:Top7.png protein was one of the first proteins designed for a fold that had never been seen before in nature.{{cite journal | vauthors = Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D | title = Design of a novel globular protein fold with atomic-level accuracy | journal = Science | volume = 302 | issue = 5649 | pages = 1364–8 | date = November 2003 | pmid = 14631033 | doi = 10.1126/science.1089427 | bibcode = 2003Sci...302.1364K | s2cid = 1939390 | url = https://semanticscholar.org/paper/3188f905b60172dcad17a9b8c23567400c2bb65f }} ]]

Natural proteins can be engineered, for example, by directed evolution, novel protein structures that match or improve on the functionality of existing proteins can be produced. One group generated a helix bundle that was capable of binding oxygen with similar properties as hemoglobin, yet did not bind carbon monoxide.{{cite journal | vauthors = Koder RL, Anderson JL, Solomon LA, Reddy KS, Moser CC, Dutton PL | title = Design and engineering of an O(2) transport protein | journal = Nature | volume = 458 | issue = 7236 | pages = 305–309 | date = March 2009 | pmid = 19295603 | pmc = 3539743 | doi = 10.1038/nature07841 | bibcode = 2009Natur.458..305K }} A similar protein structure was generated to support a variety of oxidoreductase activities{{cite journal | vauthors = Farid TA, Kodali G, Solomon LA, Lichtenstein BR, Sheehan MM, Fry BA, Bialas C, Ennist NM, Siedlecki JA, Zhao Z, Stetz MA, Valentine KG, Anderson JL, Wand AJ, Discher BM, Moser CC, Dutton PL | display-authors = 6 | title = Elementary tetrahelical protein design for diverse oxidoreductase functions | journal = Nature Chemical Biology | volume = 9 | issue = 12 | pages = 826–833 | date = December 2013 | pmid = 24121554 | pmc = 4034760 | doi = 10.1038/nchembio.1362 }} while another formed a structurally and sequentially novel ATPase.{{cite journal | vauthors = Wang MS, Hecht MH | title = A Completely De Novo ATPase from Combinatorial Protein Design | journal = Journal of the American Chemical Society | volume = 142 | issue = 36 | pages = 15230–15234 | date = September 2020 | pmid = 32833456 | doi = 10.1021/jacs.0c02954 | bibcode = 2020JAChS.14215230W | s2cid = 221308093 }} Another group generated a family of G-protein coupled receptors that could be activated by the inert small molecule clozapine N-oxide but insensitive to the native ligand, acetylcholine; these receptors are known as DREADDs.{{cite journal | vauthors = Armbruster BN, Li X, Pausch MH, Herlitze S, Roth BL | title = Evolving the lock to fit the key to create a family of G protein-coupled receptors potently activated by an inert ligand | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 12 | pages = 5163–5168 | date = March 2007 | pmid = 17360345 | pmc = 1829280 | doi = 10.1073/pnas.0700293104 | doi-access = free | bibcode = 2007PNAS..104.5163A | author5-link = Bryan Roth }} Novel functionalities or protein specificity can also be engineered using computational approaches. One study was able to use two different computational methods: a bioinformatics and molecular modeling method to mine sequence databases, and a computational enzyme design method to reprogram enzyme specificity. Both methods resulted in designed enzymes with greater than 100 fold specificity for production of longer chain alcohols from sugar.{{cite journal | vauthors = Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB | display-authors = 6 | title = Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway | journal = Nature Communications | volume = 6 | pages = 10005 | date = November 2015 | pmid = 26598135 | pmc = 4673503 | doi = 10.1038/ncomms10005 | bibcode = 2015NatCo...610005M }}

Another common investigation is expansion of the natural set of 20 amino acids. Excluding stop codons, 61 codons have been identified, but only 20 amino acids are coded generally in all organisms. Certain codons are engineered to code for alternative amino acids including: nonstandard amino acids such as O-methyl tyrosine; or exogenous amino acids such as 4-fluorophenylalanine. Typically, these projects make use of re-coded nonsense suppressor tRNA-Aminoacyl tRNA synthetase pairs from other organisms, though in most cases substantial engineering is required.{{cite journal | vauthors = Wang Q, Parrish AR, Wang L | title = Expanding the genetic code for biological studies | journal = Chemistry & Biology | volume = 16 | issue = 3 | pages = 323–36 | date = March 2009 | pmid = 19318213 | pmc = 2696486 | doi = 10.1016/j.chembiol.2009.03.001 }}

Other researchers investigated protein structure and function by reducing the normal set of 20 amino acids. Limited protein sequence libraries are made by generating proteins where groups of amino acids may be replaced by a single amino acid.{{cite journal | vauthors = Davidson AR, Lumb KJ, Sauer RT | title = Cooperatively folded proteins in random sequence libraries | journal = Nature Structural Biology | volume = 2 | issue = 10 | pages = 856–864 | date = October 1995 | pmid = 7552709 | doi = 10.1038/nsb1095-856 | s2cid = 31781262 }} For instance, several non-polar amino acids within a protein can all be replaced with a single non-polar amino acid.{{cite journal | vauthors = Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH | title = Protein design by binary patterning of polar and nonpolar amino acids | journal = Science | volume = 262 | issue = 5140 | pages = 1680–1685 | date = December 1993 | pmid = 8259512 | doi = 10.1126/science.8259512 | bibcode = 1993Sci...262.1680K }} One project demonstrated that an engineered version of Chorismate mutase still had catalytic activity when only nine amino acids were used.{{cite journal | vauthors = Walter KU, Vamvaca K, Hilvert D | title = An active enzyme constructed from a 9-amino acid alphabet | journal = The Journal of Biological Chemistry | volume = 280 | issue = 45 | pages = 37742–37746 | date = November 2005 | pmid = 16144843 | doi = 10.1074/jbc.M507210200 | doi-access = free }}

Researchers and companies practice synthetic biology to synthesize industrial enzymes with high activity, optimal yields and effectiveness. These synthesized enzymes aim to improve products such as detergents and lactose-free dairy products, as well as make them more cost effective.{{cite web|url=https://www.thermofisher.com/us/en/home/life-science/synthetic-biology/synthetic-biology-applications.html|title=Synthetic Biology Applications|website=www.thermofisher.com|access-date=2015-11-12}} The improvements of metabolic engineering by synthetic biology is an example of a biotechnological technique utilized in industry to discover pharmaceuticals and fermentive chemicals. Synthetic biology may investigate modular pathway systems in biochemical production and increase yields of metabolic production. Artificial enzymatic activity and subsequent effects on metabolic reaction rates and yields may develop "efficient new strategies for improving cellular properties ... for industrially important biochemical production".{{cite journal | vauthors = Liu Y, Shin HD, Li J, Liu L | title = Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects | journal = Applied Microbiology and Biotechnology | volume = 99 | issue = 3 | pages = 1109–18 | date = February 2015 | pmid = 25547833 | doi = 10.1007/s00253-014-6298-y | s2cid = 954858 }}

Scientists can encode digital information onto a single strand of synthetic DNA. In 2012, George M. Church encoded one of his books about synthetic biology in DNA. The 5.3 Mb of data was more than 1000 times greater than the previous largest amount of information to be stored in synthesized DNA.{{cite journal | vauthors = Church GM, Gao Y, Kosuri S | title = Next-generation digital information storage in DNA | journal = Science | volume = 337 | issue = 6102 | pages = 1628 | date = September 2012 | pmid = 22903519 | doi = 10.1126/science.1226355 | s2cid = 934617 | bibcode = 2012Sci...337.1628C | doi-access = free }} A similar project encoded the complete sonnets of William Shakespeare in DNA.{{cite web|url=http://news.sky.com/story/1041917/huge-amounts-of-data-can-be-stored-in-dna|title=Huge amounts of data can be stored in DNA|date=23 January 2013|publisher=Sky News|access-date=24 January 2013|archive-url=https://web.archive.org/web/20160531044937/http://news.sky.com/story/1041917/huge-amounts-of-data-can-be-stored-in-dna|archive-date=2016-05-31 }} More generally, algorithms such as NUPACK,{{cite journal | vauthors = Zadeh JN, Steenberg CD, Bois JS, Wolfe BR, Pierce MB, Khan AR, Dirks RM, Pierce NA | display-authors = 6 | title = NUPACK: Analysis and design of nucleic acid systems | journal = Journal of Computational Chemistry | volume = 32 | issue = 1 | pages = 170–173 | date = January 2011 | pmid = 20645303 | doi = 10.1002/jcc.21596 | s2cid = 33709556 | doi-access = free }} ViennaRNA,{{cite journal | vauthors = Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL | title = ViennaRNA Package 2.0 | journal = Algorithms for Molecular Biology | volume = 6 | issue = 1 | pages = 26 | date = November 2011 | pmid = 22115189 | pmc = 3319429 | doi = 10.1186/1748-7188-6-26 | doi-access = free }} Ribosome Binding Site Calculator,{{cite journal | vauthors = Salis HM, Mirsky EA, Voigt CA | title = Automated design of synthetic ribosome binding sites to control protein expression | journal = Nature Biotechnology | volume = 27 | issue = 10 | pages = 946–950 | date = October 2009 | pmid = 19801975 | pmc = 2782888 | doi = 10.1038/nbt.1568 }} Cello,{{cite journal | vauthors = Nielsen AA, Der BS, Shin J, Vaidyanathan P, Paralanov V, Strychalski EA, Ross D, Densmore D, Voigt CA | display-authors = 6 | title = Genetic circuit design automation | journal = Science | volume = 352 | issue = 6281 | pages = aac7341 | date = April 2016 | pmid = 27034378 | doi = 10.1126/science.aac7341 | doi-access = free }} and Non-Repetitive Parts Calculator{{cite journal | vauthors = Hossain A, Lopez E, Halper SM, Cetnar DP, Reis AC, Strickland D, Klavins E, Salis HM | display-authors = 6 | title = Automated design of thousands of nonrepetitive parts for engineering stable genetic systems | journal = Nature Biotechnology | volume = 38 | issue = 12 | pages = 1466–1475 | date = December 2020 | pmid = 32661437 | doi = 10.1038/s41587-020-0584-2 | s2cid = 220506228 | url = https://scholarsphere.psu.edu/resources/bc01023b-9262-4356-9e2a-81eb4d8e0068 | url-access = subscription }} enables the design of new genetic systems.

Many technologies have been developed for incorporating unnatural nucleotides and amino acids into nucleic acids and proteins, both in vitro and in vivo. For example, in May 2014, researchers announced that they had successfully introduced two new artificial nucleotides into bacterial DNA. By including individual artificial nucleotides in the culture media, they were able to exchange the bacteria 24 times; they did not generate mRNA or proteins able to use the artificial nucleotides.{{cite news|url=https://www.nytimes.com/2014/05/08/business/researchers-report-breakthrough-in-creating-artificial-genetic-code.html|title=Researchers Report Breakthrough in Creating Artificial Genetic Code| vauthors = Pollack A |date=May 7, 2014|work=New York Times|access-date=May 7, 2014}}{{cite journal| vauthors = Callaway E |date=May 7, 2014|title=First life with 'alien' DNA|url=http://www.nature.com/news/first-life-with-alien-dna-1.15179|journal=Nature|doi=10.1038/nature.2014.15179|s2cid=86967999|access-date=May 7, 2014|url-access=subscription}}{{cite journal|vauthors=Malyshev DA, Dhami K, Lavergne T, Chen T, Dai N, Foster JM, Corrêa IR, Romesberg FE|date=May 2014|title=A semi-synthetic organism with an expanded genetic alphabet|journal=Nature|volume=509|issue=7500|pages=385–8|bibcode=2014Natur.509..385M|doi=10.1038/nature13314|pmc=4058825|pmid=24805238}}

Synthetic biology raised NASA's interest as it could help to produce resources for astronauts from a restricted portfolio of compounds sent from Earth.{{Cite book| vauthors = Verseux CN, Paulino-Lima IG, Baqué M, Billi D, Rothschild LJ |date=2016|chapter=Synthetic Biology for Space Exploration: Promises and Societal Implications|title= Ambivalences of Creating Life|publisher=Springer-Verlag|volume=45|pages=73–100|doi=10.1007/978-3-319-21088-9_4|series=Ethics of Science and Technology Assessment|isbn=978-3-319-21087-2}}{{cite journal |vauthors=Menezes AA, Cumbers J, Hogan JA, Arkin AP |title=Towards synthetic biological approaches to resource utilization on space missions |journal=Journal of the Royal Society, Interface |volume=12 |issue=102 |pages=20140715 |date=January 2015 |pmid=25376875 |pmc=4277073 |doi=10.1098/rsif.2014.0715 }}{{cite journal |vauthors=Montague M, McArthur GH, Cockell CS, Held J, Marshall W, Sherman LA, Wang N, Nicholson WL, Tarjan DR, Cumbers J |display-authors=6 |title=The role of synthetic biology for in situ resource utilization (ISRU) |journal=Astrobiology |volume=12 |issue=12 |pages=1135–1142 |date=December 2012 |pmid=23140229 |doi=10.1089/ast.2012.0829 |bibcode=2012AsBio..12.1135M}} On Mars, in particular, synthetic biology could lead to production processes based on local resources, making it a powerful tool in the development of occupied outposts with less dependence on Earth. Work has gone into developing plant strains that are able to cope with the harsh Martian environment, using similar techniques to those employed to increase resilience to certain environmental factors in agricultural crops.{{Cite web| vauthors=Steigerwald B |title=NASA – Designer Plants on Mars |website=www.nasa.gov|language=en |url=https://www.nasa.gov/centers/goddard/news/topstory/2005/mars_plants.html |access-date=2020-05-29}}

{{Further|Artificial cell|Hypothetical types of biochemistry}}

File:Syn3 genome.svg functions in the minimal genome of the synthetic organism, Syn 3{{cite journal |vauthors=Hutchison CA, Chuang RY, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH, Gill J, Kannan K, Karas BJ, Ma L, Pelletier JF, Qi ZQ, Richter RA, Strychalski EA, Sun L, Suzuki Y, Tsvetanova B, Wise KS, Smith HO, Glass JI, Merryman C, Gibson DG, Venter JC |title=Design and synthesis of a minimal bacterial genome |journal=Science |volume=351 |issue=6280 |pages=aad6253 |date=March 2016 |pmid=27013737 |doi=10.1126/science.aad6253 |bibcode=2016Sci...351.....H |doi-access=free}}]]

One important topic in synthetic biology is synthetic life, that is concerned with hypothetical organisms created in vitro from biomolecules and/or chemical analogues thereof. Synthetic life experiments attempt to either probe the origins of life, study some of the properties of life, or more ambitiously to recreate life from non-living (abiotic) components. Synthetic life biology attempts to create living organisms capable of carrying out important functions, from manufacturing pharmaceuticals to detoxifying polluted land and water.{{cite news |url=https://www.independent.co.uk/news/science/major-synthetic-life-breakthrough-as-scientists-make-the-first-artificial-enzymes-9896333.html |url-status=live |archive-url=https://ghostarchive.org/archive/20220526/https://www.independent.co.uk/news/science/major-synthetic-life-breakthrough-as-scientists-make-the-first-artificial-enzymes-9896333.html |archive-date=2022-05-26 |url-access=subscription |vauthors=Connor S |title=Major synthetic life breakthrough as scientists make the first artificial enzymes |work=The Independent |location=London |date=1 December 2014 |access-date=2015-08-06}} In medicine, it offers prospects of using designer biological parts as a starting point for new classes of therapies and diagnostic tools.

A living "artificial cell" has been defined as a completely synthetic cell that can capture energy, maintain ion gradients, contain macromolecules as well as store information and have the ability to mutate.{{cite journal |vauthors=Deamer D |title=A giant step towards artificial life? |journal=Trends in Biotechnology |volume=23 |issue=7 |pages=336–338 |date=July 2005 |pmid=15935500 |doi=10.1016/j.tibtech.2005.05.008}} It has been claimed that this would be difficult, although researcher have created contenders for such artificial cells.{{cite journal |last=Bornscheuer |first=Uwe T. |date=2010-07-19 |title=The First Artificial Cell—A Revolutionary Step in Synthetic Biology? |url=https://onlinelibrary.wiley.com/doi/10.1002/anie.201003393 |journal=Angewandte Chemie International Edition |volume=49 |issue=31 |pages=5228–5230 |doi=10.1002/anie.201003393 |issn=1433-7851 |access-date=2025-04-12}}

A completely synthetic bacterial chromosome was produced in 2010 by Craig Venter, and his team introduced it to genomically emptied bacterial host cells.{{cite journal | vauthors = Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA, Smith HO, Venter JC | title = Creation of a bacterial cell controlled by a chemically synthesized genome | journal = Science | volume = 329 | issue = 5987 | pages = 52–6 | date = July 2010 | pmid = 20488990 | doi = 10.1126/science.1190719 | bibcode = 2010Sci...329...52G | doi-access = }} The host cells were able to grow and replicate.{{cite web| url=https://www.npr.org/templates/transcript/transcript.php?storyId=127010591| title=Scientists Reach Milestone On Way To Artificial Life| website=NPR| access-date=2010-06-09 |date=2010-05-20}}{{cite web| vauthors=Venter JC |title=From Designing Life to Prolonging Healthy Life |website=YouTube |date=25 January 2017 |publisher=University of California Television (UCTV) |url=https://www.youtube.com/watch?v=Gwu_djYMm3w&t=30s |access-date=1 February 2017 |archive-url=https://ghostarchive.org/varchive/youtube/20211221/Gwu_djYMm3w |archive-date=2021-12-21 |url-status=live}}{{cbignore}} The Mycoplasma laboratorium is the only living organism with completely engineered genome.

The first living organism with 'artificial' expanded DNA code was presented in 2014; the team used E. coli that had its genome extracted and replaced with a chromosome with an expanded genetic code. The nucleosides added are d5SICS and dNaM.

In May 2019, in a milestone effort, researchers reported the creation of a new synthetic (possibly artificial) form of viable life, a variant of the bacteria Escherichia coli, by reducing the natural number of 64 codons in the bacterial genome to 59 codons instead, in order to encode 20 amino acids.

In 2017, the international Build-a-Cell large-scale open-source research collaboration for the construction of synthetic living cells was started,{{cite web |url=http://buildacell.io/|title=Build-a-Cell|access-date=4 Dec 2019}} followed by national synthetic cell organizations in several countries, including FabriCell,{{cite web|url=http://fabricell.org/|title=FabriCell |access-date=8 Dec 2019}} MaxSynBio{{cite web |url=https://www.maxsynbio.mpg.de/home/|title=MaxSynBio – Max Planck Research Network in Synthetic Biology |access-date=8 Dec 2019}} and BaSyC.{{cite web |url=http://www.basyc.nl/|title=BaSyC|access-date=8 Dec 2019}} The European synthetic cell efforts were unified in 2019 as SynCellEU initiative.{{cite web|url=http://www.syntheticcell.eu/|title=SynCell EU|access-date=8 Dec 2019}}

In 2023, researchers were able to create the first synthetically made human embryos derived from stem cells.{{Cite news |last1=Devlin |first1=Hannah |date=2023-06-14 |title=Synthetic human embryos created in groundbreaking advance |language=en-GB |work=The Guardian |url=https://www.theguardian.com/science/2023/jun/14/synthetic-human-embryos-created-in-groundbreaking-advance |access-date=2023-11-30 |issn=0261-3077}}

In therapeutics, synthetic biology has achieved significant advancements in altering and simplifying the therapeutics scope in a relatively short period of time. In fact, new therapeutic platforms, from the discovery of disease mechanisms and drug targets to the manufacture and transport of small molecules, are made possible by the logical and model-guided design construction of biological components.

Synthetic biology devices have been designed to act as therapies in therapeutic treatment. It is possible to control complete created viruses and organisms to target particular pathogens and diseased pathways. Thus, in two independent studies 91,92, researchers utilised genetically modified bacteriophages to fight antibiotic-resistant bacteria by giving them genetic features that specifically target and hinder bacterial defences against antibiotic activity.{{Cite journal |last1=Khalil |first1=Ahmad S. |last2=Collins |first2=James J. |date=May 2010 |title=Synthetic biology: applications come of age |url=http://dx.doi.org/10.1038/nrg2775 |journal=Nature Reviews Genetics |volume=11 |issue=5 |pages=367–379 |doi=10.1038/nrg2775 |pmid=20395970 |pmc=2896386 |s2cid=2926016 |issn=1471-0056}}

In the therapy of cancer, since conventional medicines frequently indiscriminately target tumours and normal tissues, artificially created viruses and organisms that can identify and connect their therapeutic action to pathological signals may be helpful. For example, p53 pathway activity in human cells was put into adenoviruses to control how they replicated.

Bacteria have long been used in cancer treatment. Bifidobacterium and Clostridium selectively colonize tumors and reduce their size.{{cite journal | vauthors = Zu C, Wang J | title = Tumor-colonizing bacteria: a potential tumor targeting therapy | journal = Critical Reviews in Microbiology | volume = 40 | issue = 3 | pages = 225–235 | date = August 2014 | pmid = 23964706 | doi = 10.3109/1040841X.2013.776511 | s2cid = 26498221 }} Recently synthetic biologists reprogrammed bacteria to sense and respond to a particular cancer state. Most often bacteria are used to deliver a therapeutic molecule directly to the tumor to minimize off-target effects. To target the tumor cells, peptides that can specifically recognize a tumor were expressed on the surfaces of bacteria. Peptides used include an affibody molecule that specifically targets human epidermal growth factor receptor 2{{cite journal | vauthors = Gujrati V, Kim S, Kim SH, Min JJ, Choy HE, Kim SC, Jon S | title = Bioengineered bacterial outer membrane vesicles as cell-specific drug-delivery vehicles for cancer therapy | journal = ACS Nano | volume = 8 | issue = 2 | pages = 1525–1537 | date = February 2014 | pmid = 24410085 | doi = 10.1021/nn405724x }} and a synthetic adhesin.{{cite journal | vauthors = Piñero-Lambea C, Bodelón G, Fernández-Periáñez R, Cuesta AM, Álvarez-Vallina L, Fernández LÁ | title = Programming controlled adhesion of E. coli to target surfaces, cells, and tumors with synthetic adhesins | journal = ACS Synthetic Biology | volume = 4 | issue = 4 | pages = 463–473 | date = April 2015 | pmid = 25045780 | pmc = 4410913 | doi = 10.1021/sb500252a }} The other way is to allow bacteria to sense the tumor microenvironment, for example hypoxia, by building an AND logic gate into bacteria.{{cite journal | vauthors = Deyneko IV, Kasnitz N, Leschner S, Weiss S | title = Composing a Tumor Specific Bacterial Promoter | journal = PLOS ONE | volume = 11 | issue = 5 | pages = e0155338 | year = 2016 | pmid = 27171245 | pmc = 4865170 | doi = 10.1371/journal.pone.0155338 | bibcode = 2016PLoSO..1155338D | doi-access = free }} Then the bacteria only release target therapeutic molecules to the tumor through either lysis{{cite journal | vauthors = Rice KC, Bayles KW | title = Molecular control of bacterial death and lysis | journal = Microbiology and Molecular Biology Reviews | volume = 72 | issue = 1 | pages = 85–109, table of contents | date = March 2008 | pmid = 18322035 | pmc = 2268280 | doi = 10.1128/mmbr.00030-07 }} or the bacterial secretion system.{{cite journal | vauthors = Ganai S, Arenas RB, Forbes NS | title = Tumour-targeted delivery of TRAIL using Salmonella typhimurium enhances breast cancer survival in mice | journal = British Journal of Cancer | volume = 101 | issue = 10 | pages = 1683–1691 | date = November 2009 | pmid = 19861961 | pmc = 2778534 | doi = 10.1038/sj.bjc.6605403 }} Lysis has the advantage that it can stimulate the immune system and control growth. Multiple types of secretion systems can be used and other strategies as well. The system is inducible by external signals. Inducers include chemicals, electromagnetic or light waves.

Multiple species and strains are applied in these therapeutics. Most commonly used bacteria are Salmonella typhimurium, Escherichia coli, Bifidobacteria, Streptococcus, Lactobacillus, Listeria and Bacillus subtilis. Each of these species have their own property and are unique to cancer therapy in terms of tissue colonization, interaction with immune system and ease of application.

Engineered yeast-based platform

Synthetic biologists are developing genetically modified live yeast that can deliver therapeutic biologic medicines. When orally delivered, these live yeast act like micro-factories and will make therapeutic molecules directly in the gastrointestinal tract. Because yeast are eukaryotic, a key benefit is that they can be administered together with antibiotics. Probiotic yeast expressing human P2Y2 purinergic receptor suppressed intestinal inflammation in mouse models of inflammatory bowel disease.{{Cite journal |last1=Scott |first1=Benjamin M. |last2=Gutiérrez-Vázquez |first2=Cristina |last3=Sanmarco |first3=Liliana M. |last4=da Silva Pereira |first4=Jessica A. |last5=Li |first5=Zhaorong |last6=Plasencia |first6=Agustín |last7=Hewson |first7=Patrick |last8=Cox |first8=Laura M. |last9=O’Brien |first9=Madelynn |last10=Chen |first10=Steven K. |last11=Moraes-Vieira |first11=Pedro M. |last12=Chang |first12=Belinda S. W. |last13=Peisajovich |first13=Sergio G. |last14=Quintana |first14=Francisco J. |date=July 2021 |title=Self-tunable engineered yeast probiotics for the treatment of inflammatory bowel disease |journal=Nature Medicine |language=en |volume=27 |issue=7 |pages=1212–1222 |doi=10.1038/s41591-021-01390-x |pmid=34183837 |s2cid=235673499 |issn=1546-170X}} A live S. boulardii yeast delivering a tetra-specific anti-toxin that potently neutralizes Toxin A and Toxin B of Clostridioides difficile has been developed. This therapeutic anti-toxin is a fusion of four single-domain antibodies (nanobodies) that potently and broadly neutralize the two major virulence factors of C. difficile at the site of infection in preclinical models.{{Cite journal |last1=Chen |first1=Kevin |last2=Zhu |first2=Yixuan |last3=Zhang |first3=Yongrong |last4=Hamza |first4=Therwa |last5=Yu |first5=Hua |last6=Saint Fleur |first6=Ashley |last7=Galen |first7=James |last8=Yang |first8=Zhiyong |last9=Feng |first9=Hanping |date=2020-10-28 |title=A probiotic yeast-based immunotherapy against Clostridioides difficile infection |journal=Science Translational Medicine |language=en |volume=12 |issue=567 |pages=eaax4905 |doi=10.1126/scitranslmed.aax4905 |issn=1946-6234 |pmc=7692727 |pmid=33115949}} The first in human clinical trial of engineered live yeast for the treatment of Clostridioides difficile infection is anticipated in 2024 and will be sponsored by the developer [https://www.fzata.com Fzata, Inc].

The immune system plays an important role in cancer and can be harnessed to attack cancer cells. Cell-based therapies focus on immunotherapies, mostly by engineering T cells.

T cell receptors were engineered and 'trained' to detect cancer epitopes. Chimeric antigen receptors (CARs) are composed of a fragment of an antibody fused to intracellular T cell signaling domains that can activate and trigger proliferation of the cell. Multiple second generation CAR-based therapies have been approved by FDA.{{Cite journal |last1=Chen |first1=Yi-Ju |last2=Abila |first2=Bams |last3=Mostafa Kamel |first3=Yasser |date=2023 |title=CAR-T: What Is Next? |journal=Cancers |language=en |volume=15 |issue=3 |pages=663 |doi=10.3390/cancers15030663 |issn=2072-6694 |pmc=9913679 |pmid=36765623 |doi-access=free }}

Gene switches were designed to enhance safety of the treatment. Kill switches were developed to terminate the therapy should the patient show severe side effects.Jones, B.S., Lamb, L.S., Goldman, F. & Di Stasi, A. Improving the safety of cell therapy products by suicide gene transfer. Front. Pharmacol. 5, 254 (2014). Mechanisms can more finely control the system and stop and reactivate it.{{cite journal | vauthors = Wei P, Wong WW, Park JS, Corcoran EE, Peisajovich SG, Onuffer JJ, Weiss A, Lim WA | display-authors = 6 | title = Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells | journal = Nature | volume = 488 | issue = 7411 | pages = 384–388 | date = August 2012 | pmid = 22820255 | pmc = 3422413 | doi = 10.1038/nature11259 | bibcode = 2012Natur.488..384W }}{{cite journal | vauthors = Danino T, Mondragón-Palomino O, Tsimring L, Hasty J | title = A synchronized quorum of genetic clocks | journal = Nature | volume = 463 | issue = 7279 | pages = 326–330 | date = January 2010 | pmid = 20090747 | pmc = 2838179 | doi = 10.1038/nature08753 | bibcode = 2010Natur.463..326D }} Since the number of T-cells are important for therapy persistence and severity, growth of T-cells is also controlled to dial the effectiveness and safety of therapeutics.{{cite journal | vauthors = Chen YY, Jensen MC, Smolke CD | title = Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | issue = 19 | pages = 8531–8536 | date = May 2010 | pmid = 20421500 | pmc = 2889348 | doi = 10.1073/pnas.1001721107 | doi-access = free | bibcode = 2010PNAS..107.8531C }}

Although several mechanisms can improve safety and control, limitations include the difficulty of inducing large DNA circuits into the cells and risks associated with introducing foreign components, especially proteins, into cells.

The most popular biofuel is ethanol produced from corn or sugar cane, but this method of producing biofuels is troublesome and constrained due to the high agricultural cost and inadequate fuel characteristics of ethanol. A substitute and potential source of renewable energy is microbes that have had their metabolic pathways altered to be more efficient at converting biomass into biofuels. Only if their production costs could be made to match or even beat those of present fuel production can these techniques be expected to be successful. Related to this, there are several medicines whose pricey manufacturing procedures prevent them from having a larger therapeutic range. The creation of new materials and the microbiological manufacturing of biomaterials would both benefit substantially from novel artificial biology tools.

The clustered frequently interspaced short palindromic repetitions (CRISPR)/CRISPR associated (Cas) system is a powerful method of genome engineering in a range of organisms because of its simplicity, modularity, and scalability. In this technique, a guide RNA (gRNA) attracts the CRISPR nuclease Cas9 to a particular spot in the genome, causing a double strand break. Several DNA repair processes, including homology-directed recombination and non-homology end joining, can be used to accomplish the desired genome change (i.e., gene deletion or insertion). Additionally, dCas9 (dead Cas9 or nuclease-deficient Cas9), a Cas9 double mutant (H840A, D10A), has been utilised to control gene expression in bacteria or when linked to a stimulation of suppression site in yeast.{{Cite journal |last1=Katz |first1=Leonard |last2=Chen |first2=Yvonne Y |last3=Gonzalez |first3=Ramon |last4=Peterson |first4=Todd C |last5=Zhao |first5=Huimin |last6=Baltz |first6=Richard H |date=2018-07-01 |title=Synthetic biology advances and applications in the biotechnology industry: a perspective |journal=Journal of Industrial Microbiology and Biotechnology |language=en |volume=45 |issue=7 |pages=449–461 |doi=10.1007/s10295-018-2056-y |pmid=29915997 |s2cid=49296740 |issn=1476-5535|doi-access=free }}

To build and develop biological systems, regulating components including regulators, ribosome-binding sites (RBSs), and terminators are crucial. Despite years of study, there are many various varieties and numbers of promoters and terminators for Escherichia coli, but also for the well-researched model organism Saccharomyces cerevisiae, as well as for other organisms of interest, these tools are quite scarce. Numerous techniques have been invented for the finding and identification of promoters and terminators in order to overcome this constraint, including genome mining, random mutagenesis, hybrid engineering, biophysical modelling, combinatorial design, and rational design.

Synthetic biology has been used for organoids, which are lab-grown organs with application to medical research and transplantation.{{cite journal | vauthors = Hofer M, Lutolf MP | title = Engineering organoids | journal = Nature Reviews. Materials | volume = 6 | issue = 5 | pages = 402–420 | date = May 2021 | pmid = 33623712 | pmc = 7893133 | doi = 10.1038/s41578-021-00279-y | bibcode = 2021NatRM...6..402H }}

{{Transcluded section|source=3D bioprinting |part= }}

{{#section-h:3D bioprinting|Tissue engineering}}

{{crossreference|selfref=no|For bioprinted food like meat see #Food and drink.}}

There is ongoing research and development into synthetic biology based methods for inducing regeneration in humans{{Relevance inline|date=October 2021}} as well the creation of transplantable artificial organs.

{{See also|Brain–computer interface|Nanomedicine|Precision medicine}}

Synthetic biology can be used for creating nanoparticles which can be used for drug-delivery as well as for other purposes.{{cite journal | vauthors = Edmundson MC, Capeness M, Horsfall L | title = Exploring the potential of metallic nanoparticles within synthetic biology | journal = New Biotechnology | volume = 31 | issue = 6 | pages = 572–578 | date = December 2014 | pmid = 24681407 | doi = 10.1016/j.nbt.2014.03.004 | s2cid = 15790244 | doi-access = free | hdl = 20.500.11820/5cd4fa26-dee8-4862-86af-cf6a79546a13 | hdl-access = free }} Complementing research and development seeks to and has created synthetic cells that mimics functions of biological cells. Applications include medicine such as designer-nanoparticles that make blood cells eat away—from the inside out—portions of atherosclerotic plaque that cause heart attacks.{{cite web|url=https://msutoday.msu.edu/news/2020/nanoparticle-chomps-away-plaques-that-cause-heart-attacks/|title=Nanoparticle chomps away plaques that cause heart attacks|date=27 January 2020|access-date=31 January 2020|publisher=Michigan State University|archive-date=29 January 2020|archive-url=https://web.archive.org/web/20200129223019/https://msutoday.msu.edu/news/2020/nanoparticle-chomps-away-plaques-that-cause-heart-attacks/|url-status=live}}{{cite web |title=Nanoparticle helps eat away deadly arterial plaque |url=https://newatlas.com/medical/nanoparticle-eats-arterial-plaque/ |website=New Atlas |access-date=13 April 2020 |date=28 January 2020 |archive-date=1 March 2020 |archive-url=https://web.archive.org/web/20200301100247/https://newatlas.com/medical/nanoparticle-eats-arterial-plaque/ |url-status=live }}{{cite journal | vauthors = Flores AM, Hosseini-Nassab N, Jarr KU, Ye J, Zhu X, Wirka R, Koh AL, Tsantilas P, Wang Y, Nanda V, Kojima Y, Zeng Y, Lotfi M, Sinclair R, Weissman IL, Ingelsson E, Smith BR, Leeper NJ | display-authors = 6 | title = Pro-efferocytic nanoparticles are specifically taken up by lesional macrophages and prevent atherosclerosis | journal = Nature Nanotechnology | volume = 15 | issue = 2 | pages = 154–161 | date = February 2020 | pmid = 31988506 | pmc = 7254969 | doi = 10.1038/s41565-019-0619-3 | bibcode = 2020NatNa..15..154F }} Synthetic micro-droplets for algal cells or synergistic algal-bacterial multicellular spheroid microbial reactors, for example, could be used to produce hydrogen as hydrogen economy biotechnology.{{cite news |title=Research creates hydrogen-producing living droplets, paving way for alternative future energy source |url=https://phys.org/news/2020-11-hydrogen-producing-droplets-paving-alternative-future.html |access-date=9 December 2020 |work=phys.org |language=en |archive-date=16 December 2020 |archive-url=https://web.archive.org/web/20201216151601/https://phys.org/news/2020-11-hydrogen-producing-droplets-paving-alternative-future.html |url-status=live }}{{cite journal | vauthors = Xu Z, Wang S, Zhao C, Li S, Liu X, Wang L, Li M, Huang X, Mann S | display-authors = 6 | title = Photosynthetic hydrogen production by droplet-based microbial micro-reactors under aerobic conditions | journal = Nature Communications | volume = 11 | issue = 1 | pages = 5985 | date = November 2020 | pmid = 33239636 | pmc = 7689460 | doi = 10.1038/s41467-020-19823-5 | bibcode = 2020NatCo..11.5985X }}

Mammalian designer cells are engineered by humans to behave a specific way, such as an immune cell that expresses a synthetic receptor designed to combat a specific disease.{{Cite journal |last1=Xie |first1=Mingqi |last2=Fussenegger |first2=Martin |date=July 2015 |title=Mammalian designer cells: Engineering principles and biomedical applications |url=https://onlinelibrary.wiley.com/doi/10.1002/biot.201400642 |journal=Biotechnology Journal |language=en |volume=10 |issue=7 |pages=1005–1018 |doi=10.1002/biot.201400642 |pmid=26010998 |s2cid=11838264 |issn=1860-6768|url-access=subscription }}{{Cite journal |url=https://academic.oup.com/proteincell/article/13/7/476/6747017 |title=Therapeutic cell engineering: designing programmable synthetic genetic circuits in mammalian cells |access-date=2024-01-31 |journal=Protein & Cell|date=2022 |doi=10.1007/s13238-021-00876-1 |last1=Mansouri |first1=Maysam |last2=Fussenegger |first2=Martin |volume=13 |issue=7 |pages=476–489 |pmid=34586617 |hdl=20.500.11850/508471 |hdl-access=free }} Electrogenetics is an application of synthetic biology that involves utilizing electrical fields to stimulate a response in engineered cells.{{Cite journal |last1=Mansouri |first1=Maysam |last2=Fussenegger |first2=Martin |date=2022-06-01 |title=Electrogenetics: Bridging synthetic biology and electronics to remotely control the behavior of mammalian designer cells |url=https://www.sciencedirect.com/science/article/pii/S1367593122000369 |journal=Current Opinion in Chemical Biology |volume=68 |pages=102151 |doi=10.1016/j.cbpa.2022.102151 |pmid=35483127 |issn=1367-5931|hdl=20.500.11850/547194 |hdl-access=free }} Controlling the designer cells can be done with relative ease through the use of common electronic devices, such as smartphones. Additionally, electrogenetics allows for the possibility of creating devices that are much smaller and compact than devices that use other stimulus through the use of microscopic electrodes. One example of how electrogenetics is used to benefit public health is through stimulating designer cells that are able to produce/deliver therapeutics.{{Cite journal |last1=Krawczyk |first1=Krzysztof |last2=Xue |first2=Shuai |last3=Buchmann |first3=Peter |last4=Charpin-El-Hamri |first4=Ghislaine |last5=Saxena |first5=Pratik |last6=Hussherr |first6=Marie-Didiée |last7=Shao |first7=Jiawei |last8=Ye |first8=Haifeng |last9=Xie |first9=Mingqi |last10=Fussenegger |first10=Martin |date=2020-05-29 |title=Electrogenetic cellular insulin release for real-time glycemic control in type 1 diabetic mice |url=https://www.science.org/doi/10.1126/science.aau7187 |journal=Science |language=en |volume=368 |issue=6494 |pages=993–1001 |doi=10.1126/science.aau7187 |pmid=32467389 |hdl=20.500.11850/418642 |s2cid=218984797 |issn=0036-8075|hdl-access=free }} This was implemented in _ElectroHEK cells, cells that contain voltage-gated calcium channels that are electrosensitive, meaning that the ion channel can be controlled by electrical conduction between electrodes and the _ElectroHEK cells. The expression levels of the artificial gene that these _ElectroHEK cells contained was shown to be able to be controlled by changing the voltage or electrical pulse length. Further studies have expanded on this robust system, one of which is a beta cell line system designed to control the release of insulin based on electric signals.{{Cite journal |last1=McCluskey |first1=Jane T. |last2=Hamid |first2=Muhajir |last3=Guo-Parke |first3=Hong |last4=McClenaghan |first4=Neville H. |last5=Gomis |first5=Ramon |last6=Flatt |first6=Peter R. |date=2011-06-24 |title=Development and Functional Characterization of Insulin-releasing Human Pancreatic Beta Cell Lines Produced by Electrofusion* |journal=Journal of Biological Chemistry |volume=286 |issue=25 |pages=21982–21992 |doi=10.1074/jbc.M111.226795 |doi-access=free |pmid=21515691 |pmc=3121343 |issn=0021-9258}}

{{Update|section|date=January 2019}}

{{Further|Bioethics|Bioeconomy#Issues}}

The creation of new life and the tampering of existing life has raised ethical concerns in the field of synthetic biology and are actively being discussed.{{Cite web|date=2019-03-04|title=Frontiers 2018/19: Emerging Issues of Environmental Concern|url=http://www.unenvironment.org/resources/frontiers-201819-emerging-issues-environmental-concern|access-date=2021-01-03|website=UN Environment Programme|language=en}}

Common ethical questions include:

• Is it morally right to tamper with nature?
• Is one playing God when creating new life?
• What happens if a synthetic organism accidentally escapes?
• What if an individual misuses synthetic biology and creates a harmful entity (e.g., a biological weapon)?
• Who will have control of and access to the products of synthetic biology?
• Who will gain from these innovations? Investors? Medical patients? Industrial farmers?
• Does the patent system allow patents on living organisms? What about parts of organisms, like HIV resistance genes in humans?{{Cite web|url=https://www.theguardian.com/science/2018/nov/26/worlds-first-gene-edited-babies-created-in-china-claims-scientist|title= World's first gene-edited babies created in China, claims scientist | date=November 2018|website=The Guardian}}
• What if a new creation is deserving of moral or legal status?

The ethical aspects of synthetic biology has three main features: biosafety, biosecurity, and the creation of new life forms.{{cite journal |vauthors=Häyry M |title=Synthetic Biology and Ethics: Past, Present, and Future |journal=Cambridge Quarterly of Healthcare Ethics |volume=26 |issue=2 |pages=186–205 |date=April 2017 |pmid=28361718 |doi=10.1017/S0963180116000803 |s2cid=29992939}} Other ethical issues mentioned include the regulation of new creations, patent management of new creations, benefit distribution, and research integrity.{{Cite journal |vauthors=Jin S, Clark B, Kuznesof S, Lin X, Frewer LJ |title=Synthetic biology applied in the agrifood sector: Public perceptions, attitudes and implications for future studie |date=September 2019|journal=Trends in Food Science and Technology |volume=91 |pages=454–466 |doi=10.1016/j.tifs.2019.07.025 |s2cid=199632852 |doi-access=}}{{Cite journal |url=https://heinonline.org/HOL/LandingPage?handle=hein.journals/macq15&div=8&id=&page=| title=Synthetic Biology: Ethics, Exceptionalism and Expectations| pages=45| vauthors=Newson AJ |date=2015|journal=Macquarie Law Journal| volume=15}}

Ethical issues have surfaced for recombinant DNA and genetically modified organism (GMO) technologies and extensive regulations of genetic engineering and pathogen research were in place in many jurisdictions. Amy Gutmann, former head of the Presidential Bioethics Commission, argued that we should avoid the temptation to over-regulate synthetic biology in general, and genetic engineering in particular. According to Gutmann, "Regulatory parsimony is especially important in emerging technologies...where the temptation to stifle innovation on the basis of uncertainty and fear of the unknown is particularly great. The blunt instruments of statutory and regulatory restraint may not only inhibit the distribution of new benefits, but can be counterproductive to security and safety by preventing researchers from developing effective safeguards.".{{cite journal |vauthors=Gutmann A |title=The ethics of synthetic biology: guiding principles for emerging technologies |journal=The Hastings Center Report |volume=41 |issue=4 |pages=17–22 |date=2012 |pmid=21845917 |doi=10.1002/j.1552-146X.2011.tb00118.x |s2cid=20662786}}

One ethical question is whether or not it is acceptable to create new life forms, sometimes known as "playing God". Currently, the creation of new life forms not present in nature is at small-scale, the potential benefits and dangers remain unknown, and careful consideration and oversight are ensured for most studies. Many advocates express the great potential value—to agriculture, medicine, and academic knowledge, among other fields—of creating artificial life forms. Creation of new entities could expand scientific knowledge well beyond what is currently known from studying natural phenomena. Yet there is concern that artificial life forms may reduce nature's "purity" (i.e., nature could be somehow corrupted by human intervention and manipulation) and potentially influence the adoption of more engineering-like principles instead of biodiversity- and nature-focused ideals. Some are also concerned that if an artificial life form were to be released into nature, it could hamper biodiversity by beating out natural species for resources (similar to how algal blooms kill marine species). Another concern involves the ethical treatment of newly created entities if they happen to sense pain, sentience, and self-perception. There is an ongoing debate as to whether such life forms should be granted moral or legal rights, though no consensus exists as to how these rights would be administered or enforced.

Ethics and moral rationales that support certain applications of synthetic biology include their potential mitigation of substantial global problems of detrimental environmental impacts of conventional agriculture (including meat production), animal welfare, food security, and human health,{{cite journal | vauthors = Bryant CJ | title = Culture, meat, and cultured meat | journal = Journal of Animal Science | volume = 98 | issue = 8 | pages = skaa172 | date = August 2020 | pmid = 32745186 | pmc = 7398566 | doi = 10.1093/jas/skaa172 }}{{cite journal | vauthors = Hong TK, Shin DM, Choi J, Do JT, Han SG | title = Current Issues and Technical Advances in Cultured Meat Production: A Review | journal = Food Science of Animal Resources | volume = 41 | issue = 3 | pages = 355–372 | date = May 2021 | pmid = 34017947 | pmc = 8112310 | doi = 10.5851/kosfa.2021.e14 }}{{cite journal | vauthors = Treich N | title = Cultured Meat: Promises and Challenges | journal = Environmental & Resource Economics | volume = 79 | issue = 1 | pages = 33–61 | date = 1 May 2021 | pmid = 33758465 | pmc = 7977488 | doi = 10.1007/s10640-021-00551-3 | bibcode = 2021EnREc..79...33T }}{{cite journal | vauthors = Treich N | title = Cultured Meat: Promises and Challenges | journal = Environmental & Resource Economics | volume = 79 | issue = 1 | pages = 33–61 | date = May 2021 | pmid = 33758465 | pmc = 7977488 | doi = 10.1007/s10640-021-00551-3 | bibcode = 2021EnREc..79...33T }} as well as potential reduction of human labor needs and, via therapies of diseases, reduction of human suffering and prolonged life.

What is most ethically appropriate when considering biosafety measures? How can accidental introduction of synthetic life in the natural environment be avoided? Much ethical consideration and critical thought has been given to these questions. Biosafety not only refers to biological containment; it also refers to strides taken to protect the public from potentially hazardous biological agents. Even though such concerns are important and remain unanswered, not all products of synthetic biology present concern for biological safety or negative consequences for the environment. It is argued that most synthetic technologies are benign and are incapable of flourishing in the outside world due to their "unnatural" characteristics as there is yet to be an example of a transgenic microbe conferred with a fitness advantage in the wild.

In general, existing hazard controls, risk assessment methodologies, and regulations developed for traditional genetically modified organisms (GMOs) are considered to be sufficient for synthetic organisms. "Extrinsic" biocontainment methods in a laboratory context include physical containment through biosafety cabinets and gloveboxes, as well as personal protective equipment. In an agricultural context, they include isolation distances and pollen barriers, similar to methods for biocontainment of GMOs. Synthetic organisms may offer increased hazard control because they can be engineered with "intrinsic" biocontainment methods that limit their growth in an uncontained environment, or prevent horizontal gene transfer to natural organisms. Examples of intrinsic biocontainment include auxotrophy, biological kill switches, inability of the organism to replicate or to pass modified or synthetic genes to offspring, and the use of xenobiological organisms using alternative biochemistry, for example using artificial xeno nucleic acids (XNA) instead of DNA.{{Cite book |title=Opinion on synthetic biology II: Risk assessment methodologies and safety aspects |date=2016-02-12 |department=EU Directorate-General for Health and Consumers |doi=10.2772/63529 |publisher=Publications Office |author1=European Commission. Directorate-General for Health Consumers |url=https://publications.europa.eu/en/publication-detail/-/publication/bfd7d06c-d3ae-11e5-a4b5-01aa75ed71a1/language-en |isbn=9789279439162}}

Some ethical issues relate to biosecurity, where biosynthetic technologies could be deliberately used to cause harm to society and/or the environment. Since synthetic biology raises ethical issues and biosecurity issues, humanity must consider and plan on how to deal with potentially harmful creations, and what kinds of ethical measures could possibly be employed to deter nefarious biosynthetic technologies. With the exception of regulating synthetic biology and biotechnology companies,{{cite journal |vauthors=Bügl H, Danner JP, Molinari RJ, Mulligan JT, Park HO, Reichert B, Roth DA, Wagner R, Budowle B, Scripp RM, Smith JA, Steele SJ, Church G, Endy D |title=DNA synthesis and biological security |journal=Nature Biotechnology |volume=25 |issue=6 |pages=627–629 |date=June 2007 |pmid=17557094 |doi=10.1038/nbt0607-627 |s2cid=7776829}}{{cite web |url=http://www.synbioproject.org/site/assets/files/1335/hastings.pdf |archive-url=https://web.archive.org/web/20150513083105/http://www.synbioproject.org/site/assets/files/1335/hastings.pdf |url-status=usurped |archive-date=May 13, 2015 |title=Ethical Issues in Synthetic Biology: An Overview of the Debates}} however, the issues are not seen as new because they were raised during the earlier recombinant DNA and genetically modified organism (GMO) debates, and extensive regulations of genetic engineering and pathogen research are already in place in many jurisdictions.Presidential Commission for the study of Bioethical Issues, December 2010 [http://bioethics.gov/synthetic-biology-report NEW DIRECTIONS The Ethics of Synthetic Biology and Emerging Technologies] {{Webarchive|url=https://web.archive.org/web/20170118225354/http://bioethics.gov/synthetic-biology-report |date=2017-01-18 }} Retrieved 2012-04-14.

Additionally, the development of synthetic biology tools has made it easier for individuals with less education, training, and access to equipment to modify and use pathogenic organisms as bioweapons. This increases the threat of bioterrorism, especially as terrorist groups become aware of the significant social, economic, and political disruption caused by pandemics like COVID-19. As new techniques are developed in the field of synthetic biology, the risk of bioterrorism is likely to continue to grow.{{Cite web | vauthors = Hummel K |date=2020-08-31 |title=Engineered Pathogens and Unnatural Biological Weapons: The Future Threat of Synthetic Biology |url=https://ctc.westpoint.edu/engineered-pathogens-and-unnatural-biological-weapons-the-future-threat-of-synthetic-biology/ |access-date=2023-01-05 |website=Combating Terrorism Center at West Point |language=en-US}} Juan Zarate, who served as Deputy National Security Advisor for Combating Terrorism from 2005 to 2009, noted that "the severity and extreme disruption of a novel coronavirus will likely spur the imagination of the most creative and dangerous groups and individuals to reconsider bioterrorist attacks."{{Cite web | vauthors = Hummel K |date=2020-06-29 |title=A View from the CT Foxhole: A Virtual Roundtable on COVID-19 and Counterterrorism with Audrey Kurth Cronin, Lieutenant General (Ret) Michael Nagata, Magnus Ranstorp, Ali Soufan, and Juan Zarate |url=https://ctc.westpoint.edu/a-view-from-the-ct-foxhole-a-virtual-roundtable-on-covid-19-and-counterterrorism-with-audrey-kurth-cronin-lieutenant-general-ret-michael-nagata-magnus-ranstorp-ali-soufan-and-juan-zarate/ |access-date=2023-01-05 |website=Combating Terrorism Center at West Point |language=en-US}}

The European Union-funded project SYNBIOSAFE{{Cite web|url=https://www.synbiosafe.eu/ |title=Synbiosafe |website=Synbiosafe}} has issued reports on how to manage synthetic biology. A 2007 paper identified key issues in safety, security, ethics, and the science-society interface, which the project defined as public education and ongoing dialogue among scientists, businesses, government and ethicists.{{cite journal |vauthors=Schmidt M, Ganguli-Mitra A, Torgersen H, Kelle A, Deplazes A, Biller-Andorno N |title=A priority paper for the societal and ethical aspects of synthetic biology |journal=Systems and Synthetic Biology |volume=3 |issue=1–4 |pages=3–7 |date=December 2009 |pmid=19816794 |pmc=2759426 |doi=10.1007/s11693-009-9034-7 |url=http://www.synbiosafe.eu/uploads/pdf/Schmidt_etal-2009-SSBJ.pdf}}Schmidt M. Kelle A. Ganguli A, de Vriend H. (Eds.) 2009. [https://www.springer.com/biomed/book/978-90-481-2677-4 "Synthetic Biology. The Technoscience and its Societal Consequences".] Springer Academic Publishing. The key security issues that SYNBIOSAFE identified involved engaging companies that sell synthetic DNA and the biohacking community of amateur biologists. Key ethical issues concerned the creation of new life forms.

A subsequent report focused on biosecurity, especially the so-called dual-use challenge. For example, while synthetic biology may lead to more efficient production of medical treatments, it may also lead to synthesis or modification of harmful pathogens (e.g., smallpox).{{cite journal |vauthors=Kelle A |title=Ensuring the security of synthetic biology-towards a 5P governance strategy |journal=Systems and Synthetic Biology |volume=3 |issue=1–4 |pages=85–90 |date=December 2009 |pmid=19816803 |pmc=2759433 |doi=10.1007/s11693-009-9041-8}} The biohacking community remains a source of special concern, as the distributed and diffuse nature of open-source biotechnology makes it difficult to track, regulate or mitigate potential concerns over biosafety and biosecurity.{{cite journal |vauthors=Schmidt M |title=Diffusion of synthetic biology: a challenge to biosafety |journal=Systems and Synthetic Biology |volume=2 |issue=1–2 |pages=1–6 | date=June 2008 |pmid=19003431 |pmc=2671588 |doi=10.1007/s11693-008-9018-z |url=http://www.markusschmidt.eu/pdf/Diffusion_of_synthetic_biology.pdf}}

COSY, another European initiative, focuses on public perception and communication.[http://www.synbio.at/ COSY: Communicating Synthetic Biology]{{cite journal |vauthors=Kronberger N, Holtz P, Kerbe W, Strasser E, Wagner W |title=Communicating Synthetic Biology: from the lab via the media to the broader public |journal=Systems and Synthetic Biology |volume=3 |issue= 1–4 |pages=19–26 |date=December 2009 |pmid=19816796 |pmc=2759424 |doi=10.1007/s11693-009-9031-x}}{{cite journal |vauthors=Cserer A, Seiringer A |title=Pictures of Synthetic Biology: A reflective discussion of the representation of Synthetic Biology (SB) in the German-language media and by SB experts |journal=Systems and Synthetic Biology |volume=3 |issue=1–4 |pages=27–35 |date=December 2009 |pmid=19816797 |pmc=2759430 |doi=10.1007/s11693-009-9038-3}} To better communicate synthetic biology and its societal ramifications to a broader public, COSY and SYNBIOSAFE published SYNBIOSAFE, a 38-minute documentary film, in October 2009.

The International Association Synthetic Biology has proposed self-regulation.Report of IASB [http://www.ia-sb.eu/tasks/sites/synthetic-biology/assets/File/pdf/iasb_report_biosecurity_syntheticbiology.pdf "Technical solutions for biosecurity in synthetic biology"] {{webarchive |url=https://web.archive.org/web/20110719031805/http://www.ia-sb.eu/tasks/sites/synthetic-biology/assets/File/pdf/iasb_report_biosecurity_syntheticbiology.pdf |date=July 19, 2011}}, Munich, 2008 This proposes specific measures that the synthetic biology industry, especially DNA synthesis companies, should implement. In 2007, a group led by scientists from leading DNA-synthesis companies published a "practical plan for developing an effective oversight framework for the DNA-synthesis industry".

In January 2009, the Alfred P. Sloan Foundation funded the Woodrow Wilson Center, the Hastings Center, and the J. Craig Venter Institute to examine the public perception, ethics and policy implications of synthetic biology.Parens E., Johnston J., Moses J. [http://www.thehastingscenter.org/who-we-are/our-research/selected-past-projects/ethical-issues-in-synthetic-biology-2/ Ethical Issues in Synthetic Biology.] 2009.

On July 9–10, 2009, the National Academies' Committee of Science, Technology & Law convened a symposium on "Opportunities and Challenges in the Emerging Field of Synthetic Biology".{{Cite web|url=https://sites.nationalacademies.org/PGA/stl/PGA_050738|title=Policy and Global Affairs at the National Academies|website=sites.nationalacademies.org}}

After the publication of the first synthetic genome and the accompanying media coverage about "life" being created, President Barack Obama established the Presidential Commission for the Study of Bioethical Issues to study synthetic biology.Presidential Commission for the study of Bioethical Issues, December 2010 [http://bioethics.gov/node/353 FAQ] {{Webarchive|url=https://web.archive.org/web/20151224160437/http://bioethics.gov/node/353 |date=2015-12-24 }} The commission convened a series of meetings, and issued a report in December 2010 titled "New Directions: The Ethics of Synthetic Biology and Emerging Technologies." The commission stated that "while Venter's achievement marked a significant technical advance in demonstrating that a relatively large genome could be accurately synthesized and substituted for another, it did not amount to the "creation of life".{{Cite web |url=http://bioethics.gov/node/353 |title=Synthetic Biology F.A.Q.'s {{!}} Presidential Commission for the Study of Bioethical Issues |access-date=2014-10-11 |archive-date=2015-12-24 |archive-url=https://web.archive.org/web/20151224160437/http://bioethics.gov/node/353 |url-status=dead }} It noted that synthetic biology is an emerging field, which creates potential risks and rewards. The commission did not recommend policy or oversight changes and called for continued funding of the research and new funding for monitoring, study of emerging ethical issues and public education.

Synthetic biology, as a major tool for biological advances, results in the "potential for developing biological weapons, possible unforeseen negative impacts on human health ... and any potential environmental impact".{{cite journal | vauthors = Erickson B, Singh R, Winters P | title = Synthetic biology: regulating industry uses of new biotechnologies | journal = Science | volume = 333 | issue = 6047 | pages = 1254–6 | date = September 2011 | pmid = 21885775 | doi = 10.1126/science.1211066 | bibcode = 2011Sci...333.1254E | s2cid = 1568198 }} The proliferation of such technology could also make the production of biological and chemical weapons available to a wider array of state and non-state actors.{{cite report | vauthors = Sayler KM |date=June 8, 2021 |title=Defense Primer: Emerging Technologies |url=https://fas.org/sgp/crs/natsec/IF11105.pdf |publisher=Congressional Research Service |access-date=July 22, 2021}} These security issues may be avoided by regulating industry uses of biotechnology through policy legislation. Federal guidelines on genetic manipulation are being proposed by "the President's Bioethics Commission ... in response to the announced creation of a self-replicating cell from a chemically synthesized genome, put forward 18 recommendations not only for regulating the science ... for educating the public".

On March 13, 2012, over 100 environmental and civil society groups, including Friends of the Earth, the International Center for Technology Assessment, and the ETC Group, issued the manifesto The Principles for the Oversight of Synthetic Biology. This manifesto calls for a worldwide moratorium on the release and commercial use of synthetic organisms until more robust regulations and rigorous biosafety measures are established. The groups specifically call for an outright ban on the use of synthetic biology on the human genome or human microbiome.Katherine Xue for Harvard Magazine. September–October 2014 [http://harvardmagazine.com/2014/09/synthetic-biologys-new-menagerie Synthetic Biology's New Menagerie]Yojana Sharma for Scidev.net March 15, 2012. [http://www.scidev.net/global/genomics/news/ngos-call-for-international-regulation-of-synthetic-biology.html NGOs call for international regulation of synthetic biology] Richard Lewontin wrote that some of the safety tenets for oversight discussed in The Principles for the Oversight of Synthetic Biology are reasonable, but that the main problem with the recommendations in the manifesto is that "the public at large lacks the ability to enforce any meaningful realization of those recommendations".[http://www.nybooks.com/articles/archives/2014/may/08/new-synthetic-biology-who-gains/?insrc=rel#fnr-1 The New Synthetic Biology: Who Gains?] (2014-05-08), Richard C. Lewontin, New York Review of Books

{{Main|Hazards of synthetic biology}}

The hazards of synthetic biology include biosafety hazards to workers and the public, biosecurity hazards stemming from deliberate engineering of organisms to cause harm, and environmental hazards.{{cite journal |last1=Freeman |first1=Jeremy |title=Existential Risk of Synthetic Biology: How Biological Engineering Can Help the World or Destroy It |journal=Journal of Student Research |date=2023 |volume=12 |issue=4 |doi=10.47611/jsrhs.v12i4.5129 |doi-access=free}} The biosafety hazards are similar to those for existing fields of biotechnology, mainly exposure to pathogens and toxic chemicals, although novel synthetic organisms may have novel risks.{{cite journal |vauthors=Howard J, Murashov V, Schulte P |title=Synthetic biology and occupational risk |journal=Journal of Occupational and Environmental Hygiene |volume=14 |issue=3 |pages=224–236 |date=March 2017 |pmid=27754800 |doi=10.1080/15459624.2016.1237031 |s2cid=205893358}} For biosecurity, there is concern that synthetic or redesigned organisms could theoretically be used for bioterrorism. Potential risks include recreating known pathogens from scratch, engineering existing pathogens to be more dangerous, and engineering microbes to produce harmful biochemicals.{{Cite book|title=Biodefense in the Age of Synthetic Biology |date=2018-06-19 |publisher=National Academies of Sciences, Engineering, and Medicine |isbn=9780309465182 |doi=10.17226/24890 |pmid=30629396 |last1=National Academies Of Sciences |author2=Division on Earth Life Studies |last3=Board On Life Sciences |author4=Board on Chemical Sciences Technology |author5=Committee on Strategies for Identifying Addressing Potential Biodefense Vulnerabilities Posed by Synthetic Biology |s2cid=90767286}} Lastly, environmental hazards include adverse effects on biodiversity and ecosystem services, including potential changes to land use resulting from agricultural use of synthetic organisms.{{Cite web |url=http://ec.europa.eu/environment/integration/research/newsalert/multimedia/synthetic_biology_and_biodiversity.htm |title=Future Brief: Synthetic biology and biodiversity |date=September 2016|website=European Commission|pages=14–15|access-date=2019-01-14}}{{Cite book |url=https://publications.europa.eu/en/publication-detail/-/publication/9b231c71-faf1-11e5-b713-01aa75ed71a1/language-en/format-PDF |title=Final opinion on synthetic biology III: Risks to the environment and biodiversity related to synthetic biology and research priorities in the field of synthetic biology |date=2016-04-04 |department=EU Directorate-General for Health and Food Safety |pages=8, 27 |publisher=European Commission |isbn=9789279549731 |access-date=2019-01-14}} Synthetic biology is an example of a dual-use technology with the potential to be used in ways that could intentionally or unintentionally harm humans and/or damage the environment. Often "scientists, their host institutions and funding bodies" consider whether the planned research could be misused and sometimes implement measures to reduce the likelihood of misuse.{{cite journal |vauthors=El Karoui M, Hoyos-Flight M, Fletcher L |title=Future Trends in Synthetic Biology-A Report |journal=Frontiers in Bioengineering and Biotechnology |volume=7 |pages=175 |date=2019 |pmid=31448268 |pmc=6692427 |doi=10.3389/fbioe.2019.00175 |doi-access=free}}

Existing risk analysis systems for GMOs are generally considered sufficient for synthetic organisms, although there may be difficulties for an organism built "bottom-up" from individual genetic sequences.{{Cite web |url=http://www.hse.gov.uk/research/rrpdf/rr944.pdf|title=Synthetic biology: A review of the technology, and current and future needs from the regulatory framework in Great Britain| vauthors=Bailey C, Metcalf H, Crook B |date=2012 |website=UK Health and Safety Executive|access-date=2018-11-29}} Synthetic biology generally falls under existing regulations for GMOs and biotechnology in general, and any regulations that exist for downstream commercial products, although there are generally no regulations in any jurisdiction that are specific to synthetic biology.{{cite book| vauthors=Pei L, Bar-Yam S, Byers-Corbin J, Casagrande R, Eichler F, Lin A, Österreicher M, Regardh PC, Turlington RD, Oye KA, Torgersen H |display-authors=6 |chapter=Regulatory Frameworks for Synthetic Biology |date=2012| title=Synthetic Biology |pages=157–226 |publisher=John Wiley & Sons, Ltd |doi=10.1002/9783527659296.ch5 |isbn=9783527659296}}{{cite journal |vauthors=Trump BD |title=Synthetic biology regulation and governance: Lessons from TAPIC for the United States, European Union, and Singapore |journal=Health Policy |volume=121 |issue=11 |pages=1139–1146 |date=November 2017 |pmid=28807332 |doi=10.1016/j.healthpol.2017.07.010 |doi-access=free}}

{{Colbegin|colwidth=20em}}

• {{annotated link|ACS Synthetic Biology|ACS Synthetic Biology}}
• {{annotated link|Bioengineering}}
• {{annotated link|Biomimicry}}
• {{annotated link|Carlson Curve}}
• {{annotated link|Chiral life concept}}
• {{annotated link|Computational biology}}
• {{annotated link|Computational biomodeling}}
• {{annotated link|DNA digital data storage}}
• {{annotated link|Engineering biology}}
• {{annotated link|International Genetically Engineered Machine}}
• {{annotated link|Non-cellular life}}
• {{annotated link|Open synthetic biology}}
• {{annotated link|Protein design}}
• {{annotated link|Protein engineering}}
• {{annotated link|Regenerative medicine}}
• {{annotated link|Synthetic intelligence}}
• {{annotated link|Synthetic morphology}}
• {{annotated link|Synthetic virology}}
• {{annotated link|Systems and Synthetic Biology|Systems and Synthetic Biology}}
• {{annotated link|Tissue engineering}}
• {{annotated link|Xenobiology}}
• {{annotated link|Protocell#Artificial models}}
• {{annotated link|Jeewanu}}
• {{annotated link|Hypothetical types of biochemistry}}
• {{annotated link|Playing God (ethics)}}
• {{annotated link|Mirror life}}

{{Colend}}

• [https://www.genome.gov/about-genomics/policy-issues/Synthetic-Biology#:~:text=Synthetic%20biology%20is%20a%20field,in%20medicine%2C%20manufacturing%20and%20agriculture. NHGRI. (2019, March 13). Synthetic Biology. Genome.gov. https://www.genome.gov/about-genomics/policy-issues/Synthetic-Biology]

{{reflist}}

• {{cite book |vauthors=Church G, Regis E |title=Regenesis:How Synthetic Biology will Reinvent Nature and Ourselves |date=2012 |publisher=Basic Books |location=New York, NY |isbn=978-0465021758}}
• {{cite report | publisher = European Commission | date = 2016 | url = http://ec.europa.eu/environment/integration/research/newsalert/pdf/synthetic_biology_biodiversity_FB15_en.pdf | title = Synthetic biology and biodiversity; Science for Environment Policy | work = Future Brief 15. Produced for the European Commission DG Environment by the Science Communication Unit, UWE, Bristol }}
• {{cite book | vauthors = Venter C | title = Life at the Speed of Light: The Double Helix and the Dawn of Digital Life | date = 2013 | publisher = Penguin Books | location = New York, NY | isbn = 978-0670025404|oclc=834432832}}
• {{Cite book|title=Creation : how science is reinventing life itself.|last=Rutherford|first=Adam|publisher=Current|year=2014|isbn=9781617230110|oclc=880230551}}

• [https://ctc.westpoint.edu/engineered-pathogens-and-unnatural-biological-weapons-the-future-threat-of-synthetic-biology/ Engineered Pathogens and Unnatural Biological Weapons: The Future Threat of Synthetic Biology] . Threats and considerations
• [http://openwetware.org/wiki/SynBio_books Synthetic biology books] popular science book and textbooks
• [http://syntheticbiology.web.unc.edu/ Introductory Summary of Synthetic Biology] {{Webarchive|url=https://web.archive.org/web/20180402054612/http://syntheticbiology.web.unc.edu/ |date=2018-04-02 }}. Concise overview of synthetic biology concepts, developments and applications
• [http://www.wikigenes.org/e/mesh/e/27630.html Collaborative overview article on Synthetic Biology]
• [http://www.sfgate.com/business/article/Controversial-DNA-startup-wants-to-let-customers-5992426.php Controversial DNA startup wants to let customers create creatures] (2015-01-03), San Francisco Chronicle
• [https://www.youtube.com/watch?v=rU_pfCtSWF4&t=792s It's Alive, But Is It Life: Synthetic Biology and the Future of Creation] (28 September 2016), World Science Festival

{{Branches of biology}}

{{Biology_nav}}

{{Emerging technologies|topics=yes|biomed=yes}}

{{subject bar|auto=y|d=y|portal=Biology|Chemistry|Technology}}

{{Authority control}}

Category:Biotechnology

Category:Molecular genetics

Category:Systems biology

Category:Bioinformatics

Category:Biocybernetics

Category:Appropriate technology

Category:Applications of evolutionary algorithms

Category:Bioterrorism