Synthetic biology


Synthetic biology is a multidisciplinary field of science that focuses on living systems and organisms. It applies engineering principles to develop new biological parts, devices, and systems or to redesign existing systems found in nature.
It is a branch of science that encompasses a broad range of methodologies from various disciplines, such as biochemistry, biotechnology, biomaterials, material science/engineering, genetic engineering, molecular biology, molecular engineering, systems biology, membrane science, biophysics, chemical and biological engineering, electrical and computer engineering, control engineering and evolutionary biology.
It includes designing and constructing biological modules, biological systems, and biological machines, or re-designing existing biological systems for useful purposes.
Additionally, it is the branch of science that focuses on the new abilities of engineering into existing organisms to redesign them for useful purposes.
In order to produce predictable and robust systems with novel functionalities that do not already exist in nature, it is also necessary to apply the engineering paradigm of systems design to biological systems. According to the European Commission, this possibly involves a molecular assembler based on biomolecular systems such as the ribosome.

History

1910: First identifiable use of the term synthetic biology in Stéphane Leduc's publication Théorie physico-chimique de la vie et générations spontanées. He also noted this term in another publication, La Biologie Synthétique in 1912.
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.
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.
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.
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:
1988: First DNA amplification by the polymerase chain reaction using a thermostable DNA polymerase is published in Science by Mullis et al. 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.
2003: The most widely used standardized DNA parts, BioBrick plasmids, are invented by Tom Knight. These parts will become central to the International Genetically Engineered Machine competition founded at MIT in the following year.
File:Synthetic Biology Open Language standard visual symbols.svg|thumb|upright=1.5| Synthetic Biology Open Language standard visual symbols for use with BioBricks Standard
2003: Researchers engineer an artemisinin precursor pathway in E. coli.
2004: First international conference for synthetic biology, Synthetic Biology 1.0 is held at MIT.
2005: Researchers develop a light-sensing circuit in E. coli. Another group designs circuits capable of multicellular pattern formation.
2006: Researchers engineer a synthetic circuit that promotes bacterial invasion of tumour cells.
2010: Researchers publish in Science the first synthetic bacterial genome, called M. mycoides JCVI-syn1.0. The genome is made from chemically-synthesized DNA using yeast recombination.
2011: Functional synthetic chromosome arms are engineered in yeast.
2012: Charpentier and Doudna labs publish in Science the programming of CRISPR-Cas9 bacterial immunity for targeting DNA cleavage. 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.
2019: Researchers report the production of a new synthetic 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.
2020: Scientists created the first xenobot, a programmable synthetic organism derived from frog cells and designed by AI.
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.
2021: Scientists reported that xenobots are able to self-replicate by gathering loose cells in the environment and then forming new xenobots.
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.

Perspectives

Synthetic biology is a field whose scope is expanding in terms of systems integration, engineered organisms, and practical findings.
Engineers view biology as technology. 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 and our environment.
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. 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 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 synthesized DNA.
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. 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.
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. Re-writers draw inspiration from refactoring, a process sometimes used to improve computer software.

Categories

Bioengineering, synthetic genomics, protocell synthetic biology, unconventional molecular biology, and in silico techniques are the five categories of synthetic biology.
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.

Bioengineering

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, 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.