Category Archives: biology

Synthetic Biology

This exciting field is evolving so rapidly that no widely accepted definitions exist. Common across many explanations is the idea of synthetic biology as the application of engineering principles to the fundamental components of biology. Some commonly used definitions are:

“Synthetic biology is a) the design and construction of new biological parts, devices and systems and b) the re-design of existing natural biological systems for useful purposes.” “Synthetic biology is an emerging area of research that can broadly be described as the design and construction of novel artificial biological pathways, organisms or devices, or the redesign of existing natural biological systems.”

(http://www.synbioproject.org/topics/synbio101/definition/)

A lightly broader definition which also provides information on some of the areas where it is used is this: Synthetic biology aims to make biology easier to engineer. Synthetic biology is the convergence of advances in chemistry, biology, computer science, and engineering that enables us to go from idea to product faster, cheaper, and with greater precision than ever before. It can be thought of as a biology-based “toolkit” that uses abstraction, standardization, and automated construction to change how we build biological systems and expand the range of possible products. A community of experts across many disciplines is coming together to create these new foundations for many industries, including medicine, energy and the environment. (https://www.ebrc.org/what-is-synbio)

Another definition points to the link between synthetic biology and biotechnology: Synthetic biology represents the latest phase in the development of biotechnology, in which scientists are gaining unprecedented control in programming new biological functions by rewriting the genetic code. This allows them to ‘design’ and ‘create’ micro-organisms that may perform a variety of useful tasks. At the same time these organisms are becoming increasingly more estranged from those we may find in nature. (https://www.synenergene.eu/information/what-synthetic-biology). As the Synthetic Biology Center at MIT explains, “The key is the development of an engineering methodology based on standardized and well-characterized interchangeable parts. Biological systems can be a basis for practical programmable materials, providing an engineering substrate with exquisite control over and response to the chemical world” (http://synbio.mit.edu/).

Types of research

According to Newcastle University, Synthetic biology research can be split broadly into three categories: new approaches, technologies and tools, the application of synthetic biology and the ethical, legal and social implications of synthetic biology (http://www.ncl.ac.uk/csbb/research/). A research report from Allied Market Research estimated that the synthetic biology market could reach $38.7 billion by 2020 (http://www.bio-itworld.com/Press-Release/Synthetic-Biology-Market-is-Expected-to-Reach-$38-7-Billion,-Globally,-by-2020—Allied-Market-Research/). Information on another report which also provides information on the different regions in the world and the companies that dominate this field is available at https://www.futuremarketinsights.com/reports/synthetic-biology-market.

Synthetic biology and defence

It is not surprising that the Department of Defense and its research arm Defense Advanced Research Projects Agency (DARPA) have taken the lead in research in SB. It has also begun to fund it. “The organization had increased its investment to $100 million per year by 2014. Funding increases were followed by the creation of the DARPA program Living Foundries: Advanced Tools and Capabilities for Generalizable Platforms, which sought to increase the speed and decrease the cost of generating new production strains of organisms. This program started in 2012, and in 2014, Living Foundries transitioned to a new program, Living Foundries: 1000 Molecules, which will invest $110 million through 2019 to enable facilities to generate organisms capable of producing 1,000 molecules of industrial and defense interests. These funds are going to a diverse group of projects. Some are incredibly broad, such as funding provided to MIT’s Broad Institute to advance our ability to assemble large genetic systems. Other projects have a specific, discrete purpose, such as the DARPA–funded biotech startup Ginkgo Bioworks, which is developing probiotics to help prevent common infections for soldiers” https://www.oreilly.com/ideas/darpa-and-the-future-of-synthetic-biology.

Synthetic biology and health

The UK government too has been interested in SB. Asking ‘Is synthetic biology the key to health?’, Lucy Goodchild van Hilten says that “In January, the UK government announced a funding injection of £40 million to boost synthetic biology research, adding three new Synthetic Biology Research Centres (SBRCs) in Manchester, Edinburgh and Warwick. The additional funding takes the UK’s total public spending on synthetic biology to £200 million – an investment that hints at the commercial potential of synthetic biology” (https://www.elsevier.com/connect/is-synthetic-biology-the-key-to-health). Committed to research in SB, The Institut Pasteur says that “The rise of emerging pathogens and antibiotic resistances is becoming a major public health issue. Using engineering principles we are creating new strategies to quickly decipher the mechanisms of bacterial virulence and provide tools to specifically kill antibiotic resistant and virulent bacteria” (https://research.pasteur.fr/en/team/synthetic-biology/).

Developing Standards for Synthetic Biology

Clearly, in a field such as this, there is an obvious need to develop standards. RAND Corporation made a study at the behest of the British Standards Institute. As it explains,At the request of the British Standards Institution, researchers identified the impact the adoption of synthetic biology is likely to have on the global marketplace, as well as barriers to preventing the rapid scale-up and commercialisation of the technology. One notable finding is that companies think standards will help reduce uncertainty and help to overcome a variety of barriers they encounter en-route to commercialization” (https://www.rand.org/randeurope/research/projects/synthetic-biology-standards.html).

The story so far

To understand the evolution of the subject, you may consider reading this from year-2000 Nature article http://www.nature.com/nature/focus/synbio/index.html, as it provides useful information on milestones in SB and many related themes.   The United States is home to many centers and research programmes. Keen as it is retain its leadership, it has defined a roadmap as you can read at https://www.sciencedirect.com/science/article/pii/S2405805X1630031X.

An excellent introduction to the subject and its evolution to where it is today is this article in http://www.explainingthefuture.com/synthetic_biology.html, which also discusses its many applications.

 

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Quantum biology

The Physics of Life Group in the UK explains the emergence of Quantum biology: “Quantum biology is an interdisciplinary field investigating non-trivial quantum effects, such as long lived quantum coherence, that play a role, at the molecular level, within living cells. The field has emerged in recent years as a result of a number of surprising experimental discoveries, such as quantum coherence in photosynthesis, quantum tunnelling in enzyme action and olfaction, possible quantum entanglement in avian navigation and several other areas” (http://www.physicsoflife.org.uk/quantum-biology.html).

What clinches its importance is the establishment of the world’s first training Centre for Quantum Biology at the University of Surrey with £1m support from the Leverhulme Trust. “The Centre, which will be headed by Professors Johnjoe McFadden and Jim Al-Khalili, will train a new generation of scientists with the skills needed to study and even exploit the quantum underpinnings of life from efficient energy transport in photosynthesis to the quantum-guided navigational skills of Christmas robins. Up to seven PhD students will be recruited each year for the next three years who will engage in a three-year interdisciplinary training and research programme. Students will work on projects from photosynthesis to nanotechnology”. Professor JohnJoe McFadden, Director of the Centre for Quantum Biology at the University of Surrey, said: “Quantum biology may also provide insights into how our brain works and even what our thoughts are made of, or provide a new understanding the fundamental difference between living and inanimate matter. But research is currently scattered and lacks dedicated scientists and established research foci. This new interdisciplinary science requires expertise from many fields, from biology and biochemistry to physics, mathematics and computer science, yet most biologists know nothing about quantum mechanics and physicists generally shun the messy and highly complex world of living organisms. To progress, quantum biology needs a new generation of scientists who can operate across the discipline boundaries, which is what we hope to achieve within our new Centre.”

Professor Jim Al-Khalili, Co-Director of the Centre for Quantum Biology at the University of Surrey, said: “A novel aspect of the Centre is that it will also exploit cutting-edge technologies, such as nanotechnology or synthetic biology to study quantum biology. For example, studying quantum mechanics of photosynthesis is difficult inside living cells or even in test tubes so members of the team will attach chlorophyll molecules to carbon nanotubes so that the systems for energy capture can be studied more effectively. Another example is bird navigation where it has been shown that the European robin appears to use quantum entanglement – the ability of distant particles to retain ‘spooky’ connections – to navigate around the globe. But the robin is not an easy experimental model so scientists involved in the Centre will be using synthetic biology tools to move the bird’s compass into the much more tractable fruit fly, which has been the favourite animal of geneticists for more than a century. Once in the fruit fly, the genes involved in the compass can be manipulated to discover how the system works.”

(https://www.surrey.ac.uk/mediacentre/press/2018/world%E2%80%99s-first-training-centre-quantum-biology-established-university-surrey-)

Sheer diversity of research

Spin biochemistry

The diversity of such a new discipline is just staggering. The Florida Institute of Technology says that “Our group and collaborators are pioneering what appears to be a fundamentally important domain of QB: namely, the role and control of electron spin in the biological production of ROS.  This “spin biochemistry” is the study of radical pair dynamics that impact ROS partitioning into different chemical species at their points of formation.  At the heart of this QB problem lies the quantum mechanical phenomenon of singlet-triplet mixing, which is a type of superposition (coherence) of quantum states.  Understanding the fundamental quantum properties that regulate ROS production promises to open new approaches to control ROS-related signaling mechanisms.

A major challenge in QB has been the difficulty of making direct, rigorously controlled measurements of quantum processes in biological environments.  The development of new experimental techniques to probe quantum phenomena in cell biology, that accurately reflect in vivo situations, represents a transformational breakthrough.  Thus, our approach to QB will reveal quantum signatures in ROS production, resulting from the bioenergetics of normal cellular metabolism and link signatures to outcomes.  Indeed, bioenergetics and the formation of ROS are inextricably connected, contributing to various ROS signaling pathways and gene regulation.  A significant achievement in redox cell biology would be to understand the basic fundamental mechanisms of ROS signaling. Demonstration of quantum signatures in the formation of ROS and subsequent activation of specific transcriptional signaling pathways that lead to altered growth profiles could have enormous fundamental impacts on a number of agricultural and biotechnology research areas”. (http://research3.fit.edu/quantum-bio/quantum-biology.php)

Ron Naaman, who holds the Aryeh and Mintzi Katzman Chair in Chemical Physics at the Weizmann Institute of Science and David Waldeck, a professor of chemistry and Director of the Petersen Institute of NanoScience and Engineering at the University of Pittsburgh, have written a research paper on spin in Quantum Biology.  (http://inference-review.com/article/spin-in-quantum-biology)

3 of nature’s greatest mysteries

A recent article (September 3, 2017) by Philip Berry describes three of nature’s greatest mysteries that may be solved with the help of Quantum Biology. This exciting field is helping us to understand bird migration, photosynthesis, and maybe even our sense of smell. (http://bigthink.com/philip-perry/3-of-natures-greatest-mysteries-may-be-solved-thanks-to-quantum-biology)

Experiment demonstrates quantum mechanical effects from biological systems

Amanda Morris, Northwestern University (December 5, 2017), writes of experiments by Prem Kumar, professor of electrical engineering and computer science in Northwestern’s McCormick School of Engineering and of physics and astronomy in the Weinberg College of Arts and Sciences. He asks: “Can we apply quantum tools to learn about biology? People have asked this question for many, many years—dating back to the dawn of quantum mechanics. The reason we are interested in these new quantum states is because they allow applications that are otherwise impossible.” Partially supported by the Defense Advanced Research Projects Agency, the research was published Dec. 5 in Nature Communications. “Researchers have been trying to entangle a larger and larger set of atoms or photons to develop substrates on which to design and build a quantum machine,” Kumar said. “My laboratory is asking if we can build these machines on a biological substrate.” In the study, Kumar’s team used green fluorescent proteins, which are responsible for bioluminescence and commonly used in biomedical research. The team attempted to entangle the photons generated from the fluorescing molecules within the algae’s barrel-shaped protein structure by exposing them to spontaneous four-wave mixing, a process in which multiple wavelengths interact with one another to produce new wavelengths.

Through a series of these experiments, Kumar and his team successfully demonstrated a type of entanglement, called polarization entanglement, between photon pairs. The same feature used to make glasses for viewing 3D movies, polarization is the orientation of oscillations in light waves. A wave can oscillate vertically, horizontally, or at different angles. In Kumar’s entangled pairs, the photons’ polarizations are entangled, meaning that the oscillation directions of light waves are linked. “When I measured the vertical polarization of one particle, we knew it would be the same in the other. If we measured the horizontal polarization of one particle, we could predict the horizontal polarization in the other particle. We created an entangled state that correlated in all possibilities simultaneously.” (https://phys.org/news/2017-12-quantum-mechanical-effects-biological.html)

Physicists and quantum biology

Many physicists are engaged in work on quantum biology. Adriana Marias, a theoretical physicist, says that, “The most well-established area in quantum biology is the study of photosynthesis. There exists a body of evidence that the primary photosynthetic processes of energy and charge transfer exhibit quantum mechanical properties essential for function and that cannot be described by classical physics” (http://www.adrianamarais.org/research). The University of Crete, places Quantum physics and Quantum biology together as it engages in research on a range of areas (http://www.quantumbiology.gr/). For a look at research in the European Union, take a look at http://www.quantumbiology.eu/research-groups.html.

Cancer research

To better understand cancer, The Quantum Biology Institute has “recently used advanced methods in Quantum Physics, Topology, Differential and Algebraic Geometric, Modular and fractal geometry to unravel peculiar aspects of Cancer, which for decades, have stumped Biologists. As a result, we made significant breakthroughs in Cancer genesis, and in tumors formation. These findings are opening up novel means and platforms to develop new cures and to eradicate Cancers. Research conducted at the Institute, using Quantum Biology probes, concludes that Cancer is first and foremost a Quantum Disease. Research conducted at the Institute investigate the feasibility to experimentally test predictions from our findings in atom smashers and in plasma laboratories. Protocols for experiments are being investigated. We are currently looking to expand this work by collaborating with other laboraties–FERMILAB, SLAC, CERN, BROOKHAVEN, The Princeton Plasma Laboratory”, (https://www.quantumbiologyinstitute.org/). The Institute has many other research interests.