Synthetic Biology: Engineering Life To Examine It

Two scientific papers that were published in the journal Nature in the year 2000 marked the beginning of engineering biological circuits in cells. The paper "Construction of a genetic toggle switch in Escherichia coli" by Timothy Gardner, Charles Cantor and James Collins created a genetic toggle switch by simultaneously introducing an artificial DNA plasmid into a bacterial cell. This DNA plasmid contained two promoters (DNA sequences which regulate the expression of genes) and two repressors (genes that encode for proteins which suppress the expression of genes) as well as a gene encoding for green fluorescent protein that served as a read-out for the system. The repressors used were sensitive to either selected chemicals or temperature. In one of the experiments, the system was turned ON by adding the chemical IPTG (a modified sugar) and nearly all the cells became green fluorescent within five to six hours. Upon raising the temperature to activate the temperature-sensitive repressor, the cells began losing their green fluorescence within an hour and returned to the OFF state. Many labs had used chemical or temperature switches to turn gene expression on in the past, but this paper was the first to assemble multiple genes together and construct a switch which allowed switching cells back and forth between stable ON and OFF states.

The same issue of Nature contained a second land-mark paper which also described the engineering of gene circuits. The researchers Michael Elowitz and Stanislas Leibler describe the generation of an engineered gene oscillator in their article "A synthetic oscillatory network of transcriptional regulators". By introducing three repressor genes which constituted a negative feedback loop and a green fluorescent protein as a marker of the oscillation, the researchers created a molecular clock in bacteria with an oscillation period of roughly 150 minutes. The genes and proteins encoded by the genes were not part of any natural biological clock and none of them would have oscillated if they had been introduced into the bacteria on their own. The beauty of the design lay in the combination of three serially repressing genes and the periodicity of this engineered clock reflected the half-life of the protein encoded by each gene as well as the time it took for the protein to act on the subsequent member of the gene loop.


Both papers described the introduction of plasmids encoding for multiple genes into bacteria but this itself was not novel. In fact, this has been a routine practice since the 1970s for many molecular biology laboratories. The panache of the work lay in the construction of functional biological modules consisting of multiple genes which interacted with each other in a controlled and predictable manner. Since the publication of these two articles, hundreds of scientific papers have been published which describe even more intricate engineered gene circuits. These newer studies take advantage of the large number of molecular tools that have become available to query the genome as well as newer DNA plasmids which encode for novel biosensors and regulators.

Synthetic biology is an area of science devoted to engineering novel biological circuits, devices, systems, genomes or even whole organisms. This rather broad description of what "synthetic biology" encompasses reflects the multidisciplinary nature of this field which integrates ideas derived from biology, engineering, chemistry and mathematical modeling as well as a vast arsenal of experimental tools developed in each of these disciplines. Specific examples of "synthetic biology" include the engineering of microbial organisms that are able to mass produce fuels or other valuable raw materials, synthesizing large chunks of DNA to replace whole chromosomes or even the complete genome in certain cells, assembling synthetic cells or introducing groups of genes into cells so that these genes can form functional circuits by interacting with each other. Synthesis in the context of synthetic biology can signify the engineering of artificial genes or biological systems that do not exist in nature (i.e. synthetic = artificial or unnatural), but synthesis can also stand for integration and composition, a meaning which is closer to the Greek origin of the word.  It is this latter aspect of synthetic biology which makes it an attractive area for basic scientists who are trying to understand the complexity of biological organisms. Instead of the traditional molecular biology focus on studying just one single gene and its function, synthetic biology is engineering biological composites that consist of multiple genes and regulatory elements of each gene. This enables scientists to interrogate the interactions of these genes, their regulatory elements and the proteins encoded by the genes with each other. Synthesis serves as a path to analysis.

One goal of synthetic biologists is to create complex circuits in cells to facilitate biocomputing, building biological computers that are as powerful or even more powerful that traditional computers. While such gene circuits and cells that have been engineered have some degree of memory and computing power, they are no match for the comparatively gigantic computing power of even small digital computers. Nevertheless, we have to keep in mind that the field is very young and advances are progressing at a rapid pace.
One of the major recent advances in synthetic biology occurred in 2013 when an MIT research team led by Rahul Sarpeshkar and Timothy Lu at MIT created analog computing circuits in cells.

Most synthetic biology groups that engineer gene circuits in cells to create biological computers have taken their cues from contemporary computer technology. Nearly all of the computers we use are digital computers, which process data using discrete values such as 0's and 1's. Analog data processing on the other hand uses a continuous range of values instead of 0's and 1's. Digital computers have supplanted analog computing in nearly all areas of life because they are easy to program, highly efficient and process analog signals by converting them into digital data. Nature, on the other hand, processes data and information using both analog and digital approaches. Some biological states are indeed discrete, such as heart cells which are electrically depolarized and then repolarized in periodical intervals in order to keep the heart beating. Such discrete states of cells (polarized / depolarized) can be modeled using the ON and OFF states in the biological circuit described earlier. However, many biological processes, such as inflammation, occur on a continuous scale. Cells do not just exist in uninflamed and inflamed states; instead there is a continuum of inflammation from minimal inflammatory activation of cells to massive inflammation. Environmental signals that are critical for cell behavior such as temperature, tension or shear stress occur on a continuous scale and there is little evidence to indicate that cells convert these analog signals into digital data.

Most of the attempts to create synthetic gene circuits and study information processing in cells have been based on a digital computing paradigm. Sarpeshkar and Lu instead wondered whether one could construct analog computation circuits and take advantage of the analog information processing systems that may be intrinsic to cells. The researchers created an analog synthetic gene circuit using only three proteins that regulate gene expression and the fluorescent protein mCherry as a read-out. This synthetic circuit was able to perform additions or ratiometric calculations in which the cumulative fluorescence of the mCherry was either the sum or the ratio of selected chemical input concentrations. Constructing a digital circuit with similar computational power would have required a much larger number of components.

The design of analog gene circuits represents a major turning point in synthetic biology and will likely spark a wave of new research which combines analog and digital computing when trying to engineer biological computers. In our day-to-day lives, analog computers have become more-or-less obsolete. However, the recent call for unconventional computing research by the US Defense Advanced Research Projects Agency (DARPA) is seen by some as one indicator of a possible paradigm shift towards re-examining the value of analog computing. If other synthetic biology groups can replicate the work of Sarpeshkar and Lu and construct even more powerful analog or analog-digital hybrid circuits, then the renaissance of analog computing could be driven by biology.  It is difficult to make any predictions regarding the construction of biological computing machines which rival or surpass the computing power of contemporary digital computers. What we can say is that synthetic biology is becoming one of the most exciting areas of research that will provide amazing insights into the complexity of biological systems and may provide a path to revolutionize biotechnology.

An earlier version of this article was first published at 3Quarksdaily.


Daniel R, Rubens JR, Sarpeshkar R, & Lu TK (2013). Synthetic analog computation in living cells. Nature, 497 (7451), 619-23 PMID: 23676681

The Prize in Biology in Memory of Alfred Nobel

The days leading up to the announcements of the Nobel Prizes as well as the aftermath are gossip heaven for us scientists. We love to speculate who will win and after the announcements, we exchange wild conspiracy theories, talk about the painful snubs and pontificate on whether or not the recipients deserve the honors. Our dark side also tends to chime in and we exhibit some Schadenfreude when the more pompous leaders in a field are snubbed and some of us also salaciously look forward to another Nobel scandal.

The announcement that John Gurdon and Shinya Yamanaka are the recipients of the 2012 Nobel Prize in Physiology or Medicine was a special treat for me. Usually, when I hear about the Physiology or Medicine Nobel Prizes, the discoveries for which the recipients are honored either occurred decades ago or were in areas of biomedical research that are not directly my area of interest.

Wikimedia / Marcela

This year’s Nobel Prize was awarded to Gurdon and Yamanaka for their ground-breaking work, which showed that adult, mature cells can be reprogrammed to an immature, stem cell state. This discovery is the basis of much of the work in my own laboratory and as I write this, I know that stem cells are being cultured in my laboratory using the methods that Yamanaka developed only six years ago. When I read the paper by Takahashi and Yamanaka published in the journal Cell in 2006, I knew that I was witnessing a land-mark discovery by brilliant scientists, and many of us in the stem cell field have been expecting that Yamanaka would receive the Nobel Prize for his work, we just seemed to disagree about the year in which he would receive it.

John Gurdon’s work dates back to the 1950s and 1960s, when he showed that nuclei from adult cells of the Xenopus frog could be transplanted into an enucleated egg and give rise to healthy frogs – the first example of animal cloning. Gurdon challenged the older paradigm that once a cell becomes mature, it cannot go back. His work was a conceptual revolution and many of his colleagues were initially resistant to embracing this paradigm shift. Gurdon’s seminal findings gradually convinced many other scientists to embrace his ideas and he inspired numerous other scientists to attempt cloning of other animals. The mechanisms of how the reprogramming occurred remained a mystery. How could a nucleus of an adult cell suddenly activate the transcriptional program of its embryonic past simply by being transplanted into an egg cell without a nucleus?

This type of nuclear reprogramming was also rather cumbersome, especially in adult mammals. Extracting the nucleus of an adult cell and then injecting it into a single egg cell required a lot of expertise and was not ready for a widespread use in stem cell laboratories. When Yamanaka published a method nearly 50 years later in which the reprogramming to the embryonic-like state could be initiated by merely implanting four genetic regulators into an adult mouse cell, the idea of reprogramming adult cells suddenly caught on. Within a matter of months, other laboratories confirmed the findings and his paper became one of the most highly cited papers in recent history. In a period of just six years, Yamanaka’s paper has been cited more than 4,000 times! Yamanaka then published a second paper in 2007, showing that adult human skin cells could be reprogrammed to the embryonic-like induced pluripotent stem cell (iPSC) state and this has lead to the generation of stem cell lines from numerous patients.

I think most stem cell biologist will agree that both Gurdon and Yamanaka deserve the Nobel Prize for their discoveries. Some may ask why the first author Kazutoshi Takahashi on the landmark 2006 paper was not a co-recipient. Others may wonder about whether the scientists who developed techniques to culture human embryonic stem cells should also have been honored, because without their hard work, Takahashi and Yamanaka may not have been able to culture the human iPSCs. Such questions common after all Nobel Prize announcements, and are in part due to the stringent requirement that the Nobel Prize can be shared by no more than three researchers, a requirement that should perhaps be reconsidered in our age of collaborative and networked discovery.

The question that bothers me, however, is why John Gurdon had to wait so long for his Nobel Prize. He had published many of the papers that convincingly documented successful reprogramming of adult Xenopus cells nearly 50 years ago. This was a pioneering discovery that challenged the paradigm of irreversible differentiation during development and had a major impact on the thinking of not just developmental biologists, but biologists from numerous disciplines.

The Lasker Foundation also recognized the importance of John Gurdon’s work, when it awarded the prestigious Lasker Basic Medical Research Award to both, Gurdon and Yamanaka in 2009. I think the obvious reason for Gurdon’s recognition in recent years is that Yamanaka’s method of reprogramming allowed for a much broader application of Gurdon’s idea to mammalian and human cells, in a manner that can will likely be used for regenerative therapies, disease modeling and screening of patient specific pharmaceutical agents.

If Yamanaka had not published his work on reprogramming mouse and human cells, would Gurdon have still received the Nobel Prize? This is a speculative question, but I think the answer is “No”, because the awarded Nobel Prize is in “Medicine or Physiology“. The title of the prize implies that the discovery has to have a link to medicine or normal physiology, but this makes it difficult to justify awarding the prize for ground-breaking discoveries in biology without a direct relevance for medicine or physiology. When the Nobel prizes were established more than a century ago, biology as an independent science was still in its infancy. The past century has brought us remarkable discoveries in biology, such as those in the areas of evolution or photosynthesis, which do not have a direct medical application. Just like the Nobel Prize in Physics honors great intellectual feats in the field of physics without documenting that these discoveries will lead to new technologies, biological discoveries should be similarly recognized without having to await imminent medical relevance.

Even though Nobel did not establish a Nobel Prize in Economics, the Sveriges Riksbank responded to the recognition for the need of such a Nobel Prize by donating the required money to the Nobel Foundation to establish “The Sveriges Riksbank Prize in Economic Sciences in Memory of Alfred Nobel“. It has this convoluted name, because it is technically not a “Nobel Prize” and was not part of Nobel’s will, but it is still administered by the Nobel Foundation like all the other Nobel prizes and this is why in common parlance, we all refer to it as the Nobel Prize in Economics. I think that we have to realize there is a similar need for a Nobel Prize in Biology, to honor outstanding biological discoveries that stand on their own, without having to prove their medical relevance. Establishing the “The Prize in Biology in Memory of Alfred Nobel“, would be one way to recognize discoveries in biology and also foster even greater interest in this field, that will likely become one of the most important sciences of the 21st century.

This article was originally published on the Scientific American Guest Blog.