Monday, June 16, 2014

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

Tuesday, June 3, 2014

Sharing Our Sorrow Via Facebook

Geteiltes Leid ist halbes Leid ("Shared sorrow is half the sorrow") is a popular German proverb which refers to the importance of sharing bad news and troubling experiences with others. The therapeutic process of sharing takes on many different forms: we may take comfort in the fact that others have experienced similar forms of sorrow, we are often reassured by the empathy and encouragement we receive from friends, and even the mere process of narrating the details of what is troubling us can be beneficial. Finding an attentive audience that is willing to listen to our troubles is not always easy. In a highly mobile, globalized world, some of our best friends may be located thousands of kilometers away, unable to meet face-to-face. The omnipresence of social media networks may provide a solution. We are now able to stay in touch with hundreds of friends and family members, and commiserate with them. But are people as receptive to sorrow shared via Facebook as they are in face-to-face contacts?

A team of researchers headed by Dr. Andrew High at the University of Iowa recently investigated this question and published their findings in the article "Misery rarely gets company: The influence of emotional bandwidth on supportive communication on Facebook". The researchers created three distinct Facebook profiles of a fictitious person named Sara Thomas who had just experienced a break-up. The three profiles were identical in all respects except for how much information was conveyed about the recent (fictitious) break-up. In their article, High and colleagues use the expression "emotional bandwidth" to describe the extent of emotions conveyed in the Facebook profile.
In the low bandwidth scenario, the profile contained the following status update:

"sad and depressed:("

The medium bandwidth profile included a change in relationship status to "single" in the timeline, in addition to the  low bandwidth profile update "sad and depressed:(".

Finally, the high emotional bandwidth profile not only contained the updates of the low and medium bandwidth profiles, but also included a picture of a crying woman (the other two profiles had no photo, just the standard Facebook shadow image).

The researchers then surveyed 84 undergraduate students (enrolled in communications courses, average age 20, 53% female) and presented them with screenshots of one of the three profiles.

They asked the students to imagine that the person in the profile was a member of their Facebook network. After reviewing the assigned profile, each student completed a questionnaire asking about their willingness to provide support for Sara Thomas using a 9-point scale (1 = strongly disagree; 9 = strongly agree). The survey contained questions that evaluated the willingness to provide emotional support (e.g.  "Express sorrow or regret for her situation") and network support (e.g. "Connect her with people whom she may turn to for help''). In addition to being queried about their willingness to provide distinct forms of support, the students were also asked about their sense of community engendered by Facebook (e.g., "Facebook makes me feel I am a part of a community'') and their preference for online interactions over face-to-face interactions  (e.g., "I prefer communicating with other people online rather than face-to-face'').

High and colleagues hypothesized that the high emotional bandwidth profiles would elicit greater support from the students. In face-to-face interactions, it is quite common for us to provide greater support to a person – friend or stranger – if we see them overtly crying and therefore the researchers' hypothesis was quite reasonable. To their surprise, the researchers found the opposite. The willingness to provide emotional or network support was significantly lower among students who viewed the high emotional bandwidth profile! For example, average emotional support scores were 7.8 among students who saw Sara entering the "sad and depressed:(" update (low bandwidth) but the scores were only 6.5 among students who also saw the image of Sara crying and updating her relationship status to single (high bandwidth). Interestingly, students who preferred online interactions over face-to-face interactions or those who felt that Facebook created a strong sense of community responded positively to the high bandwidth profile.

There are some important limitations of the study. The students were asked to evaluate whether they would provide support to a fictitious person by imagining that she was part of their Facebook friends network. This is a rather artificial situation because actual supportive Facebook interactions occur among people who know each other. It is not easy to envision support for a fictitious person whose profile one sees for the first time. Furthermore, "emotional bandwidth" is a broad concept and it is difficult to draw general conclusions about "emotional bandwidth" from the limited differences between the three profiles. Increasing the sample size of the study subjects as well as creating a broader continuum of emotional bandwidth differences (e.g. including profiles which include pictures of a fictitious Sara Thomas who is not crying, using other status updates, etc.), and also considering scenarios that are not just related to break-ups (e.g. creating profiles of a fictitious grieving person who has lost a loved one) would be useful for an in-depth analysis of "emotional bandwidth".

The study by High and colleagues is an intriguing and important foray into the cyberpsychology of emotional self-disclosure and supportive communication on Facebook. This study raises important questions about how cyberbehavior differs from real world face-to-face behavior, and the even more interesting question of why these behaviors are different. Online interactions omit the dynamic gestures, nuanced intonations and other cues which play a critical role in determining our face-to-face behavior. When we share emotions via Facebook, our communication partners are often spatially and temporally displaced. This allows us to carefully "edit" what we disclose about ourselves, but it also allows our audience to edit their responses, unlike the comparatively spontaneous responses of a person sitting next to us. Facebook invites us to use the "Share" button, but we need to remember that online "sharing" is a sharing between heavily edited and crafted selves that is very different from traditional forms of "sharing".     


Acknowledgments: An earlier version of this article was first published at 3Quarksdaily. The images from the study profiles were provided by Dr. Andrew High, copyright of the images - Dr. Andrew High. 

Reference: Misery rarely gets company: The influence of emotional bandwidth on supportive communication on Facebook, AC High, A Oeldorf-Hirsch, S BellurComputers in Human Behavior (2014) 34, 79-88 High, A., Oeldorf-Hirsch, A., & Bellur, S. (2014). Misery rarely gets company: The influence of emotional bandwidth on supportive communication on Facebook Computers in Human Behavior, 34, 79-88 DOI: 10.1016/j.chb.2014.01.037