Oscillator

Electronic Noses

Biomimetic electronic noses are designed to mimic the olfactory system of mammals, with receptors that respond to certain chemicals, sending an electronic signal to a computer that can integrate the responses in order to identify the odorant. These systems are useful in industrial food preparation, where contamination by microorganisms must be detected as soon as possible. A fascinating new paper attempts to improve these electronic noses my linking the combinations of receptor signals to common smell metaphors used by real humans, like “This flavour is sweet”.

From the paper’s abstract:

Smell provides important information about the quality of food and drink. Most well-known for their expertise in wine tasting, sommeliers sniff out the aroma of wine and describe them using beautiful metaphors. In contrast, electronic noses, devices that mimic our olfactory recognition system, also detect smells using their sensors but describe them using electronic signals. These devices have been used to judge the freshness of food or detect the presence of pathogenic microorganisms. However, unlike information from gas chromatography, it is difficult to compare odour information collected by these devices because they are made for smelling specific smells and their data are relative intensities. Here, we demonstrate the use of an absolute-value description method using known smell metaphors, and early detection of yeast using the method. This technique may help distinguishing microbial-contamination of food products earlier, or improvement of the food-product qualities.

This idea is so interesting; combining in a biomimetic system not only the molecular components of chemical sensing in the nose, but also the integrative aspects of smell and taste and flavor that the brain does. Will there be an electronic sommelier someday?

Synthetic Biology and the Scientific Analogy

Scientists love analogies; they make it easier to discuss and understand complicated systems in terms of things that are familiar to many people. Synthetic biology is still trying to define itself, but the analogy that prevails thus far is synthetic biology:biology/life::electrical engineering:physics. With the data from decades of biological research, we can put together novel biological pathways and maybe even whole genomes, creating new living “circuitry”.

Since the industrial revolution, Nature has been seen as both a source of resources to be used and shaped into human invention, but also as somewhat of a machine itself, something that has parts that can be systematically understood and then used as a tool [1]. As technology has developed to embrace the digital machine, our analogies for Nature and specifically biology have changed with it. In synthetic biology we have DNA as “software”, genes as “parts”, biochemistry as “logic gates”, all the way up to cells as computers and networks [2].

With this kind of analogy in place, synthetic biology can make “devices” that behave like toggle switches, logic gates, diodes, or oscillators, and even develop real computer software to help build living circuits like you would electronic circuits. This intertwining of biology and electrical engineering has almost moved beyond simple analogy, that biological molecules are electrical components (I too am guilty of this) and that progress in synthetic biology will mirror progress in computer engineering in the 20th century.

This analogy is useful, and certainly interesting, but is it limiting? Biology does a lot of amazing things that computers can’t (yet?), and vice-versa. There are some people working on cyborg interfaces between computers and cells as a way to take advantage of both (see the Harvard 2008 iGEM project, for example) but in a lot of ways cells and computers are not alike in what they are, what they do, and how we interact with them (and that’s ok). I think most importantly, this kind of analogy doesn’t really take into account the basic science implications of synthetic biology as a tool.

I’m not sure if we need an analogy at all, but the one that I like the best is synthetic biology:biology::synthetic chemistry:chemistry from Brian Yeh and Wendell Lim’s 2007 Commentary “Synthetic biology: lessons from the history of synthetic organic chemistry” [3].

Chemical synthesis of organic compounds in the mid 1800’s shattered the notion that there is something magical about the chemicals that make up living systems. Most importantly, synthesis led to enormous insights into the physical structure of molecules. Despite the very limited knowledge of chemistry that existed at the time of the first synthetic projects, attempts at creating molecules opened up new avenues for learning about chemistry, with obvious implications for how we make drugs, dyes, plastics, food etc.

We may be at such a turning point now. There is a lot that we don’t know about how cells work, but attempts at synthesizing rudimentary biological pathways will possibly allow synthetic biologists to better understand how cells work, and will very likely develop many useful technologies and research tools along the way. In the end synthetic biology may redefine biological engineering and the study of biology into something uniquely different.

Synthetic Biology 1’s and 0’s

I’m fascinated by the ways that people discuss biological engineering, the language that they use to talk about what cells, proteins, and DNA do. Often, these words come from computer engineering: DNA is the code, proteins are machines, cells can interact to form networks, etc.

A recent article in the UK version of Wired points out that even though we like to talk about biology as machines, the reality is that while “the 1s and 0s of software live in shiny metals shielded by colourful plastics; biological data lurks in dampness, in pipettes and test tubes.” How does the grossness associated with bacteria affect how synthetic biology and biotechnology are received?

I love the idea that if the domestication of biotechnology is going to dominate our life for the next 50 years, as Freeman Dyson predicts, the aesthetics and perceptions surrounding biology are going to change dramatically. Will germophobes be the new luddites? Will bacteria be beautiful? How about lab supplies?