Monthly archives of “May 2015

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The “smart” in synbiosmart


“If you look up consciousness in the dictionary, it says, “awareness of the world around you,” and that’s because you lose it somehow when you become unconscious, right? Well, you can show that microorganisms, or bacteria, are certainly conscious. They will orient themselves, they will work together to make structures. They’ll do a lot of things. This ability to respond specifically to the environment and to act creatively, in the sense that that precise action has never been taken before, is a property of life. “

-Lynn Margulis

While synthetic biology research is often creative and innovative, the true intelligence is that of the microbes,  plants and eukaryotic cells involved. I am most familiar with the intelligence of bacteria. The best studied bacterium, E. coli, has roughly 4,000 genes and we are lucky if we know the function of 50% of these genes. Humans have an estimated 25,000 genes, which was an unexpected and lower number of genes than was originally thought to explain the differences between humans an bacteria.

Microbiology has a rich history of study, with the first microscopes of Richard Hooke and Anton van Leeuwenhoek in the 1600s, followed by the isolation of specific pathogens and the demonstration of the germ theory by Louis Pasteur and others in the 1800s. The first microbial genome was sequenced in 1995 (Haemophilus influenza) and now with 1000s of complete or draft genome sequences, and new ones added to the list every day. Despite this rich history, and our ability to interrogate the function of each gene in a given genome, we still are lucky to experimentally confirm the function of 50% of a given bacterial genome. Any scientist who has spent his graduate degree trying to characterize the function of one or a handful of genes will attest to the challenge to understanding a microbe – or even a single gene function.

A central illustration of the intelligence of microbes is their ability to survive, to colonize any and all environments on planet earth. The staggering diversity of microbes attests to their ability to evolve, to acquire the genetic potential to thrive, to  produce energy, to multiply. The diverse behaviours of microbes also marks their true intelligence. They may have large genomes but not all genes are expressed at any given time. Bacteria use an economical approach for expressing genes, where only those genes that are needed are expressed, and many are only expressed under specific conditions. For example, when in the presence of specific carbon sources, only then are the genes required to take in and metabolize the substrate are expressed.

This ability to sense and respond to changing and diverse conditions is a hallmark feature of microbes. They possess a large variety of environmental sensing mechanisms, with abilities to sense environmental threats, changes in temperature, viscosity, surfaces, concentration gradients of nutrients. The sensing ability is often mediated by surface bound protein machines and sensors, but also by internal protein sensors of a myriad of chemical signals. Microbes are multilingual and are capable of communicating with related species types, but also adept at communicating with diverse numbers of species. The ability to communicate with a population has a profound affect on their behaviour, as it allows the population to coordinate a virulent attack on the host during infection, or to produce bioluminescence at the appropriate stages of their symbiotic relationships with many higher marine organisms.

Microbes are sophisticated architects and builders of complex structures known as biofilms. These aggregate ‘towers’ and ‘mushrooms’ allow them to survive harsh environmental conditions, and resist the grazing behaviour of hungry amoeba in the wild, or evade our white blood cells that are constantly on the patrol for microbes in locations like the blood and tissues, where they are not supposed to be.  The list of sophisticated behaviours includes hunting and biodegrading. We are currently gaining an increased appreciation for the importance of all microbes in the human body – now referred to as the human microbiome. In this context, microbes are supremely helpful, where they are required to digest our food, train our immune system, influence our brain and behaviour, and protect us from infection by the relative minority of bacterial pathogens. Microbes seem to be peace loving creatures that by and large evolve to greater degrees of symbiosis with their host. However, we can’t put microbes in a box,  they are also adept warriors and have developed sophisticated weapons to kill neighbouring and therefore competing bacterial species in a dramatic display of “survival of the fittest”.

These diverse behaviours and attributes are the result of a very long period of learning over the last few billion years, and the acquisition and sharing of a diverse gene pool.  This intelligence in the form of features, gene functions and behaviours is now being exploited for the design of new products and technologies. We are mining this potential for new ideas and there are limitless possibilities. From this biological intelligence, we will design our future factories, environmental detox kits, monitoring stations, computers, medicines and much more.


microbial intelligence.

Photo taken from The Incredible Book Eating Boy – Oliver Jeffers

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Synthetic Biology has great potential to transform health and the environment


By way of introduction, I am scientist with 20 years of experience at the lab bench. Most of my research has been working with bacterial pathogens and trying to understand how they cause disease, resist antibiotics and evade the immune system. To accomplish this goal, we use molecular biology and recombinant DNA approaches to engineer these strains to answer basic research questions. These methods are the same tools needed for synthetic biology, which is the use of an engineering and design approach to create new cell lines with new features and to create new biotechnologies.

The path of drug discovery is long, possibly as long as your career. Although it is possible to discover a new antibiotic to combat infections, there is a tremendous regulatory process to bring that drug to market. In my career, I have known very few scientists to complete this cycle. This is one of the reasons I am attracted to synthetic biology, where the time needed to create something is very short, on the order of a few weeks in the lab. We are just beginning to consider the ethical implications of using synthetic biology, so it is hard to say how and when these technologies will be of use in the market. In my opinion, with access to new technologies such as next generation sequencing and custom DNA synthesis, the rapid pace of discovery will force the system to catch up and establish the appropriate ethics and guidelines to bring these technologies online.

The goal of this blog is to discuss new ideas and discoveries that arise in the area of synthetic biology. The focus will be those ideas that will help us clean up and protect our environment, and also to maintain and improve our health. I also hope to educate the non-scientists on some of the details regarding the science behind synthetic biology. We will explore the science of Canadian and international researchers who are working in this area, and the various entrepreneurial communities developing around the science of synthetic biology.

As a final thought, I am not one who proposes that new technologies will save us from our human-imposed environmental and health crises. There are some who are eternal optimists with a touch of denial believing that all will be sorted out in the future, with the advent of new technology. In fact, I often think that many of our problems could be avoided or mitigated or even solved  by changing our behaviour, changing our conditioning and ways of safely living with the status quo. While the ideas presented on this blog may have potential to help solve some of major challenges, this is only one piece of the puzzle. Human beings must ultimately wake up and exercise a higher level of awareness expressed through our thoughts, words and actions, so that when we look back on the past, we have pride in what was accomplished.