What is Synthetic Biology?

In my work I write about nanotechnology and synthetic biology and over the next couple of weeks I would like to describe what is happening in these high technology fields. I start with synthetic biology. I am not a scientist and cannot give any form of technical description of how they do what they do. I can present a kind of sketch though of what they are doing and their aims.

The first question then must be what is synthetic biology? Well it is something that can be described as engineering, biology, genetics or nanotechnology, the most common description is that of applying the concept of engineering to biological organisms. But what does that actually mean?

Well, synthetic biology aims to design and engineer biologically based parts, novel devices and systems as well as redesigning existing, natural biological systems. Practitioners use a systems approach, an organism is seen as a whole, or a system, and can therefore be engineered, very much like a machine.

you see, kid's stuff

The system is reduced to biological parts (bioparts) whose function is expressed in terms of input/output characteristics. Once these parts have been described in terms of their function, isolated, standardised and syntheticaly reproduced, they can then be combined to from new organisms, very much in the way that an engineer would build a machine using standard devices built from standard parts. It is just that they are parts of a living organism.

These standard parts are defined by their DNA, and this can be manipulated in order to make the perfect part for the perfect device. Parts of the DNA can be removed and synthetic pieces used to replace them. Create the right part that does the right job, put in it a carrier cell (known as chassis) and Bob’s your Uncle, you can start to construct your organism.

The Biobricks Foundation is a not for profit organization that aims to keep a register of these standard parts, maintaining open access and promoting technical standardization, something that is seen as holding the key to the further development of synthetic biology.

Obviously to do all of the above you require technical expertise, the process requires computational modeling in order to analyze the complexities of biological entities and to predict system performance. You require DNA sequencing in order to describe the genome and then of course DNA synthesis, to re-produce either part of or the entire genome itself.

But what are the potential areas of application for this technology, and what can they actually do now?

One of the main fields is undoubtedly medicine. Drugs can be produced that are more effective or have fewer or even no side effects, as the genomes of their active components can be adjusted and synthesized. An example is the development of a synthetic version of the anti-malarial drug Artermisinin that could be industrially and cheaply mass produced, and in the near future antibiotics could become much more efficient.

Another existing application is water that changes colour when in contact with different polluting agents making them instantly recognizable. Switches already exist that react to certain types of input. An example could be a cell that is part of a person’s body that reacts to the stimulus of a certain chemical that in turn stimulates the production of another. Imagine for example a device that reacts to a chemical produced by a cancerous cell. This input causes a reaction that produces another chemical to counteract this presence. All working naturally using the body’s energy to function.

Other developments involve the energy sector, the production of plants for bio mass that are not as wasteful as those used today and even the development of synthetic aviation fuels.

In other fields a synthetic form of the silk produced by the Golden Orb spider is under development. This is an extremely strong, fine and lightweight material that could lead the way towards new specialist engineering materials.

They are even working on living computer memory, and  this article describes breakthroughs and results in DNA computing.

Well this is nothing but reasonable, my memory lives in my brain and the memory of my ancestors in my DNA, and now they have the technology to read it and even change it, so why not use it in a computer?

I have written several articles on this and other related topics on the Bassetti Foundation website, and as I said I am no scientist, so all comments and criticism invited and accepted.

How to proceed in the age of big data?

A couple of weeks ago I read an article in the New York Times about the age of big data, and today at a science and technology conference I got into a conversation about the same thing with a US public health official.

Much has been written (and I am a guilty party) about Google’s quest for information, including allegations of infringements of privacy etc, but not all of this capability should be seen in a negative light. I would like to give you a few examples of why.

A wealth of data

Google collect all of the search terms used by every user and categorize them. Let’s take a hypothetical situation. You are director of a large hospital inManchester. What can Google tell you about your job? Well probably a lot, let’s say that this week there is an enormous peak in the search terms “Flu symptoms” used across the Greater Manchester area, or “rash on back and neck”. Indirectly the knowledge of these search trends tells you that you should prepare your hospital, because late next week you will have a massive influx of patients with the Flu or some other contagious disease as it takes hold of the population.

This information is potentially lifesaving, as one of the main problems with epidemics is they come out of nowhere and so health centres are not properly prepared.

Search terms can also give an indication of how the housing market will behave too, with a rise in searches for houses in a certain area being reflected 6 months later in new sales. The type of house searched could also improve planning, as developers would see what people were looking for and where.

Analysts and programmers are currently working on how to expand on the simple examples above using search terms as wider indicators, a system called ‘sentiment analysis’ looks particularly promising.

This form of analysis looks at terms used during on line communication and categorizes them in terms of their sentiments. The logic is that in an area that is prospering terms will be generally positive, but in an area that is threatened by demise, such as the closure of industry or other societal problems, the terms will differ. This is not dissimilar to the conversation analysis sociologists use to obtain a person’s own sentiments about their position in life, with their true feelings reflected in the terms they use without thought. The hope is that an accurate analysis of this type might signal unfolding problems before they become a reality so that action can be taken in specific areas to avoid social breakdown.

I have addressed these issues in more depth on the Bassetti Foundation website, but want to conclude by saying the following; in my posts I have often raised the issue of data collection as a problem, and collection of personal data for advertising or any other purpose for that matter does raise serious ethical issues, but here Google et al could be sitting on a mine of extremely useful and possibly globally important data if the technology and political will is developed to use it correctly.

Scientists grow artificial meat

In my work at the Bassetti Foundation I have written extensively about food, its production and how technology has entered and continues to encroach on everyday provisioning.

I wrote an article about how milk from cloned cows entered the food chain last year, and then how some cloned cows went missing in Scotland, probably ending up at the butcher’s shop and on to somebody’s table, but this week I let you in to a story that goes much further.

A very fat cow

A fat cow

Scientists in Holland have managed to grow meat from stem cells and later this year aim to have enough to make a hamburger. I don’t know if they plan to eat it though, it will cost about $300 000 to produce. Although this sounds abhorrent as well as quite expensive, they have good reason to try it. Many experts believe that current food provisioning techniques are non sustainable. As the population grows more people require more food, but leave less land to use in its production, and this presents one problem. The second issue is that large scale meat production is one of the biggest carbon producing industries on the planet.

Meat production is also physically very damaging for the environment, there have been many articles written about beef production in Argentina and Brazil causing problems for the rainforests. Meat production is also inefficient. In order to produce meat (for example beef again) you need to feed up a cow, and cows eat a lot. The protein gained from the cow is equal to 15% of the protein it eats, so you have to feed a herd of cows 100 tons of protein for every 15 tons produced.

So could this new type of production help feed the planet? It will certainly have to overcome a few hurdles, production price will have to come down obviously and I imagine protests and general dislike of the idea, but OGM is everywhere nowadays (unmarked in the US I believe) and you can get used to anything if you try. The point is that it can be done, the technology exists and once done on mass it will be done cheaply.

If you are interested in learning more take a look at the article on the BBC website, my interview with Prof Andrew McMeekin of the University of Manchester Business School on the subject of food provisioning and my other meanderings on the Bassetti Foundation website.