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.

A review of the environment and power series

Here I would like to review the series and look at the way people commented the individual posts, before concluding with a few lines about the experience.

Renewable energy renewing the Earth

In my first post I introduced the idea of environmental cost. This was the measurement that I wanted to use to address the issue of pollution, and more specifically that produced through energy use.

I tried to avoid the term ‘clean energy’, as I feel this overlooks certain aspects of all forms of production. Modern solar panels for example may provide clean energy from the sun but they themselves present issues during their manufacturing and disposal phases.

Another point I hoped to raise is that the problem needs to be viewed from a realistic standpoint. We are not all going to convert to a zero emissions life overnight any more than we are going to return to being a hunter and collector society that lives in caves. The world will continue to operate more or less as it does now, and it is through this framework that the problem should be addressed.

The first comment I received contained the following line from Vicky, and it really is worthy of note:

“I believe that each of us can help a lot in improving the health of our planet, the only problem is that we have great vision but no action. Why don’t we act first and through that action we start making some vision?” This is echoed by the quote from Gandhi that I used to open the first post, and could really be a manifesto for the series.

The second post was about cutting fuel emissions from transport systems, and it received a couple of interesting comments. Darci commented that even cutting emission by 30% (referring to the commercial use of Kites on ships) would be a great improvement, and I must agree with her. Neil’s comment included the following lines that are worth thinking about:

“It seems to me that over the past decade the builders of internal combustion engines have made some great breakthroughs in generating more energy from their engines with the same amount of input and we have seen the KW output of many engines jump significantly. It would be good to see these same producers working backwards to produce smaller engines that produce an adequate amount of power from a minimal amount of fuel.” An extremely astute comment I would say.

Post 3 entitled Cleaner Energy Production was one of the most commented of the series. I think this is because the technology described is on the verge of becoming commercially available, and because solar panels are now an every day piece of urban furniture.

The article also provoked a series of comments lead by the following from Custom Items:

“These are a great bunch of suggestions. It’s really sad that we all what we need and what is right but can’t do anything about it. I’ve always felt that the government was taking sides with the big corporations. In this world of ours, money and power talks.”

This obviously provoked discussion with the other commenters in agreement with the sentiment, some seeming to suggest that development is hindered by large corporations and governments and that although the people recognize the need for change they may be incapable of achieving it.

Not all doom and gloom though and I for one am optimistic and agree with some of the brighter outlooks expressed.

Post 4 was all about a report published by the Royal Society for Engineering in which they looked at possible ways of artificially cooling the planet. Again many comments were left, a couple of which raise issues that should be addressed.

The post involves the problematic debate around global warming. Two comments really show the diversity of belief that surrounds the issue, even though not taking radical standpoints. The following comment was made by Shane Ryans:

“In my opinion the earth has gone through many different cycles, throughout its lifetime. The earth has gone through ice ages so why would there not have been, for lack of a better word, “hot” ages. What makes today so different from the past. We are just going into yet another cycle. Now that being said, I am sure that we as a race have made the circumstances different and added to the problem and sped up the process, with all the different chemicals and air pollutants we have introduced into our environment. I do hope that scientists can come up with a viable solution”.

Although Shane does not make the line that humans do not contribute to the problem, many people do, and go on to argue that the greenhouse effect does not exist. From their point of view any change is merely a product of nature. People that espouse this line have powerful lobbies, and invest large sums of money to promote their line to the point that the debate has become a business, and dirty tricks and smear campaigns abound. See this page on Wikipedia for plenty of information and links to further reading

Returning to the post a second comment made by Virtual Stock Trading runs as follows, the edit is mine but you can see the original comment where it was left:

“I don’t think there is any doubt on global warning…….. But the process is very gradual and will not significantly affect anyone living today.”

I cannot agree with the final line. Global warming is affecting communities all over the world as we speak. Sea levels are rising and threatening the very survival of some of theMaldivesIslands, flooding is rife in low-lying countries and London has to thank the Thames Barrier to avoid Joe Strummer’s classic prediction. And a simple look at its use tells a story, it was closed four times in the 1980s, 35 times in the 1990s, and 80 times since 2000.

Post 5 was a review of inventions and power generating machines that profess to generate free or pollution free energy. It did not generate the number of comments that the previous posts managed, but Samantha returned to the non support from governments and big business argument once more:

“Actually, there are so many inventions nowadays that can actually lessen our cost and pollution as well. However, they are having problems of getting support from our government. Of course, this body is after of money from businesses like big petroleum companies.”

From a personal point of view writing the series gave me great satisfaction. I have all the articles on a single file and it looks like a small book! I wrote 2 of the articles before posting the first, as Christopher suggested, and it was a very good idea. I wanted to reply to each comment and that took a lot of time, so I found it quite a strain researching while the series was running (each post took about 6-8 hours to research and write).

I found all of the comments interesting, and thank everyone who took the time to post. I did not have the problem that I sometimes have of people missing the point. I do not like to express my arguments too openly and rely on a bit of intuition, and sometimes this is lacking and I find comments that express the opposite of what I wanted to convey. This was not the case during the series, and that pleases me.

I can definitely recommend the experience, and will undoubtedly write another.

UPDATE: Jonny has compiled a fantastic PDF publication of his series which contains every article in the series, and the responses each article got. You can view it on the blog here Can We Improve the Health of the Planet? A series by Jonny Hankins.

Nanobots – The future in Nanotechnology

This is Technology Bloggers 150th article 🙂
Well done and thank you to all our brilliant writers (Hayley included), as well as readers and commenters who have helped us get here!

A fraction of the ever-expanding field of nano-technology, nano-robots, a.k.a. nanobots, hold some of the most promising possibilities in the fields of technology, engineering and medicine. They also pose some of the most complex hurdles, such as automation, replication, control and finding viable energy sources to enable movement.

The Nano-Scale

Nanotechnology involves the study and micromanipulation of anatomic particles up to 1 nanometer, with scientists working to develop nanobots in fields less than 100 nanometers in size. Transmission electron (TEM), scanning electron (SEM), scanning tunneling (STM) and Atomic Force (ATM) microscopes are large, powerful machines that make all aspects of nanotechnology, including nano-robotics, possible.

Nano-microscopes allow researchers to isolate and observe single molecules, including chemical reactions that occur upon moving, eliminating and rearranging molecular structures. This base knowledge is essential to understanding, creating and ultimately finding solutions so that nanobot technology will reach its full potential.

Bottoms Up

Up until recent years, the development of nanotechnologies maintained “top-down” construction. The advent of “bottom up” creations on the nano-scale provide scientists the ability to create smaller objects; in addition, components can be “grown” to allow greater adaptation to specific environments or inclusion of specific properties.

Scientists are literally able to “grow” carbon nanotubes and “string” together nanowires, creating desired properties such as hastening conduction or reducing heat output – properties that make for tiny, efficient particles. In theory, by building a nanobot from the bottom up, scientists begin to find solutions that allow for greater control mechanisms and possibly self-replication of the nanobot.

A carbon nanotube

Carbon nanotubes – building nanotechnology from the bottom up.

The greatest benefit of working bottom-up is that, rather than altering materials to work in a desired fashion, scientists build nanostructures and nanobots with proper compounds from the outset.

The Present

Although practical applications in medicine and technology have yet to be fully realized, nanobots are no longer figments of science-fiction imagination.

Lack of autonomy, largely associated with insufficient or unrealistic sources of energy, leaves a large barrier to the potential uses of nanobots. Batteries and solar sources are impractical due to size and, although a scientist can guide the nanobot with the use of magnets, they are not ideal. For example, a physician using a nanobot to treat a patient would need to maneuver the nanobot from outside the skin while also observing inner structures of the body.

Within the past year, scientists announced the creation of a nano “electric motor.” Utilizing principles of adsorption, a molecule attaches itself to the outside of a piece of copper; an STM probe focuses electrons onto the molecule, providing a source of energy and means to control direction. The large, cumbersome STM still makes this impractical in many ways; however, scientists are able to study this single motor and hypothesize ways to alter this and thus to apply it to nanobots.

In addition, micromanipulation made possible by electron microscopes allows for “DNA-walkers.” Essentially reprogramming a portion of a DNA strand, “molecular robots” or “spiders” walk autonomously; ultimately, scientists hope to further develop this technology, creating nanobots that fix genetic diseases.

The Future

Many scientists believe self-replication, most likely by programming the nanobot to micromanipulate surrounding atoms to create duplicates of its self, is essential to the realization of the many medical and technological applications.

In addition, a truly autonomous nanobot would be able to recognize, react and/or adjust to varying environmental conditions, including the presence of other nanobots; scientist could also program them for molecular assembly.

Many believe nanobots will allow for precise diagnostic capability and treatment of diseases such as cancer, as well as genetic disorders. Advances in communications, green energy, computer electronics and semi-conductors appear limitless.

Summary

Although still in its infancy, scientists across many fields hold much promise for nanobot technology. An autonomous nanobot, able to adapt its environment and self-replicate, could be the key to early detection and the cure of many diseases; in addition, nanobots will play an important role in sustainable or renewable energy sources, engineering and advancing computer technology. What do you think?

For further information check out the article on nanobots over at MicroscopeMaster. Links in my bio.