Synthetic biology is great, I really like everything about it. I truly do. I had the privilege of meeting and seeing the work of some of the pioneers in this exciting new approach to genetic engineering last year at MIT.
I must emphasize something about these bioengineers. They are extremely smart, hard working, innovative and, did I say it? smart biological engineers!

So what is it that ticks me off about some of the synthetic biology related articles? It’s not the “Frankenstein” remarks, it’s not the bioterrorism worries and it’s not even the JC Venter veneration!
Nope, it’s the constant comparison between synthetic biology now and computer science in the mid-80′s.

This comparison just brings along a whole truck load of babble that I think is incorrect. Mentioning that synthetic biology makes engineering biology so easy you can do it in your garage as if putting together a new lego set. Stating that people are sequencing their own genomes in their closet as if it were something like baking a cake in your microwave.

These stories are either incomplete or incorrect. You choose. I think that the average reader is going to misinterpret these articles. It’s quite notorious by looking at the comments made on the online news articles.

No doubt that synthetic biology makes engineering biology easier but it’s not something you’ll be doing in your garage/kitchen/bedroom closet. At least not legally, or with much success. Besides, the people that seem to be championing such efforts are mostly graduate students in fields related to biological sciences, not your regular Make magazine reader or science buff.

I’m not against the DIYBio movement. I just don’t think it should be synonymous with “garage synthetic biology”, because it’s not. They have a ton of really interesting projects that I believe would make more sense to put effort into.

So yeah, let’s not get ahead of ourselves.

In summary: Synthetic biology is great awesome! But unlike Obama, it’s not your new bicylce.

[Photo: Alexander van Dijk]

Synthetic Biology is not your new bicylce

GOOGLE SQUARED AND GENETICS
Search terms: DNA sequence

Search terms: Genomes

Search terms: Genetic Diseases

Search terms: Genes

WOLFRAM|ALPHA AND ENGINEERING
And now, let me just put in my quick 2 eurocents (roughly 2.84 US cents) regarding Wolfram|Alpha.
I’ve found it to be a really valuable tool with any work that requires looking up tabulated data and proceeding with any type of calculations upon such data.

Wolfram|Alpha would have been such a time saver while I was working on my biotech industries project. Loads of engineering calculations and data to look up that would have been made so much easier. No need to skim through Perry’s handbook, through process engineering and transport phenomena books looking for figures, graphs and constants. Wolfram|Alpha would have made most of it a simple search.

In summary, Wolfram|Alpha is, in my opinion, a really large and structured Almanac with a super scientific calculator mashed-up into it and therefore a very useful reference tool. However, it’s pretty poor when it comes to anything outside it’s “comfort zone”, like life sciences. I’ll have more to say about this in a future post.

Google Squared and genetics, Wolfram Alpha and engineering

The new journal will be published by Wiley & Sons and has a respectable editorial board headed by Adam P. Arkin (Berkeley). The board includes well known researchers in this emerging field of bioengineering like Pamela Silver (Harvard), Luis Serrano (EMBL Spain), Ron Weiss (Princeton), Christina Smolke (Caltech) and more.

The new journal is described as follows:

Synthetic Biology as a journal will provide a forum for scientific inquiry in this field. The core will be publishing of Research Articles and Technical Reports that exemplify the cutting edge in both foundations and application for synthetic biology. Perspectives and Reviews will help track the major technical innovations and challenges and the rapid evolution of thought that characterizes this new field and engage the community in discussion of the impact of this science on biology, biotechnology, society, and the economy.

The journal is now accepting research articles, perspectives, reviews and spec sheets. I find the idea of spec sheets in biology, just brilliant (ex: BBa_F2620 Data Sheet pdf).
From some research presentations/articles I’ve already had a chance to look at, the first issue of Synthetic Biology will surely be a success.

Synthetic Biology – the journal

The creation of a synthetic organism and related work being done by the Venter Institute has been running the press/blogs for quite some time now. The organism, also known as Synthia, is not yet a reality but the genetic structure seems well on it’s way.

Dr. Craig Venter doesn’t see himself as playing God, it’s more like using the building blocks of life to build new life forms.

“I don’t view that we’re creating life,” Venter told The Associated Press last year in describing this series of experiments. “I view that we’re modifying life to come up with new life forms by designing and synthetically constructing chromosomes.”

More on this:
- Venter Institute Scientists Create First Synthetic Bacterial Genome
- Scientists Create Synthetic Genome

Dr. Craig Venter and Synthia’s genome

The project title is “Production of Potassium Cephalosporin-C” and it was a hell of a ride. It’s a nice 300 pages worth of engineering and another 500 pages of annexes to follow along.

And to top off that nice heap of dead trees, we have our industrial process all laid out and programmed in the engineering software we used.

Mission accomplished!

I recently found this site dedicated to nanoscience and nanotechnology called nanoHUB. bought to the web by the NCN (Network for Computational Nanotechnology) at Purdue University.

It’s a beautifully designed and structured website that provides visitors with valuable information, for beginners and experts alike.

Although not an area that I’m too familiar with (other than some simple stuff about biosensors which is not really nanotech…) I’ve found this site to be a good example of how the use of great design and new web technologies can make room for a better user experience, be it for proper research or simply learning a bit about nanotechnology.

nanoHUB brings nanotechnology to the web

The research I’m referring seems to take a good step forward regarding the propagation of synthetic genomes after the transfer of the entire genome of one species of bacteria to another made the later become of the same species as the donor. Confused?

Well, remember the Matrix: Revolutions? They had that spiteful Agent Smith that could sort of touch anyone and have that person become an Agent of the matrix just like himself?
Well, instead of transferring his bits and bytes over to the next person and making them a copy of himself, we’re talking about DNA, more DNA and bacteria.

The study shows a success rate of 1 in 150 000 but this is not that bad if we take into account that we are talking about bacteria and that this is in fact a great step for the synthetic biology folks.

Sr. Anderson, mi genome es su genome!

Synthia, or Syn for friends, is none other than The Venter Institute’s own human-made life form. In fact, the very first made.

It seems that The Venter Institute is proceeding to patent this life form worldwide and there is some opposition by the ETC Group that is afraid this could be the opening of Pandora’s box.

Statements like the following are among the basis of their opposition towards this monopolistic patenting of life forms.

“For the first time, God has competition, Venter and his colleagues have breached a societal boundary, and the public hasn’t even had a chance to debate the far-reaching social, ethical and environmental implications of synthetic life…”

So, although this is true, I’d like to see a debate regarding this issue. There are indeed a lot of bones to pick, and I’d like to hear the opinions from professionals on both sides.

But there is a great question that floats around…

Will Venter’s company become the ‘Microbesoft’ of synthetic biology?

What do you have to say about this, are we going a little too far? Or is this a great step ahead?

Via ETC Group news release.

The Venter Institute patenting synthetic life

Sound odd? Well, it’s more than you think. These little guys are genetically engineered pets – GenPets. And they come in cool packages where they stay in hibernation until they are picked up at the shop.

These packages are extremely high-tech with heart monitor, fresh strip (to see how long the GenPet has been waiting on the shelves), Bio-Genica IV System (to feed the GenPet) and Color Strip that shows the GenPet’s personality type (?!).

Some other info about Bio-Genica‘s GenPet:

• Allergen free
• Child safe
• Low maintenance
• 1 or 3 years life span
• 7 different personalities available

So, are you going to be the first one in your neighborhood to get one? Let’s hope your cat or dog gets along with the little guy!

Note: For anyone that is completely loosing it by now… This is biotech art!

Via: Genetics and Health & Medgadget

Bioengineering brings you GenPets

SuperPro Designer facilitates modeling, evaluation and optimization of integrated processes in a wide range of industries (Pharmaceutical, Biotech, Specialty Chemical, Food, Consumer Goods, Mineral Processing, Microelectronics, Water Purification, Wastewater Treatment, Air Pollution Control, etc.). The combination of manufacturing and environmental operation models in the same package enables the user to concurrently design and evaluate manufacturing and end-of-pipe treatment processes and practice waste minimization via pollution prevention as well as pollution control. (in Intelligen.com)

I used it last year, along with my work group, to project an industrial plant capable of producing Vitamin B. From raw material through all the different processes involved right down to the final product and all calculations needed in between.

This year, I’m starting it up again and we’re planning out a Cephalosporin C industrial bioprocessing plant. Calculations are done on the side using Microsoft Excel and a little brain power and the information is then introduced into the program and we go from there.

I’ll most probably spend some more time explaining my experience with this great application in the future, but for now I’ll just leave it up to you to check it out at Intelligen‘s website.

Oh! Yeah… it’s extremely expensive (~13k!) for a students pocket change but luckily we have it running on some computers at the university, even though it is an older version… (we’re using v4.9 and the latest release is 6.1 I think…)

SuperPro Designer – Making life (a little) easier