My Biotech Life » Biotechnology

Synthetic Biology is not your new bicylce

Ricardo Vidal — Sun, 23 Aug 2009 18:25:57 +0000

There’s been a recurring topic showing up in prominent news outlets that has been getting on my nerves. Well, not really on my nerves but something that I consider to be wrong and was hoping someone would make it stop or at least correct it.

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

Everybody is into bio these days…

Ricardo Vidal — Sun, 27 Jul 2008 02:50:14 +0000

I was returning home on the MIT shuttle yesterday, when these two guys got on and sat on the bench behind me. They were talking rather loudly because the shuttle was full and noisy.
From what I could understand they were high school buddies. The conversation was about how they just graduated, one from MIT and the other from BU.

The MIT kid, possibly a computer science graduate, was going on about how all his friends were coders working at Cisco earning 33 bucks an hour. Some where at Google, got paid less but had better perks.

The BU guy followed by saying something along the lines: “Wow, 33 an hour! I should have gone into computer sciences…”. To what the MIT kid replied “Nah, everybody is into bio these days… That’s where the money is!”.

Shortly after, the MIT kid said “Anyways, I hate bio!”. The BU guy concurred with a simple “Me too”.

Everybody is into bio these days…

Mendeley = paper management + collaboration goodness

Ricardo Vidal — Tue, 01 Jul 2008 03:35:07 +0000

Some months ago, I was looking for software to manage the papers I had been consulting for a large group project I had been working on. At the time, the best (aka cheap or free!) available options where either for Mac or Linux, nothing for Windows.

Mac users have an award winning software application called Papers (not free) that is all the rage or even Yep (free?), the Linux gang have some options like Referencer that did a decent job of organizing and downloading metadata for the files. But Windows users were stuck with… well, expensive software packs like Endnote. Oh, and maybe Zotero that is a Firefox addon.

Well, it seems that this is not an issue anymore, someone has been hard at work and there is now a real option for Windows users (Mac & Linux too (sort of…)), it is called Mendeley.

Mendeley is still in closed beta but it is already packing a punch with some features that make it much more than just a paper manager. In their words:

Mendeley Desktop helps you to manage your research papers as easily as MP3s. When you import your research papers (in text PDF format), Mendeley Desktop will try to automatically extract the metadata (authors, title, journal, etc.), thus giving you a hand in setting up your digital library. In the next versions, we will also introduce Microsoft Word integration, OCR for converting your image PDFs, sharing and collaboration features, and exciting 3D visualizations of your library.

But Mendeley Desktop is just the starting point to get more out of your research papers. In the coming weeks and months, Mendeley Web will begin to provide you with personalized reading recommendations, statistics about your own publications, up-and-coming topics in your academic discipline, a network of fellow researchers, and much more

One of the cool features here is that there is a Desktop and a Web component that leverage the strengths of each platform. It will be interesting to see how the collaborative features in Mendeley Web work.
I’ve just began to use the software today so I can’t really get into any technical issues I may have noticed, but from what I’ve seen so far, it looks great. The user interface is functional and the overall design is also quite pleasant, on both Mendeley Desktop and Web.

The friendly folks at Mendeley have given me access to beta test their reference management application along with 20 no more invites for my readers. If you are interested in being a beta tester, feel free to comment below and I’ll send out invites first come, first served.

I’m sure we’ll be hearing much more about Mendeley in the near future as the features start rolling out. Meanwhile, take a look at this demo (youtube) and let me know what you think about this app.

Mendeley = paper management + collaboration goodness

Synthetic Biology – the journal

Ricardo Vidal — Thu, 05 Jun 2008 04:59:02 +0000

It’s just come to my attention that there will soon be a new scientific journal totally dedicated to this fascinating area of science engineering named accordingly Synthetic Biology.

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

Fold it – Solve puzzles for science

Ricardo Vidal — Sat, 10 May 2008 05:28:40 +0000

Jason from Free Genes pointed me in the direction of this cool project called Fold It that just caught my eye. It’s a game but it’s a game with serious impact.
Based upon a similar concept of grid processing like the protein folding project (folding@home) or the search for ETs (SETI@home), this new approach makes the collective effort of players directly impact the processing.
It’s as if Fold It is an upgraded version of folding@home with the extra special new feature called: human interaction.

The concept is quite simple at the gaming point of view where you try to make the protein fold in the best way possible with points being given for stability through hydrogen bonding, compacting, hydrophobic and hydrophilic positioning of lateral protein chains, etc
The “better” you fold your protein, the more points you achieve.

These conformations are registered by the software and then processed furthermore thus contributing to the overall effort of predicting protein folding and therefore solving puzzles for science!

Fold it – Solve puzzles for science

Gene Genie: the better late than never personal genomics special edition

Ricardo Vidal — Wed, 16 Apr 2008 06:18:08 +0000

It’s a couple of days off schedule but Gene Genie has arrived. I’d like to thank Berci for the opportunity once again. That said, here goes the juicy genetic content.

NAVIGENICS GETS SOME LINK LOVE
Hsien-Hsien Lei over at Eye on DNA gives us an inside look at Navigenics with an interview with Genetic Counseling Program Director Elissa Levin.

Genetics and Health also had the privilege of interviewing Navigenics with a 7 part (long!) blog post with some great topics.

Looking into Navigenics entrance into the personal genomics market, Thomas Goetz from Epidemix goes local and delivers some inside observations.

THE WOES OF PERSONALIZED GENOMICS
The personalized genomics hype is bringing up the good and the bad. By making genetic testing a spit & pay easy one-click process, the science behind the actual testing becomes somewhat doubted upon by the general public. This may not be the case but it has been seen in the media where words such as “snake oil” have been associated with genetic tests.

Lisa over at DNA Direct Talk gives us a look into this topic with a great post packed with related links.

As we can see, not all companies can be put in the same basket, but there are clues here and there that some of them “haven’t really done their homework“, says Sandra Porter over at Discovering Biology in a Digital World.

THE WHO, WHAT AND WHERE IN PERSONAL GENOMICS
The who, what and where on personalized genomics
Berci from ScienceRoll has done a great job compiling a load of links, videos and quotes regarding personalized genomics that will certainly put you up-to-date.

GENOMICS GOSSIP
And finally, The Gene Sherpa brings us some tabloid style gossip regarding the Navigenics opening cocktail parties. Find the details hiding at the very bottom of a another one of his great posts.

Thanks to all those that submitted links for this edition of Gene Genie. I’m sorry I couldn’t get you all in. Maybe next time :)
The next Gene Genie will be hosted at Gene Expression on the 27th of April.

Gene Genie: the better late than never personal genomics special edition

Dr. Craig Venter and Synthia’s genome

Ricardo Vidal — Fri, 25 Jan 2008 01:02:46 +0000

The ever-pioneering Dr. Craig Venter and his Institute have just published their latest genetic feat in Science.

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

BioBeers – The Premiere Life Science Start-up Club in Colorado

Ricardo Vidal — Sun, 09 Dec 2007 00:14:09 +0000

A buddy of mine recently told me about a new life science start-up club he was involved in called BioBeers. I thought the idea was quite cool, not only the actual start-up club, but also the name they had come up for the monthly gathering.

So, what necessarily is BioBeers?

A fundamental component to accelerate the region towards achieving a top-tier bio-cluster ranking is a thriving and nurturing bio-entrepreneurial community. BioBeers is designed to function as such an accelerant, where like minded bio-preneurs gather once a month to share ideas, cultivate business relationships and build life long friendships.

If you are located in the Colorado region, I’d recommend a visit to the official BioBeers website and get in contact. Who knows, there might just be free beer!

BioBeers – The Premiere Life Science Start-up Club in Colorado

Quote of the day by Joe Cibelli (Michigan State University)

Ricardo Vidal — Wed, 21 Nov 2007 10:00:44 +0000

Regarding the recent studies demonstrating the possibility of inducing pluripotency in Human somatic cells, Joe Cibelli researcher at Michigan State University said:

“Anybody can do this procedure. It’s a very simple recipe,” … “A combination of three or four genes, and in a couple of weeks, you go from a skin cell to an embryonic stem cell. It’s remarkable.”

Quote of the day by Joe Cibelli (Michigan State University)

Quick publishing for embryonic stem cell research (without embryos)

Ricardo Vidal — Wed, 21 Nov 2007 01:04:35 +0000

I was under the assumption that the publishing of papers in top of the line subscription journals like Nature, Cell and Science was a long and sluggish process that could take from months. But the latest research in stem cells seems to have access to the fast lane.

On the stands this week (in Cell and Science), two recent and independent papers demonstrating the capacity to induce pluripotency in human somatic cells present their results similar to those found in studies performed last year on mice by the same authors (Thomson et al, 2007; Yamanaka et al, 2007).

These papers were submitted at the end of October and within 20 days they were revised and now published. Ba-da-bing ba-da-boom!

I’ll certainly get back to these papers this week, but for now I recommend David Hamilton’s great piece over at VentureBeat Life Sciences.

Quick publishing for embryonic stem cell research (without embryos)