Startup Offers Pre-Built Biological Parts 71
TechReviewAl writes "A new startup called Ginkgo BioWorks hopes to make synthetic-biology simpler than ever by assembling biological parts, such as strings of specific genes, for industry and academic scientists. While companies already exist to synthesize pieces of DNA, Ginkgo assembles synthesized pieces of DNA to create functional genetic pathways. (Assembling specific genes into long pieces of DNA is much cheaper than synthesizing that long piece from scratch.) Company cofounder Tom Knight, also a research scientist at MIT, says: 'I'm interested in transitioning biology from being sort of a craft, where every time you do something it's done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things.'"
First-post question recycling! (Score:2, Interesting)
So, to reprise a previous question, in an improved form...
If we synthesize a living organism in totality, does Common Descent become untrue?
If so, how will we know when Common Descent became no longer true?
Re:Does this mean... cyborgs? (Score:4, Interesting)
Apparently they've streamlined a technique whereby the biological mishmash of understanding is standardized into 'code-like' organization. So instead everyone looking up how to make their own gene of their liking, knowing everything about the whole process from the DNA, to the organism to output, you instead just plug in what you want.
In biology there are known 'promoters' (that say "Start"), terminators ("END"), with the gene in the middle, and a number of other little addons and 'features'. Currently in the lab I have to paste these together on my own, from different sources, using different techniques on each. I have to bring each piece into my local standard before I can put them all together. Because it is MUCH easier to change a few bases, or add/delete, than it is to synthesize de novo entire strands of DNA, there exists a need to have modular, standardized 'code' that can easily be swapped from one project to another. These guys make that easy, I guess. When your goal is not just to change/alter a gene, but to set up a few altered/new/engineered genes (or even an entire pathway) at once, this could save a lot of headache.
Re:Does this mean... cyborgs? (Score:5, Interesting)
Oh, and by the way, if there are any ambitious young coders who want to revolutionize bioengineering, all you have to do is write some decent software which can objectively navigate the complicated but exceedingly logical rules of basic cloning. Someone who could write a program with a nice GUI where you just dragged around genes along a plasmid backbone, told it what organism you're to be working in, and have it spit out the plasmid one should use, the oligos & primers needed to be ordered, along with the enzymes to be used could enable a lot of time to be saved in the lab and make a lot of synthetic biology MUCH more accessible. It's a simple kind of code. Great fun for the programming mind. But the current software is god-awful, and exceedingly limited.
Re:Hey wow (Score:3, Interesting)
But it is mandatory to be because this is progress. </sarcasm>
CC.
Plasmids kinda do this already. (Score:3, Interesting)
'I'm interested in transitioning biology from being sort of a craft, where every time you do something it's done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things.'"
To some extent, this is already done with common bacterial strains, and the plasmid vectors we already use. Most of the plasmids we use in the industry have specific sets of features such as multiple cloning sites, inducible repressors, ORIs, antibiotic resistance sites etc... You need a plasmid that has a kanamycin resistance gene, high copy number, will add a His tag to your product, and lacks cut sites for a particular restriction enzyme? It's likely in the catalogues already. And if what you're trying to assemble is already in the catalogues, it's a target that may not be worth pursing anyway, since you're unlikely to get a publication or a patent off of it.
The approach he seems to be pushing here seems to be analogous to buying a car piece by piece rather than as a pre-assembled package. The difference is that while average joe has no idea how to fabricate a synchro for his transmission, your average molecular biologist is already quite adept at designing primers and cloning fragments out of a cDNA library. The hard part for the scientists is then characterizing, validating and optimizing the expression of their target; and then later demonstrating the functionality of the product. To continue the analogy, it would be showing that the car ran, was reliable, and was safe for the passengers. Having readily available gene circuits (the famous lac operon for instance) may help with the planning and initial development, but it really won't speed up the bulk of the work we do.
I'll readily admit that many of the expression/knockout constructs are somewhat ad hoc in nature, but interoperability isn't typically a concern. The thing is that evolution is a pretty laissez faire system where "duct tape and bailing wire" construction is more often the rule than the exception. Nature cares about what works, not about what conforms to standards (codon-amino acid translation being the biggest exception that comes to mind). As a result, expression systems have to be tailored to the organism that they'll be expressed in. For instance, bacteria cannot express functional mammalian genes unless the introns are removed from the sequence first. Sufficiently large yeast proteins will cause an immune reaction because the glycosylation patterns are recognized as foreign. Many genes won't be expressed very well at all unless the regulatory elements in the flanking sequences are also included. Once you start looking at things like inducible expression and tissue-specific expression, things get even more complicated, and more varied between species. In short, it's complicated, and the idea of instituting standards to achieve interoperability between expression systems is pretty much a pipe dream.
In short, I have my doubts about the plausibility of this plan, and I'll be mighty impressed if he pulls it off.
agreed! (Score:4, Interesting)
I'd just like to add in a quick feature request. It would be very nice if it could take the
The software that I'm using now does allow you to figure out situations like the above, but all it does is alignments; Analyzing the reasons why something didn't work out takes guesswork, and the comparisons prettymuch have to be done manually. For the concatomers example, I'd have to back to my original insert sequence, make a text document of the DNA sequence, import multiple copies into the program, reverse a couple of them (sense/anti-sense), and then manually align the second and third copies. It's very time consuming when it really shouldn't be.
Re:Does this mean... cyborgs? (Score:4, Interesting)
+1. It blows my mind how terrible the software is. Bioedit has some powerful tools in it, but finding out whether or not it has a tool you haven't used before, and then figuring out how to use it often takes hours. But it's really the little things that it does to you when you are worn down from trying to make it do new things that really goes above and beyond, to that realm of "Oh my god, whoever made this was an evil genius."
For instance if you tell it to line the similar parts of two sequences it asks you if you want to save the statistics. Then while you're annoyed with that, it resizes the window to almost fullscreen. You go to close it, and it closes the window behind it, usually the page for the genomic sequence.
I would generalize it to any young coder should consider bio-related software. For instance imaging software for microscopy is also terrible in my experience. Imaris is useful for pulling together multiple microscope images over time to make a 3d movie. Importing multiple files to stitch together, the version we have invariably puts what should be the last frame as the second frame. I'm told the more current version fixes that, but as far as I can tell the solution is that the new version doesn't even attempt to put the movies together.
brrr... (Score:3, Interesting)
I just do eyes. Just - just eyes. Just genetic design. Just eyes!
Re:Hey wow (Score:3, Interesting)
Are you sure about that [virology.ws]...?