Slashdot Mirror
Startup Offers Pre-Built Biological Parts
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.'"
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?
~ Whence do you come, slayer of men, or where are you going, conqueror of space?
5' 5", 110lbs, female, further details can be found in attached magazine. Do you give volume discounts?
Seems that ordinary people may soon be able to do synthetic biology. No wet lab required.
I could imagine getting into that. Design a few "circuits", send away for them to be built, unpack the slides and.. expose em to ultraviolet light and see if they turn yellow, I guess.
How we know is more important than what we know.
Are they saying they can "program" the human genetic code and create an improved species? Or that they can grow body parts? Because either way, cybernetics is sure to follow in this field footsteps.
"Chance favors only the prepared mind." -Archimedes
The key innovation of the BioBrick assembly standard is that a biological engineer can assemble any two BioBrick parts, and the resulting composite object is itself a BioBrick part that can be combined with any other BioBrick parts.
Sounds great in theory. In reality, you'll always be missing one of those stupid little yellow bricks and they won't sell them individually.
So instead of "enlarge your penis" emails we will get "get a larger penis" emails.
Do the founders wear bras on their heads?
"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.'"
Boy is this guy in for a wake up. No matter how well you replicate a strand, you can't replicate the environment without violating the exclusion principle -- the two can't be in the same place. And with different environments comes different expressions. It says he's a "research scientist". I'm betting the field isn't biology.
"I may be synthetic, but I'm not stupid." -- Bishop 341-B
TFA:
I'm interested in transitioning biology from being sort of a craft....to an engineering discipline with standardized methods...
Good! Geneticists would benefit from getting smarter. Anybody taken a look at Monsanto's work? I don't think "train wreck" quite captures the epic fail quality they've managed to achieve.
I want my monkey-man!
'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.
"Operating systems suck: you're better off using only the BIOS" --trainsaw.com
It's called "bio bricks", and it's old news.
I read about before 2006.
Any sufficiently advanced intelligence is indistinguishable from stupidity.
First, I agree completely. I can't tell you how much time a program like that would save.
.ab1 files from sequenced clones and quickly align and compare them to the theoretical construct, and then indicate what needed to be done differently. For example, "your inserts are forming concatemers: adjust their concentration relative to the vector during the ligation step, or treat them with CAP (alkaline phosphatase)." or "this particular sequence has internal cut sites: use this restriction endonuclease instead."
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.
"Operating systems suck: you're better off using only the BIOS" --trainsaw.com
Are they saying they can "program" the human genetic code and create an improved species?
This is not cybernetics, it's eugenics (not the obviously unethical "extermination" eugenics but the more deviously unethical establishment of a 'genetic elite').
In star trek they're called "augments", in gundam seed they're called "coordinators", but im sure in practice it will be called "oops!, we accidentally gave you gills!"
VLC FOR MAC IS DYING! IF YOU DEVELOP, PLEASE SAVE IT!!
I just do eyes. Just - just eyes. Just genetic design. Just eyes!
"...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."
Like Software Engineering, then. Good luck with that. -j
Bioshock IRL?
Consider getting Tom Hall to publish the source
Otherwise no BioEdit fixes unless Tom can get around to them.
-- Terry
I began my course in genetics with essentially this programming goal in mind (making bad biological software better). Now I've got enough genetic theory under my belt to have a crack at something like this (although my practice is mostly low-level clinical biochemistry). Just a few more months...
Ask me about repetitive DNA
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.
Well, that's nice. I want a pony, too. But that's not how biology works.
In fact, it's not even how engineering works anymore.
A century ago, people built big things from small numbers of standardized parts. People could buy devices, take them apart, repair them, modify them, etc. These days, many mass produced products are built around custom-designed and custom-manufactured parts, from specially moulded cases to custom integrated circuits.
Building things from standardized parts really only works if performance and efficiency are secondary; they rarely are in biology.
ImageJ - free and Open Source, and consequently plugins to do pretty much everything you can think of (or if not, roll your own) (see here for a good bundle).
The next millionaires?
I have a strange desire to have a bunch of 3 inch long cats, as smart as regular cats, smaller brain cells, I guess, all optimized to breed true and live long and prosper. Why? I have this desire to have about 100 of them as pets and be a catherd.
Can you imagine sitting down with 100 of them all over you, little tiny whiskers, higher frequency purrs. Have to keep them in, I guess, or they would take over