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?
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i'm sorry, but your violating my copyright on DNA gene vG10.974.4485.011 revision 76.
Under the licence that i released that DNA sequence, it STATED that any use of it in a living being, that living being must pay a royalty of $5,000 a month or be terminated within 3 days.
gah, brings a new meaning to copyrighting life
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Um, no, I haven't been asking this question for weeks.
I have not the slightest idea what you mean by "ignoring" the answers. I found such answers as I received interesting, as I expressed. The answers I saw indicated a continuum of opinion--if simple genetic manipulation, no, if complete synthesis, perhaps. Now I'm inquiring on more views on that "perhaps", because that type of edge-case is where it's philosophically and scientifically interesting. I'm sorry you feel so defensive about what to me is an
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"Now I'm inquiring on more views on that "perhaps", because that type of edge-case is where it's philosophically and scientifically interesting. I'm sorry you feel so defensive about what to me is an interesting question of science, apart from your ad hominem fantasies and clear defensiveness regarding why I'm asking."
Yes, you enquire initially, then you just put words into people's mouths to draw your own conclusions, or simply resort to insulting people when they do not agree with your intelligent design
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So, if I had a sympathetic view toward ID, at any time, I am not entitled, somehow, to ask a purely scientific question?
Is it significant, from a purely scientific standpoint, if in 10 years Common Descent will no longer be true? YES.
Would it be useful and necessary, purely scientifically, to specify when that point occurred, that is, to have clear criteria on such questions as "what is 'descent'" and related scientific and definitional questions? YES.
Others actually contributed to these questions. I cre
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So, if I had a sympathetic view toward ID, at any time, I am not entitled, somehow, to ask a purely scientific question?
You're perfectly entitled to do so, and when you come up with one please ask it.
Is it significant, from a purely scientific standpoint, if in 10 years Common Descent will no longer be true? YES.
Nope. What currently active research questions depend on the truth or falsity of common descent? For example, most scientists currently believe that there are other life systems in the universe, s
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If we synthesize a living organism in totality, does Common Descent become untrue?
Common descent will have been true, which is the important part. It's a fundamental part of evolutionary history, crucial to understanding what has gone before.
There's no reason that this planet couldn't have had several parallel threads of common descent. It would have made evolutionary history harder to unravel, adding more noise to a signal that turned out to be pretty clear once we found it.
It means that future biologists will find the state of evolution on this planet harder to untangle, but that's t
I'm ready to place my order (Score:5, Funny)
5' 5", 110lbs, female, further details can be found in attached magazine. Do you give volume discounts?
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5' 5", 110lbs, female, further details can be found in attached magazine. Do you give volume discounts?
Should the mood code be rotary adjustable?
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Buy five with hardwired moods (since it is a volume discount). Probably less prone to faults.
Re:I'm ready to place my order (Score:5, Funny)
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By "volume discounts" I hope you don't mean if she turns out to be 250lbs, you don't have to pay as much?
No, weight has to be 110.
(not enough Neil Young fans here apparently).
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Which volume do you want to be discounted?
Hey wow (Score:2)
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.
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kinda like this,
"Scientists create synthetic polio virus from genetic sequence"
http://news.bbc.co.uk/2/hi/science/nature/2122619.stm [bbc.co.uk]
Several articles on this back in 2002.
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But it is mandatory to be because this is progress. </sarcasm>
CC.
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An average idiot like you perhaps? Did ya know that DNA does not a virus make? Of course not. Basically what you're suggesting is that "oh no, someone might be able to download the plans for a nuclear weapon of the internets!!"
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Are you sure about that [virology.ws]...?
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If you're not worried, you're not paying attention... if you're interested in this stuff, I'd suggest you watch this: http://fora.tv/2008/11/17/Drew_Endy_and_Jim_Thomas_Debate_Synthetic_Biology [fora.tv]
It really is an excellent discussion of all of the salient issues pertaining to synthetic biology. It's not going to make your hair curl or keep you amazingly excited like the mostly terrible edutainment st
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.
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Mostly to satisfy my own curiosity, is this written up somewhere outside of the academic literature? Or, if not, any pointers to a good place to start reading?
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You'll probably want a decent background in molecular biology -- equivalent to one or two intermediate college courses, or whatever you can self-learn from the right t
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Awesome, thanks!
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NEB catalog & technical reference for actual enzyme data and a few conceptual tips at the end: http://www.neb.com/nebecomm/neb_mail_form.asp
Molecular Cloning for actual protocols: http://molecularcloning.com/
Molecular Biology of the Cell for conceptual background: http://www.garlandscience.com/textbooks/0815332181.asp
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.
Consider getting Tom Hall to publish the source (Score:2)
Consider getting Tom Hall to publish the source
Otherwise no BioEdit fixes unless Tom can get around to them.
-- Terry
Almost there (Score:2)
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...
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I consider myself comfortable with software - and I'm fascinated by the prospect of synthetic DNA. A glitch is that I don't have a degree-level background in either chemistry or biology - and this makes it very hard for me to appreciate what sort of things are viable. I would definitely like to know more about this field...
Can you recommend a text-book that explains the relevant biochemistry for this from-the-ground-up?
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see my post above.
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I'm a little lost here. In my lab we already engineer discrete parts like promoters, terminators, resistance makers and individual genes all by their lonesome into plasmids that we use as starter material. Then we cut and paste with restriction enzyme and T4 ligase to make our "composite material" or BioBrick as they would call it. How is this product better? Its only 235 dollars per 50 reactions according to the NEB website...maybe their way saves a dollar or two when you buy the kit....
But the current software is god-awful, and exceedingly limited.
I know its a
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"Augments" (Score:2)
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!"
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Building blocks (Score:5, Funny)
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.
Oh Great (Score:1, Funny)
So instead of "enlarge your penis" emails we will get "get a larger penis" emails.
Obligatory reference: (Score:3, Funny)
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Of course. It's ceremonial.
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Obigitory - "didn't look very hard before spouting off did ya."
You might want to give a read here. [wikipedia.org]
Ohhh and maybe here [unizar.es]too.
Or here. [biobricks.org]
These two guys are formidable minds, so ya just might want to think before you blast your mouth off.
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Obigitory - "didn't look very hard before spouting off did ya."
You might want to give a read here. [wikipedia.org]
Ohhh and maybe here [unizar.es]too.
Or here. [biobricks.org]
These two guys are formidable minds, so ya just might want to think before you blast your mouth off.
Ah. Appeal to authority, the refuge of the science fanboi.
I know Harold Morowitz from our visits to the Santa Fe Institute and from George Mason (my daughter studies there). I quote him here regularly, especially his "Energy Flow In Biology". I've also quoted his story about being the first to try to sell fairy shrimp. It was a miserable failure. If he can tell you he can be wrong, so can I.
I don't know Knight, but I was right -- he's an engineer, not a biologist. And it was his statements I took issue with
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I replied do to your overwhelming bombast.
And you might be correct that the process might not work.
And since you have zero cred ( at least as far as I can tell ) in the field, and Knight does ( hence my references ), coupled with the fact that the guy was accepted to MIT at the age of 14, his accomplishments are massive, he studied biology under a guy who is a very well respected professor in the field, I am thinking that I would not make the flat out assertion that he is dead wrong on pretty much ANY subje
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I didn't think your response was a troll at all since most of the "modding" that gets done around here is done by fanbois.
And just for your edification, I am not any kind of a fanboi, but long ago I did learn not to make absolute statements regarding someones research as it is unwise.
Good (Score:1)
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.
God Chmod! (Score:2)
I want my monkey-man!
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.
Re:Plasmids kinda do this already. (Score:4, Informative)
Wow. Retarded reply gets modded up to the highest post.. I'd be surprised, but hey, it's a non-IT article on Slashdot.
How would you feel if I told you that teenagers have been using biobricks to do some of this "pipe dream" stuff for about 10 years now. That there's an annual international competition to showcase what they come up with and that has been running since 2003? That biobricks are a standard part of genetic engineering of microbes for industrial use? That basically everything you said was so horrendously outdated and ignorant that you sound like someone talking about the impossibility of heavier than air flight in 1913.
I know things have been bad around here for a long time and we've all come to just accept it, but would it be too much to ask that the moderation system undergo a little bit of review? I'm gunna ask the Taco.
Old news. (Score:3, Informative)
It's called "bio bricks", and it's old news.
I read about before 2006.
brrr... (Score:3, Interesting)
I just do eyes. Just - just eyes. Just genetic design. Just eyes!
Good luck (Score:1, Insightful)
"...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
I want a pony! (Score:2)
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. P
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At the moment, biology is where engineering was a century ago. We NEED standardized parts. We have lots of ground that we could cover very quickly if we didn't have to reinvent the wheel each time we wish to make a small machine.
We now know there are all these different parts. We want to put them together into small mini-machines with anywhere from 2 to 10 parts working together or so. But each one has to be taken from different sources, put together in a completely arbitrary and new manner in order to
And some journalist (Score:1)
Awesome (Score:1)
Mini Moggies (Score:1)
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