Software Lets Scientists Assemble DNA
Velcroman1 writes "Biochemical engineers can now download a piece of software and with a few simple clicks, assemble the DNA for new life forms through their laptops. 'With the proper computer tools, biologists can write their own genetic code — and then turn that code into life,' said biochemist Omri Amirav-Drory, who founded Genome Compiler Corp., the company that sells the software. He demonstrated at a coffee shop early one morning by manipulating a bacteria's genes on his laptop. The synthetic biology app is still in beta; on Jan. 15, the company added an undo feature and support for new DNA file formats. Building creatures is increasingly like word processing, it would seem. But such is the strange reality in the age of cheap genome sequencing, DNA synthesizing and 'bioinformatics.'"
And how long will it be until extremists design and assemble a lethal and unstoppable virus this way and trigger a global epidemic that wipes out humanity in the name of Allah? Nice work, Omri; you've just handed them the tools.
licet differant, aequabitur
It was called Spore.
The guy who said the election was rigged won the presidency with the second-most votes.
DNA is a programming language after all... but knowing the character set is far from understanding the foibles of the programming language itself. We need to have a deeper and more complete understanding before distributing this kind of power.
Not cool.
"Undo feature?" Shouldn't the command to eliminate your unwanted DNA creations be called "Abort?"
We don't have a state-run media we have a media-run state.
I have a degree in it. (More specifically B.Sc in Computer Science specializing in Bioinformatics)
Wow, that is really a misleading title for those in the field. "Assemble" generally refers to solving the jigsaw puzzle of putting digitized DNA fragments generated from a sequencing machine together to form contigs which can eventually be assigned to a chromosome.
See:
http://en.wikipedia.org/wiki/Sequence_assembly
Oliver's law of assumed responsibility: If you're seen fixing it, you will be blamed for breaking it.
...by 'DNA 2.0', which seems to hold an absurdly broad patent on DNA editors:
http://holmansbiotechipblog.blogspot.co.uk/2012/12/dna-20-sues-genome-compiler-corp-for.html
I seem to recall that the complete genome was published a few years ago. I'll be in my sealed bunker.
any one got some dino DNA?
I need backers to fund a zoo.
... achoo ...
I've been considering taking up study in this field. As a software developer I can see benefits for both sides. I'm curious if we could develop a suitable runtime environment to express the code rather than just "build and lets see".
Where genius and insanity become confused true wisdom is found
When the compiler can show eventual protein expression in the resulting virtual organisms I'll be really impressed. Wonder what the output device will look like?
Organization? You must be joking..
This kind of software tools have been available to genetics/molecular biology reserchers for the last 4-5 decades, only the computer nerds don't know it. When my friends told me 10 years ago that Linux is the best platform and I told them that the software I use at work does not run on Linux they couldn't believe it: what kind of software do I need that isn't free, open source, and available in a Linux repository? Well, it may come as a shock to some but almost all specialty, proprietary software runs on Windows or Max OS.
Yeah, I can see where that could be useful:
Nuoh my god we're cylons.
While amazing progress has been made, genetic engineering and synthetic biology are still very young fields. In spite of what this company (and scientists like Craig Venter) would like you to believe, the field is no where near being able to engineer organisms or even simple biochemical pathways in the same efficiency as we are able to in mechanical/electrical engineering.
This drawback shouldn't prevent the development of more sophisticated tools, but it seems disingenuous to pitch their solution as the last piece left in the puzzle.
Not that it matters, but IAASB (I am a synthetic biologist).
In the late 1980s or 1990ish, I attended a meeting sponsored by the National Science Foundation, to promote interaction between biologists and computer scientists. Much of the discussion focussed on designing algorithms and producing programs to answer questions posed by biologists. That part of the discussion was dominated by laments: biologists describe problems, computer scientists create programs to solve them, biologists find that the solution isn't really what they wanted.
Gerald Sussman (MIT, creator of Scheme) was at the meeting. At one point he got excited, and captured the podium. Alas, there is no transcipt, but here's my paraphrase of his inspiring speech:
I have a great memory. I remember good stuff, and some of it happened. Please don't blame Mr. Sussman for any idiocies in my paraphrase. Maybe I projected the prehensile tail from my own repressed desires. But, I do think Mr. Sussman deserves great credit for observing the deep conceptual connections between CS and genetics at a time when very few of us thought beyond the idea of writing computer programs to help solve genetic problems.
Mike O'Donnell http://people.cs.uchicago.edu/~odonnell/
Read War of the Worlds. Then read The Hot Zone.
No virus is unstoppable; unless you consider humanity a mega-macro-virus.
Basically I'm not scared. I can always live underground for a few years while the unprepared/weak succumb.
Does the tool let people specify various epigenetic factors, such as methylation? This is a thing that's pretty important, but that a lot of people don't understand well (and some refuse to believe there's anything to understand there).
If so, wow.
If not, this is going to have some severe limits in utility. Useful, certainly, but completely incapable of producing working DNA for, say, a human being or a giraffe.
How long until we see a GCC release implementing this?
Bioweapons.
Careful what you wish for.
Just a wish list...
Kinda like ponies, rainbows and sparkly vampires
If a powerful tool can be invented, it will be invented. That is how humans are. You can't stop that. No amount of sentiment, moral pontification, or law will stop scientific progress (for any length of time). It is just too much a part of our basic nature.
The only question is who gets it first.
If you want to blame someone for evil, don't blame the scientists who make the tools. Blame the specific people who use the tools for evil.
Integrate this software with the Sims game and you will have a winner!!!
Karma: Bad
....to Jurassic Park!
I thought they were talking about a 3D printer app...
It's no more appropriate to say "bioinformatics" than it is to say "algebra" - they're well defined fields.
We can print a new one.
why the fuck would you put bioinformatics in quotes?
Once satisfied with the results, a scientist can save her invention to a file, click the order button and ship the virtual creature’s specs to a DNA synthesizing lab such as GenScript or GeneArt, which can assemble actual physical DNA based on the specs. Read more: http://www.foxnews.com/science/2013/02/27/programming-life-with-click-mouse/#ixzz2M8XF9cfu
So my question is: are the DNA synthesizing labs regulated? Will they just synthesize anything that is submitted, or is there some scrutiny? And what is the risk if they do synthesize something bad? What is the amount of effort needed to weaponize even dangerous DNA? If it is relatively easy, then regulation of the synthesizing labs is well advised.
The genetic code is indeed a programming language. It was designed by evolution, while the artificial programming languages for digital computers were at worst (Ada?) designed by government-appointed committee. The user's manual hasn't been written yet, and of course the notion that we know how to program a prehensile tail is a joke. We know how to program sequences of amino acids. We know that there are conditional mechanisms, but they are more numerous and trickier than if ... then ... else. We can learn a lot, but not by a long shot everything, by investigating the control mechanisms in nucleic acid expression, using insights that were stimulated by computer programming languages.
Sigh. Can we stop extrapolating useful ideas in silly ways in order to ridicule them, and put more effort into squeezing out insight in many different ways? I have met a few thousand computer scientists, and not one of them expressed such an opinion, or anything near to it. It was certainly not the spirit in which I understood Sussman. Come to think of it, I don't know anyone who thinks that computer programming languages are easy to understand and hack, so the notion doesn't even start with computer languages much less carry over to an attitude about biology.
Mike O'Donnell http://people.cs.uchicago.edu/~odonnell/
All in all you would need to have access to a lot of the equipment and skills found in molecular biology and virology labs to get the job done, not just mail order DNA.
Of Microsoft buying them.
And then, adding Clippy support in the UI.
"It looks like you're trying to make a weaponizable ebola virus. Do you want some help with that?"
Carrier pigeon. Carolina Parakeet. Mastodon. Elephant bird.
Contribute to civilization: ari.aynrand.org/donate
Unless I'm missing something, couldn't you then easily code for a batch of bacteria that produces morphine, or cocaine, THC, mescaline, psilocybin, or any other number of natural, and possibly synthetic drugs, grown in a jar in the privacy of your own home? ... cool!
It's a better, modernized, interface for essentially pre-existing sequence technologies. Vector NTI does the same thing and has been around for ever. So have other applications. The only thing "new" here is it makes it easier to export the data in a format readily importable by the DNA synthesis vendors.
I'm not saying it's not a useful tool, sequence applications are notable for being distinctly user UNfriendly. If this tool simplifies the interface it could be very useful in research.
As for the actual, physical sequencing side. It's one thing to create DNA sequence on the computer, another to create the physical sequence, yet another to accurately sequence a viable sequence hundreds of millions, of base pairs long, and finally and quite a bit another to build a living cell from scratch. As far as I am aware, the second-to-last item is yet to be accomplished, and the last being something we've only accomplished in a limited fashion with a very persmissive yardstick. We've created a small, artificial chromosome and replaced the natural one inside a cell, letting the new chromosome take control of the cellular machinery and propagation.
But all of that cellular machinery was pre-existing. We have NOT created a synthetic cellular membrane, filled it with synthetic cellular machinery, and controlled it with synthetic DNA/RNA. We haven't even taking natural bits and re-assembled a cell. "All" we've done is irradiate an existing, whole cell and inject an artificial chromosome.
And this speaks nothing of higher-order organisms, or things that utilize linear chromosomes rather than the much more simplistic circular chromosomes used in experiments to date.
That's not to say that the research done, and in progress, isn't anything short of amazing. But it's no where near the level of sophistication suggested by headlines and fear-mongers.
Source: ima genetic engineer.
I have to ask myself, since the biochemists are limited to biochemical knowledge at the time of technology release, how this will work with Circular RNA, or all the other forms of RNA such as microRNA, miRNA, mRNA, siRNA, and so on.
Just in the past five years, so much has changed that a true understanding of proper DNA regulation, while better than before, is a moving target.
It's like building a solar house while unaware that we can now 3D print biofilm shaped solar windows that power the house, have algae digestation of household wastes used to run fuel cell power plants, and use green walls and other methods to achieve Platinum LEEDS levels of efficiency.
-- Tigger warning: This post may contain tiggers! --
Writing programs to serve biologists is cool as far as it goes, but our collaboration should cut much deeper. The genetic code is a programming language, and we should help biologists figure out the structure of the programs written in the alphabet of the bases. What I really want is the Emacs mode to edit the genome, so I can give myself a prehensile tail.
Of course, if he is correct and the genetic code is a programming language, then genome is merely various algorithms combined to express various desired traits. And as we have been told over and over again, algorithms cannot be patented, so this would be doomed to fail because there is no money to be made.
'With the proper computer tools, biologists can write their own genetic code — and then turn that code into life...
Err...not exactly, Mr. article author. It takes two things, a) copying of the genetic material, and b) expression of the genetic material. The expression of the genetic material is much more significant than the mere assembling and duplicating of DNA code and is only very roughly understood by biologists. It's analogous to an architect showing up at your door with a set of plans and saying 'there you go...you can turn those plans into your dream home' but there has to be the carpenters, plumbers, electricians, and whatnot that read the plans and build the home. Similarly, the way that genetic material is expressed determines if a hand develops or a flipper. The smallest, simplest forms of life are nevertheless far more complex than the most complex device ever constructed by people. It is a form of institutional hubris to suggest or believe that new life can be created by stitching together some DNA. The best we can manage at the present is to modify some tiny function of an existing life form in a hopefully beneficial direction. Anyone who thinks otherwise can volunteer to deal with the next influenza outbreak.
Awesome! Now we just need someone to create a Vindaloo Monster, which could help to feed the poor and starving. Or have it feed on the poor or starving. Either way, it resolves a need.
It's the perfect solution. I mean, what could possibly go wrong?!
The term has been around for over a decade now. Placing it in single quotes implies that it is very new or not well accepted; neither of which are correct for bioinformatics. As someone who has been to bioinformatics conferences in the past I can tell you there are thousands of scientists who would agree with this.
Damn_registrars has no butt-hole. Damn_registrars has no use for a butt-hole.
The technology to synthesize DNA has existed for decades, but is limited in the length of DNA pieces that it can produce. Companies like genescript (mentioned in the article) can put the pieces together for you, but there's even a limit to how much they can put together for you. Plus they've been around for many years now. So first off, this is nothing new.
Second, the program that's reference here isn't really that amazing. There are scores of tools that exist for copying and pasting DNA sequences. Back in the day I used to do it in notepad (and still do from time to time). The fact that they let you essentially "edit the text of your essay" and that it integrates databases of "essays" is cool, but there have been lots of tools like this in the past, (I use them all the time).
I guess what I'm saying is this: there's nothing new here, and even if it was... all you're getting in the mail is DNA -- not the organism. As others have stated, it's an entirely different thing. DNA is completely benign and is just a dry powder at the bottom of a vial. You could eat the suff, no matter the sequence.
And how long will it be until extremists design and assemble a lethal and unstoppable virus this way and trigger a global epidemic that wipes out humanity in the name of Allah?
Really? This nonsensical fear comes up all the time. If you RTFA (I know, not fashionable here but try it some time, you might like it) you can find that even Fox News includes some factual information on occasion:
You can send them a text file and they'll send you back physical DNA
For those who are not familiar with molecular biology, having the DNA is only one step; it doesn't do much of anything on its own. If you're trying to alter a bacteria (anthrax, e coli, etc) you need to get the DNA in to the bacteria of your choice and get it to take it up in a way that results in a persistent change in order for it to hang around. Most of the time when foreign DNA is introduced into a bacteria it is promptly spat back out; so you need to overcome this hurdle. And if you're working with a virus it is even more technically challenging.
Nice work, Omri; you've just handed them the tools.
No, no, no. He has not handed them the tools. He basically just wrote a piece of software that brings different resources together into one simpler package.
If anything perhaps your comment deserved to be moderated up as "funny". It most certainly did not in any way earn "interesting".
Damn_registrars has no butt-hole. Damn_registrars has no use for a butt-hole.
Doctor Who: Davros, if you had created a virus in your laboratory, something contagious and infectious that killed on contact, a virus that would destroy all other forms of life, would you allow its use?
Davros: It is an interesting conjecture.
Doctor Who: Would you do it?
Davros: The only living thing, a microscopic organism reigning supreme... A fascinating idea.
Doctor Who: But would you do it?
Davros: Yes... Yes...
[raises hand as if holding the metaphorical capsule between thumb and forefingers]
Davros: To hold in my hand a capsule that contains such power, to know that life and death on such a scale was my choice... To know that the tiny pressure of my thumb, enough to break the glass, would end everything... Yes, I would do it! That power would set me up above the gods! AND THROUGH THE DALEKS, I SHALL HAVE THAT POWER!
The smallest, simplest forms of life are nevertheless far more complex than the most complex device ever constructed by people. It is a form of institutional hubris to suggest or believe that new life can be created by stitching together some DNA. The best we can manage at the present is to modify some tiny function of an existing life form in a hopefully beneficial direction. Anyone who thinks otherwise can volunteer to deal with the next influenza outbreak.
I seem to recall a "minimal genome" project that now seems as though it involved catenating a selection of genes sufficient for life. I'd have to search what came of it, but if you or anyone else could shed some light on it, I'd welcome it.
To-do List: Receive telemarketing call during a tornado warning. Check.
gcc is already taken
Spore