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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.'"
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.
"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.
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
So what you mean is that we should be monitoring Linux users?
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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.
It may be inevitable. The more accessible the tools the higher the odds of it happening. Then again toxic gases are incredibly easy to make and yet few even attempt it. Terrorists tend not to be the sharpest tools in the shed. If a super virus is engineered the odds are it will be fairly selective about who it can infect. It could wipe out most of the general population but pockets would likely survive. Once most carriers are dead the virus should be wiped out. It's what happened to smallpox except we made the carriers immune so it was left without hosts. Bird flues and swine flues are scary because common animals can carry them. Mutating an avian flu would probably be the scariest scenario but if it's equally lethal to birds then the same limiting factors would come into play. The odds of us being rendered extinct are small but the odds of a significant percentage of the population dying are quite high.
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
Probably longer than it will take them to build an atomic bomb from scratch.
Making an a-bomb isn't much of a technical challenge. It's only got a few thousand pieces and specs for those pieces are pretty easy to come by. You can actually buy the majority of them premade. Once you've got the thing, it's pretty reliable. No worries about dispersion patterns, vaccines, resistant populations.
Now, putting together a killer virus from scratch, that's hard. Nobody's ever done it before.
Yeah, I can see where that could be useful:
QUICK, STOP ALL SCIENCE
It takes a special kind of terrorist to deploy a bioweapon, because bioweapons don't distinguish based on religion (although you could theoretically make one that distinguishes on race, it's a bit tricky). That means it'll hit everyone indiscriminately, and not even most terrorists want that. The only ones who would use something like that are people who want to destroy everyone, and finding a large enough group of people (as you would need to create and deploy such a weapon) willing to do that is quite difficult.
Also even the most lethal bioweapons won't kill everyone, whether thanks to natural immunity or proper quarantine procedures, a lot of people will survive. Anything nasty enough to actually kill everyone will almost certainly burn out very rapidly.
"None can love freedom heartily, but good men; the rest love not freedom, but license." --John Milton
The plan to get the NSA using our code is proceeding well.
Initiate phase 2: Open source all their data.
Oh wait did I say that out loud?
Read Frank Herbert's book "White Plague" that was written back in the early 70's. The scariest part of the tale is that even back then, I knew enough to engineer such a virus and had enough access to the stuff needed for it.
Mod me up/Mod me down: I wont frown as I've no crown
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/
Wonder what the output device will look like?
Genitalia.
An enigma, wrapped in a riddle, shrouded in bacon and cheese
This was published couple of years ago by Gibson and Venter. You can even buy a kit from New England Biolobas (very fine company I must say). What the software does is to save you little effort in writing the perl/python scripts for automating the design. I wouldn't call this a big hurdle for the would be terrorists.
Except that in the case of the atomic bomb, the materials for the bomb itself are scarce and require refinement. The materials for a weaponized virus or pathogen are ubiquitous, require no sophisticated means of delivery, and will evade all types of detection currently used to screen against threats.
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.
Probably forever, because:
On the other hand, idiots who think other people are cartoon supervillains and appeal to that caricature to argue against new tools are certainly capable of killing millions by hindering the War on Disease. You and everyone who modded you up ought to be ashamed of yourselves. You're just as bad as the anti-vaccine people, except you don't even have misfiring parental instincts as an excuse.
Forget magic. Any technology distinguishable from divine power is insufficiently advanced.
Integrate this software with the Sims game and you will have a winner!!!
Karma: Bad
It's no more appropriate to say "bioinformatics" than it is to say "algebra" - they're well defined fields.
You don't want a real mermaid: Let Shel Silverstein explain why.
I am officially gone from
Race is a social construct that has only a loose connection to biology, so it would only be even theoretically possible to have a bioweapon that distinguishes by genetic (or other biological) characteristics that loosely correspond to race, rather than race itself.
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?"
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! --
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?!
What happens when the "lab" is a consumer device the size of a desktop printer?
We'll just ban them? What happens when consumer grade 3D printers are capable of building the parts necessary to make the desktop microbiology lab? We'll just ban them too? I don't want to live in a world where a technology as liberating, powerful, and cheaply available as such a 3D printer exists, but its use is forbidden. That prohibition would eventually have to be enforced through draconian means; house to house searches for machine tools and computer hardware, etc. So to save ourselves from horrific annihilation through a man-made virus we impose on ourselves horrific man-made slavery and oppression.
I also don't want to live in a world where any human with a few thousand/hundred dollars can purchase a device capable of killing millions. Throughout human history the arms race between defense and offense has been fairly neck and neck. It's gotten a lot more lopsided in recent history, since the invention of the gun. If I wanted to kill you, really, really wanted to kill you and didn't care about the consequences to myself after the fact, you're dead. It's just that simple. I can buy a gun, maybe I'll have to wait a few days and pass a background check (and I would pass, clean record) and I'd find you and kill you. I'd probably be arrested, incarcerated/executed, but you'll still be dead. Even a bullet proof vest won't make much of a difference. I could buy a 60 year old Soviet-made carbine that'll defeat any vest commonly used today. Or I'll just get close enough to shoot you in the head.
There's no defensive technology available today, on the personal level or on the national level, capable of defeating a determined opponent who is not rational (this does not mean unintelligent), and does not care about the consequences of their actions, including their own survival.
And guns are toys compared to what is already possible today, though not cheaply possible. What happens when the expensive super-weapons of our time are as cheap as the "toy" weapons we have now? Could humanity survive if everyone can walk around with a nuclear bomb or a deadly virus?
I think I see the problem, actually. Humans just suck at living together when the power to destroy is cheap and ubiquitous. Eventually an individual will be born with a genetic mutation that makes them irrational but with the amoral guile of a sociopath. They'll acquire the latest weapon of their time, and they'll use it; just because they can. It only takes one of such a person if the technology is available to everyone. I have a deep and terrifying fear that this is the reason the universe appears so empty of intelligent life. I'm hoping we just haven't looked hard enough, and that the ashes and fossils of millions of dead races don't liter the cosmos, entombed on long-barren hellscapes once lush as Earth.
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