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.'"

Comments

So -- the terrorists win in the end

[Rudisaurus]

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.

Re:So -- the terrorists win in the end

[emagery]

Heh; while we hold on to weaponized smallpox stockpiles ... yeah; totally an islamic thing, eh? Any sufficiently disenfrachised, abused, and under-represented individual or group will have similar motivations.

Re:So -- the terrorists win in the end

[ArcadeMan]

So what you mean is that we should be monitoring Linux users?

Re:So -- the terrorists win in the end

[Grayhand]

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.

Re:So -- the terrorists win in the end

[ceoyoyo]

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.

Re:So -- the terrorists win in the end

[Anonymous Coward]

Evolution has been trying to bump us off for 2 billion years and failed.

Re:So -- the terrorists win in the end

[StripedCow]

Nah, this technology will first be used by a slashdotter. The virus will be targeted at males that don't match his specific DNA profile. When the virus is done, he will be the only man midst of three billion women! At last!! Muhahahaha.

Re:So -- the terrorists win in the end

[micromoog]

QUICK, STOP ALL SCIENCE

Re:So -- the terrorists win in the end

[Baloroth]

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.

Re:So -- the terrorists win in the end

[cheater512]

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?

Re:So -- the terrorists win in the end

[Alopex]

You have to remember that -all- of cell biology and biochemistry is rapidly advancing, not just synthetic biology. Even though we are rapidly approaching the point at which anyone can develop a flu-like weapon with relatively basic tools, we are also rapidly developing the knowledge base and tools that will enable us to neutralize threats at will.

Re:So -- the terrorists win in the end

[fast turtle]

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.

Re:So -- the terrorists win in the end

[CanHasDIY]

If you knew anything about the American government's historic propensity for secretly testing dangerous chemicals and weapons on their own populace, I wager you'd spend less time worrying about what imaginary brown boogeymen might do with the technology, and far more time concerning yourself with what the government will do with it.

Re:So -- the terrorists win in the end

[spxZA]

Here's a man that managed to infect Madagascar.

Re:So -- the terrorists win in the end

[CanHasDIY]

What makes you think they don't already?

Re:So -- the terrorists win in the end

[pesho]

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.

Re:So -- the terrorists win in the end

[Alopex]

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.

Re:So -- the terrorists win in the end

[tibman]

oh, but this will be intelligently designed : P

Re:So -- the terrorists win in the end

[ultranova]

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?

Probably forever, because:

1. Wiping out humanity is the one thing anyone - including the extremists - ought to understand is guaranteed to royally piss off any creator god that might be behind human existence (or any being even remotely interested in humanity, for that matter).
2. Politically motivated terrorism doesn't exactly have many scenarios where actually ending the world would get you what you want either.
3. It's pretty hard to imagine that fundamentalists could outsmart biologists who, after all, also have access to this tool to make a cure.

Nice work, Omri; you've just handed them the tools.

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.

Re:So -- the terrorists win in the end

[ShanghaiBill]

Making an a-bomb isn't much of a technical challenge.

The hard part is getting the uranium and/or plutonium. Once they have that, everyone who has ever attempted to build an a-bomb has succeeded on the first try.

Now, putting together a killer virus from scratch, that's hard. Nobody's ever done it before.

It will be hard the first time. After that, you can just follow the recipe.

Re:So -- the terrorists win in the end

[Anonymous Coward]

LOL: cartoons! The irony probably wasn't intentional but it's appreciated nonetheless. Your faith in the abilities of extremists to self-limit and of biologists to cope with outbreaks in a timely fashion does indicate a certain sunny optimism to your personality that, sadly, is not universal. Do keep posting, however; it's nothing if not entertaining.

Re:So -- the terrorists win in the end

[loufoque]

People need to be educated to use this..

Re:So -- the terrorists win in the end

[dkleinsc]

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?

Al Qaida and their friends do not want the entire world to die, they want the entire world to live under Muslim religious law. A global epidemic doesn't help them reach their goals, because that would kill off good Muslims as much as anyone else.

In other words, they're fanatics, and not generally suicidal. They think more like Vo Nguyen Giap than like Dr Evil.

Re:So -- the terrorists win in the end

[DragonWriter]

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).

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.

Re:So -- the terrorists win in the end

[nbauman]

The most obvious difference in circumstances is that we've let terrorists use our biological weapons to kill people http://en.wikipedia.org/wiki/2001_anthrax_attacks and Pakistan hasn't.

Re:So -- the terrorists win in the end

[bdwebb]

Please mod parent up. I wish I had mod points.

Re:So -- the terrorists win in the end

[Anonymous Coward]

You're perpetuating the myth that terrorists are all a bunch of fundamentalist yokels. In fact if you look at the membership of real terrorist groups you'll find many of their members have a Western university education and come from a wealthy background. It's not at all hard to imagine that they could indeed get the resources to construct a biological weapon.

While you admit you may not understand the motives for wiping out much of the human population, the motive doesn't have to make sense to you. The point is that there are people out there who would have no qualms with that. All part of the reason why the government does take the concept of bioterrorism seriously.

Idiots who think that scientific advances represent an unending march toward progress without analyzing the potential negative consequences ought to be ashamed of themselves.

Re:So -- the terrorists win in the end

[ranton]

It's pretty hard to imagine that fundamentalists could outsmart biologists who, after all, also have access to this tool to make a cure.

It is usually incredibly easier to destroy than it is to create. Creating a virus that does just enough to kill people is probably much easier than finding a cure. Just like it is easier to smash up a car than it is to fix a totalled car.

It may be different in this specific case, but I doubt it.

Re:So -- the terrorists win in the end

[nbauman]

Sounds like somebody who wants to see his midterms cancelled.

Re:So -- the terrorists win in the end

[Jessified]

"Wiping out humanity is the one thing anyone - including the extremists - ought to understand is guaranteed to royally piss off any creator god that might be behind human existence (or any being even remotely interested in humanity, for that matter)."

That is unless, of course, the "creator" likes all of its creations equally, in which case it would be thrilled to see humanity wiped from the face of the planet.

Re:So -- the terrorists win in the end

[ChrisMaple]

Sure. Cool it until it freezes.

Re:So -- the terrorists win in the end

[pepty]

It's pretty hard to imagine that fundamentalists could outsmart biologists who, after all, also have access to this tool to make a cure.

It's always easier to break stuff than it is to fix it. There are plenty of viruses and bacteria out there that we can't touch despite years of trying. I don't see much chance of rapidly taking out a novel pathogen except with RNA-interference or antisense treatments, and those have had a checkered history so far.

Re:So -- the terrorists win in the end

[Hotawa Hawk-eye]

It's pretty hard to imagine that fundamentalists could outsmart biologists who, after all, also have access to this tool to make a cure.

It is usually incredibly easier to destroy than it is to create. Creating a virus that does just enough to kill people is probably much easier than finding a cure. Just like it is easier to smash up a car than it is to fix a totalled car.

It may be different in this specific case, but I doubt it.

True, but the number of people interested in curing the virus will be much larger than the number of people interested in creating it. Even if governments have to implement isolation protocols that keep people in shelters while the virusCure@Home community works on a cure, some small group of humanity will survive.

Re:So -- the terrorists win in the end

[ceoyoyo]

Just dig them up. It's not technically difficult. Yes, it's a lot of work, and if someone notices what you're doing they might come and stop you, but it's not technically challenging.

If you DID manage to build yourself the blueprints for a killer virus with this software you still have to send it to a lab to get it made for you. Then someone is very likely to come and stop you. Same end result, but a whole lot more technical hurdles.

Re:So -- the terrorists win in the end

[Genda]

No, Windows 8 users...

Re:So -- the terrorists win in the end

[ceoyoyo]

Uh, no. The materials to make a weaponized virus are scarce, tightly controlled, and concentrated in only a few places. You weren't thinking you hook up a virus printer to your computer, were you? This software is kind of a drag and drop RAD application to make a blueprint for an organism which you then e-mail to a lab that actually does the work.

It's pretty widely agreed that a nice atomic bomb would be pretty trivial to deliver to most places you'd want to, with very few orries about detection. A shipping container is not a sophisticated means of delivery. A biological agent, on the other hand, DOES require sophisticated delivery. The literature on delivery methods for biological agents is extensive. It's not easy. To get any sort of worthwhile effect you don't just drop a beaker on the sidewalk.

Re:So -- the terrorists win in the end

[sqrt(2)]

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.

Re:So -- the terrorists win in the end

[tr897]

Very well put. I wish I had mod points...

Re:So -- the terrorists win in the end

[Sigg3.net]

You seem to indicate that Islamic fundamentalists are historically and socioeconomically detached from the world and evil to the tune of evil for evil's sake?

You know the Bible and the Qu'uran are more or less the same, but that followers of the first just happened to colonize the latter first with great financial gain which we still reap the benefits of? While they pay?

Don't get me wrong, extremists are insane. But they were not born extreme, so explain the interlude before going all judgmental.

Think I've played this game already

[dywolf]

It was called Spore.

Re:Think I've played this game already

[Anonymous Coward]

Seems like an upgrade to it :)
It could make me replay at least ;)

Re:Think I've played this game already

[Anonymous Coward]

I think you're confusing Spore with that vaporware game that once held the same name.

Re:Think I've played this game already

[drinkypoo]

I think you're confusing Spore with that vaporware game that once held the same name.

Vehement Agreemsg. If Spore were this good, or even say two-thirds as good as they made me think it would be, I'd still be playing it.

Re:Think I've played this game already

[wanzeo]

A cool game with more potential than was realized.

On a more serious note, you can build genomes in any molecular editor. Try the open source Coot.

Or, use your favorite text editor (GATACGGTACAT....). This commercial gimmick software is not newsworthy, even here.

Sounds great

[emagery]

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.

Re:Sounds great

[ArcadeMan]

Distribute that kind of power, you say? Let's make a beowolf cluster of DNA! We'll call it.... Earth.

Re:Sounds great

[geekoid]

DNA is a programming language after all...

no it isn't. I'm not sure if you are ignorant in genetic, programming, or just stupid.

Re:Sounds great

[GodfatherofSoul]

I see your analogy. We understand the syntax of DNA, but we don't completely understand the semantics of the tokens. So, we're haphazardly slapping together tokens to form grammatically correct sentences with limited comprehension of their meanings. This is like the opposite of a new language speaker who puts the correct words together with improper syntax. We're like new programmers who are giddy thinking they're done because the code compiled.

Re:Sounds great

[maxwell demon]

Programming language: The computer executes a sequence of commands.

DNA: The cell translates genes into proteines which then either get part of the structure of the cell, or perform a specific, continuous function until they are destroyed.

Maybe an FPGA would be a better analogy to DNA, because there again the code isn't executed but determines the elements which perform the requested function.

Re: Sounds great

[Anonymous Coward]

I'm building a prototype in a sock that I keep underneath my bed.

Re:Sounds great

[loufoque]

Programming language: The computer executes a sequence of commands.

That only covers the imperative paradigm.

Re:Sounds great

[Anne Thwacks]

How do you write "My Hovercraft is full of eels" in DNA? and can you compile it from C++?

"a bacteria"

[Anonymous Coward]

Not cool.

Re:"a bacteria"

[mark-t]

Yeah, I kind of mentally tripped over that expression myself. My first thought was "what? bacteria is a singular form noun now? when did that happen?"

Undo?

[meta-monkey]

"Undo feature?" Shouldn't the command to eliminate your unwanted DNA creations be called "Abort?"

Re:Undo?

[Rhacman]

It's not a choice, it's a chimera!

Re:Undo?

[bobthesungeek76036]

"Undo feature?" Shouldn't the command to eliminate your unwanted DNA creations be called "Abort?"

Actually I think it's called "genocide"...

Why is bioinformatics in inverted commas?

[spxZA]

I have a degree in it. (More specifically B.Sc in Computer Science specializing in Bioinformatics)

Re:Why is bioinformatics in inverted commas?

[ceoyoyo]

Because the submitter doesn't understand what it is.

Misleading title

[subanark]

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

Re:Misleading title

[Hythlodaeus]

The whole post reads like a bio version of "And then I cloud-sourced an internet to my giga-drive!"

Re:Misleading title

[Pseudonym]

I know! When I read that you can assemble DNA on a desktop computer, my first thought was: Hell, the assembler I wrote did that years ago, and I didn't get a Slashdot writeup!

Can't wait for...

[roc97007]

...the blue screen of giant grasshoppers.

Already being sued...

[RDW]

...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

Smallpox, anyone?

[sehlat]

I seem to recall that the complete genome was published a few years ago. I'll be in my sealed bunker.

3dPrint: "Goodbye, World"

[ankhank]

... achoo ...

Re:any one got some dino DNA?

[geekoid]

You don't need dino DNA. You just need to figure out what it was and you can make your own.

That's the cool bit.

Next phase of career?

[DontLickJesus]

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".

Re:Next phase of career?

[DontLickJesus]

"Very few acquire sufficient mastership of the physics to make a dent. And even if you do, you'll be in a rat race against other geniuses. New discoveries spur new ideas, but discoveries are published worldwide and ideas are also a dime a dozen as well. Even if you have the gift to derive a really good and worthwhile idea from a given recent discovery, you can be sure that at least two of your competitors around the world will have thought of it, and then it comes down to who is fastest and who can deliver the most generally useful implementation or variant of the idea." Sounds exactly like programming actually :-). Seriously, though, thank you for your insight.

Protein expression?

[h8sg8s]

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?

Re:Protein expression?

[CanHasDIY]

Wonder what the output device will look like?

Genitalia.

Undo feature?

[Hartree]

Yeah, I can see where that could be useful:

BSGtruth

[Korruptionen]

Nuoh my god we're cylons.

Sussman: Emacs mode to edit genome

[ODBOL]

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:

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.

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.

Re:Sussman: Emacs mode to edit genome

[RDW]

Inevitably there is a DNA editing mode for Emacs, though unfortunately there don't seem to be any 'insert tail' commands available:

http://www.mahalito.net/~harley/elisp/dna-mode.el

Re:Sussman: Emacs mode to edit genome

[ColdWetDog]

The problem here is the coding libraries. The 'tail' library exists but if you think documentation is bad now, just wait until you hit biological organisms: While we might know what language the library uses, we don't understand the versioning system, we don't understand the dependencies, we don't know which compiler was used and there are over a billion years of garbled, deprecated code to deal with.

If you think that bozo who had your job before you was bad at spaghetti code, just you wait until you see what His Noodliness has in store for you.

Re:Sussman: Emacs mode to edit genome

[Daniel Dvorkin]

The problem is that the genetic code alone isn't a programming language. It looks deceptively like a programming language, and that fact has deceived a generation of computer scientists into thinking biology is easy to understand and hack. But it's really better thought of as a collection of heuristics. Edit your genome to get a prehensile tail, and you might get that, or you might get a blob of useless flesh hanging off your ass (and the latter outcome is a lot more likely).

Now, it may be that once we understand all the regulatory mechanisms that turn a couple of DNA strands into a complete organism, it will turn out that the whole thing is nicely deterministic and we can reprogram at will. But at this point, talking about adding new anatomical features is like talking about writing an operating system right after you've learned "Hello world."

Re:Sussman: Emacs mode to edit genome

[Bob the Super Hamste]

or you might get a blob of useless flesh hanging off your ass (and the latter outcome is a lot more likely).

So how is that different than most people I see with the grocery cart full of diet food and diet pop?

Re:Sussman: Emacs mode to edit genome

[brausch]

In 1986, Pacfic Northwest (National) Laboratory won an R&D 100 award for:

"Computer Aided Genetic Engineering/Genetic Engineering Machine (CAGE/GEM)—;Richard J. Douthart, James J. Thomas

CAGE/GEM is a software toolkit that can help researchers design genetic structures before performing expensive laboratory experiments. By using the system, scientists can analyze sequences from both a broad and specific viewpoint with integration of expert knowledge. They can isolate a genetic element in DNA sequence, then graphically manipulate the element to create and explore new genetic constructs."

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC339405/figure/F1/ shows some screen shots.

It was written on Dec MicroVAX computers and was a complete GUI environment back when those were still rare. It could do all of the design and analysis work but there wasn't any technology to actually create the resulting physical constructs. It merely provided guidance to the laboratory folks doing gene sequencing and early genetic manipulation experiments. DOE installed the software at quite a few universities as part of some research projects.

Re:Sussman: Emacs mode to edit genome

[mdielmann]

If you think that bozo who had your job before you was bad at spaghetti code, just you wait until you see what His Noodliness has in store for you.

I think code written up on little twisted strings of material pretty much by definition has to be spaghetti code.

Re:Sussman: Emacs mode to edit genome

[Luyseyal]

Ha! Thanks for making my day.

-l

Re:any one got some dino DNA?

[marcosdumay]

any one got some dino DNA?

Try asking some birds.

epigenetics?

[DdJ]

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.

Re:epigenetics?

[Anonymous Coward]

Sort of.

Using it to build all enzymatic pathways needed to produce and excrete oil from large tanks of bugs.

Managing bottles necks is a nightmare, it's far harder than getting the synthesis correct, the whole system needs regulation.

Methylation is part of it, controlling localized pH via modifications is too.

Re:epigenetics?

[Anonymous Coward]

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).

Excellent point. I have recently read some papers that imply methylated cytosine can significantly change the meaning of the expressed gene. I am hopeful that this is one more step along the way. As with most complex software it will probably take a few years. But this sure seems like an exciting step in the right direction: synthetic biology as opposed to just trying to measure and draw statistical conclusions about genetics.

Re:epigenetics?

[kwyjibo87]

As far as I know, bacteria don't use epigenetics in the same way we would associate with eukaryotes. First off, bacteria don't have histones and are thus limited to DNA methylation in terms of types of epigenetic modifications they can employ (bacteria do have DNA-binding proteins that help package DNA, but I don't believe anyone has shown they are used to control gene expression in a heritable manner -- the definition of epigenetics). In terms of how bacteria use DNA methylation, there are two cases I am aware of: (1) distinguishing between newly synthesized and "template" DNA just after DNA replication to help fix errors (if the DNA repair machinary detects a mis-matching base-pair, it corrects based on the template, methylated strand; and (2) to distinguish between self and non-self DNA, particularly in anti-phage (viral) defense, so that enzymes that have evolved to destroy foreign DNA can avoid destroying the bacterial DNA.

In general, epigenetic markers are controlled by protein interactions, which can of course be very complex, including kinetic competitions between proteins that write the markers, and proteins that erase the markers. To build a genetic pathway that regulates epigenetic markers beyond simple sequence recognition (such as GAmTC methylation in E. coli that regulates the origin of DNA replication) is probably beyond the capability of current synthetic biology.

Point and Click

[ThatsNotPudding]

Bioweapons.

Careful what you wish for.

Sims...

[bobthesungeek76036]

Integrate this software with the Sims game and you will have a winner!!!

Re:Pet Dragons, Griffins, and REAL MERMAIDS!

[bobthesungeek76036]

Don't forget Sokoblovsky's miniature giraffes...

Aww....

[sabt-pestnu]

I thought they were talking about a 3D printer app...

Scare Quotes Not Needed

[me01chanl]

It's no more appropriate to say "bioinformatics" than it is to say "algebra" - they're well defined fields.

Re:Pet Dragons, Griffins, and REAL MERMAIDS!

[dkleinsc]

You don't want a real mermaid: Let Shel Silverstein explain why.

are the dna synthesisers regulated?

[bityz]

from the article:

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.

It's an evolved programming language with variatio

[ODBOL]

The problem is that the genetic code alone isn't a programming language.

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.

deceived a generation of computer scientists into thinking biology is easy to understand and hack

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.

not so ubiquitous

[pepty]

The article breezily mentions creating a genome from scratch, but it's not really that easy. Say you wanted to use the services mentioned in the article to create smallpox, a 186 kb (kilobase) virus, from scratch. Genome compiler software would be a way to design the project on a computer, but that's about it. The services mentioned in the article will certainly synthesize oligonucleotides into genes (100 to 10000 base pairs) and put those genes or operons into vectors and ship them to you, but building a whole virus would be a long involved project and would get special attention. Even having them just make parts of smallpox genes would probably throw up red flags in the software; it would be pretty trivial for checks like that to be automatic. But say you get your genes or operons in the mail. You would then need to assemble all of those bits into one genome. That involves a lot of intermediary steps of cutting and pasting, replicating (first by a PCR machine, then in host organisms when the pieces get too big for PCR), purifying, and then cutting and pasting again. Fairly standard molecular biology, but harder with such long pieces of DNA. Then it's off to the biosafety level 5 lab to package the DNA into chickenpox viral capsids or find some other way to get your viral genome into human cells intact. Then you'll need to culture the virus in (presumably) human cells, yet another skill set.

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.

Re:not so ubiquitous

[Genda]

Exactly, you would be much more likely to see bad men creating biotoxins like botulina toxin keyed to a specific persons genome. The Perfect assassination tool. Go after entire families. The stuff of science fiction!

I have this horrible vision...

[dlingman]

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?"

Dodo

[ChrisMaple]

Carrier pigeon. Carolina Parakeet. Mastodon. Elephant bird.

How does this work with Circular RNA?

[WillAffleckUW]

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.

No money to be made.

[Dcnjoe60]

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.

There's more to the problem than duplicating genes

[dtjohnson]

'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.

Vindaloo Monster

[deek]

  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?!

Bioinformatics does not need single quotes

[damn_registrars]

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.

WHY was this moderated up?

[damn_registrars]

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".

Re:There's more to the problem than duplicating ge

[whovian]

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.

EA got to this already...

[The_Star_Child]

Spore

Re:Goldilocke's Zone

[Raenex]

Basically I'm not scared. I can always live underground for a few years while the unprepared/weak succumb.

Assuming you didn't get infected before the threat was known. The nastiest virus would lay dormant for a year or so.