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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.'"

149 comments

  1. So -- the terrorists win in the end by Rudisaurus · · Score: 1, Interesting

    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
    1. Re:So -- the terrorists win in the end by emagery · · Score: 1, Insightful

      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.

    2. Re:So -- the terrorists win in the end by ArcadeMan · · Score: 4, Funny

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

    3. Re:So -- the terrorists win in the end by Grayhand · · Score: 2

      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.

    4. Re:So -- the terrorists win in the end by ceoyoyo · · Score: 2

      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.

    5. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 1

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

    6. Re:So -- the terrorists win in the end by StripedCow · · Score: 1

      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.

      --
      If Pandora's box is destined to be opened, *I* want to be the one to open it.
    7. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      Maybe mankind will be saved by the patent trolls suing these guys out of existence?

    8. Re:So -- the terrorists win in the end by micromoog · · Score: 5, Insightful

      QUICK, STOP ALL SCIENCE

    9. Re:So -- the terrorists win in the end by Baloroth · · Score: 3, Insightful

      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
    10. Re:So -- the terrorists win in the end by cheater512 · · Score: 2

      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?

    11. Re: So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      Broad definition of "us" you have there. If you're counting everything from eukaryotes to humans, evolution has succeeded countless times in wiping things out. But yes, collectively, the entire biomass of the planet survives...for now.

    12. Re:So -- the terrorists win in the end by Alopex · · Score: 1

      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.

    13. Re:So -- the terrorists win in the end by fast+turtle · · Score: 2

      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
    14. Re:So -- the terrorists win in the end by CanHasDIY · · Score: 1

      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.

      --
      An enigma, wrapped in a riddle, shrouded in bacon and cheese
    15. Re:So -- the terrorists win in the end by spxZA · · Score: 1

      Here's a man that managed to infect Madagascar.

    16. Re:So -- the terrorists win in the end by CanHasDIY · · Score: 1

      What makes you think they don't already?

      --
      An enigma, wrapped in a riddle, shrouded in bacon and cheese
    17. Re:So -- the terrorists win in the end by pesho · · Score: 2

      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.

    18. Re:So -- the terrorists win in the end by Alopex · · Score: 2

      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.

    19. Re:So -- the terrorists win in the end by tibman · · Score: 1

      oh, but this will be intelligently designed : P

      --
      http://soylentnews.org/~tibman
    20. Re:So -- the terrorists win in the end by ultranova · · Score: 4, Insightful

      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.

      --

      Forget magic. Any technology distinguishable from divine power is insufficiently advanced.

    21. Re: So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      Open your closed mind it is pretty clear he means humans

    22. Re:So -- the terrorists win in the end by ShanghaiBill · · Score: 1

      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.

    23. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      Oh, get off your high horse. We haven't used it. The Islamic fanatics have displayed time and time again that they will do and use whatever it takes to achieve their goal.

      The US having weaponised small pox and Pakistan having it are two completely different circumstances.

    24. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 1

      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.

    25. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      This was my immediate thought, though I was going to spare males related to me, and include women over 30 in the kill to crush potential opposition.

    26. Re:So -- the terrorists win in the end by loufoque · · Score: 1

      People need to be educated to use this..

    27. Re:So -- the terrorists win in the end by dkleinsc · · Score: 1

      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.

      --
      I am officially gone from /. Long live http://www.soylentnews.com/
    28. Re: So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      Humans have been around 200000 years, not two billion. Or maybe the op meant 2 million instead of billion, if he's starting from Homo Erectus.

      My mind is open, my friend. I'm just looking for clarification.

    29. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      Read Chicken Little. I first read that back in the 70's, the scariest part of that was that people openly dismiss the possibility of the sky falling. They'll be sorry when it does!

    30. Re:So -- the terrorists win in the end by DragonWriter · · Score: 2

      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.

    31. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      Read Chicken Little. I first read that back in the 70's, the scariest part of that was that people openly dismiss the possibility of the sky falling. They'll be sorry when it does!

      Yeah, but did you know how to make it fall? Even back then?

      (captcha: bottoms)

    32. Re:So -- the terrorists win in the end by nbauman · · Score: 1

      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.

    33. Re:So -- the terrorists win in the end by bdwebb · · Score: 1

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

    34. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 1

      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.

    35. Re:So -- the terrorists win in the end by ranton · · Score: 1

      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.

      --
      -- All that is necessary for the triumph of evil is that good men do nothing. -- Edmund Burke
    36. Re:So -- the terrorists win in the end by nbauman · · Score: 1

      Sounds like somebody who wants to see his midterms cancelled.

    37. Re:So -- the terrorists win in the end by Jessified · · Score: 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)."

      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.

    38. Re:So -- the terrorists win in the end by ChrisMaple · · Score: 1

      Sure. Cool it until it freezes.

      --
      Contribute to civilization: ari.aynrand.org/donate
    39. Re:So -- the terrorists win in the end by pepty · · Score: 1

      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.

    40. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      Oh, I get it.

      Man creates virus.
      Virus destroys men.
      Women destroy man who killed their friends & family.
      Women inherit the earth.

    41. Re:So -- the terrorists win in the end by Hotawa+Hawk-eye · · Score: 1

      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.

    42. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      No, the scary part is that such a plague would be unthinkable, but the reverse would apparently not- and there are people who openly wish for such a genocide and talk about it freely (see: femitheist, radfem hub).

    43. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      High horse?

      Have you ever used a mirror?

    44. Re:So -- the terrorists win in the end by ceoyoyo · · Score: 1

      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.

    45. Re:So -- the terrorists win in the end by Genda · · Score: 1

      No, Windows 8 users...

    46. Re:So -- the terrorists win in the end by ceoyoyo · · Score: 1

      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.

    47. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      You're thinking about formulations of anthrax that can be stored dry for months and then infect lots of people all at the same time, but delivering a contagious virus doesn't have to be any more sophisticated than a pump spray bottle. Or some "cooling mist" stations. Heck, hide a mister in a truck and drive wherever there are pedestrians. Unlike anthrax powders you only need to give a few people that flu or SARS derivative; so long as the virus is highly contagious well before the symptoms become dire the rest happens on its own.

      Creating long pieces of DNA is a specialized skill, but not that specialized. Getting the DNA packaged as the first generation of your virus, then growing more of that virus, purifying out viable virus for distribution, all without killing yourself ... much trickier, but in many cases wouldn't take anything you wouldn't find in academic cell biology/virology labs.

    48. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      this i believe is the end of the human race, it just takes one really bright under achiever in a basement who is pissed off at the world for all its injustices. blamo airborn herpes.

    49. Re:So -- the terrorists win in the end by sqrt(2) · · Score: 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.

      --
      If you build it, nerds will come. Soylentnews.org
    50. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      Don't worry. There's now an undo function. ;)

    51. Re:So -- the terrorists win in the end by tr897 · · Score: 1

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

    52. Re:So -- the terrorists win in the end by Sigg3.net · · Score: 1

      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.

    53. Re:So -- the terrorists win in the end by Anonymous Coward · · Score: 0

      only SELinux users, they are the ones hiding something

  2. Think I've played this game already by dywolf · · Score: 4, Funny

    It was called Spore.

    --
    The guy who said the election was rigged won the presidency with the second-most votes.
    1. Re:Think I've played this game already by Anonymous Coward · · Score: 1

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

    2. Re:Think I've played this game already by Anonymous Coward · · Score: 2, Funny

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

    3. Re:Think I've played this game already by drinkypoo · · Score: 1

      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.

      --
      "You're right," Fisheye says. "I should have set it on 'whip' or 'chop.'"
    4. Re:Think I've played this game already by wanzeo · · Score: 2

      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.

  3. Sounds great by emagery · · Score: 3, Interesting

    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.

    1. Re:Sounds great by ArcadeMan · · Score: 2

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

    2. Re:Sounds great by geekoid · · Score: 2, Informative

      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.

      --
      The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
    3. Re:Sounds great by Anonymous Coward · · Score: 0

      Why, because you need to know C++ before using a text editor? Or running gcc?

      Somebody's got to be the first person to write "Hello World".

    4. Re:Sounds great by Anonymous Coward · · Score: 0

      I can't seem to get an analogy. Please help. Here are the pieces.

      High level programming language/low level programming language
      Compiled binaries
      010101

      Dna
      Mrna and trna--> protein

    5. Re:Sounds great by GodfatherofSoul · · Score: 1

      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.

      --
      I swear to God...I swear to God! That is NOT how you treat your human!
    6. Re:Sounds great by maxwell+demon · · Score: 1

      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.

      --
      The Tao of math: The numbers you can count are not the real numbers.
    7. Re: Sounds great by Anonymous Coward · · Score: 1

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

    8. Re:Sounds great by loufoque · · Score: 1

      Programming language: The computer executes a sequence of commands.

      That only covers the imperative paradigm.

    9. Re:Sounds great by Anne+Thwacks · · Score: 2

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

      --
      Sent from my ASR33 using ASCII
  4. "a bacteria" by Anonymous Coward · · Score: 1

    Not cool.

    1. Re:"a bacteria" by mark-t · · Score: 1

      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?"

    2. Re:"a bacteria" by Anonymous Coward · · Score: 0

      No, no, it fits. A bacteria. Some bacterium. Standard preposition ending agreement.

    3. Re:"a bacteria" by Anonymous Coward · · Score: 0

      Offtopic.

      IMO ending form agreement is a stupid linguistic mechanic. It just introduces complexity while adding little value.

      Better for endings (or any change in form) to indicate function and modifiers, with placement (and punctuation) indicating relationship.

  5. Undo? by meta-monkey · · Score: 4, Funny

    "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.
    1. Re:Undo? by Rhacman · · Score: 1

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

      --
      Account -> Discussions -> Disable Sigs
    2. Re:Undo? by bobthesungeek76036 · · Score: 1

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



      Actually I think it's called "genocide"...
      --
      Karma: Bad
    3. Re:Undo? by Anonymous Coward · · Score: 0

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

      The damn "Abort" button isn't working. I keep pressing it, but you're still here!

    4. Re:Undo? by Anonymous Coward · · Score: 0

      I can hear them now: "What do we need an 'undo' feature for? What could possibly go wrong..?"

      (captcha: humanity)

  6. Why is bioinformatics in inverted commas? by spxZA · · Score: 1

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

    1. Re:Why is bioinformatics in inverted commas? by ceoyoyo · · Score: 1

      Because the submitter doesn't understand what it is.

    2. Re:Why is bioinformatics in inverted commas? by Anonymous Coward · · Score: 0

      Velcroman1 perhaps has a better "degree"

  7. Misleading title by subanark · · Score: 4, Informative

    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

    1. Re:Misleading title by Hythlodaeus · · Score: 3, Insightful

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

      --
      For great justice.
    2. Re:Misleading title by Pseudonym · · Score: 1

      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!

      --
      sub f{($f)=@_;print"$f(q{$f});";}f(q{sub f{($f)=@_;print"$f(q{$f});";}f});
  8. Can't wait for... by roc97007 · · Score: 1

    ...the blue screen of giant grasshoppers.

    --
    Oliver's law of assumed responsibility: If you're seen fixing it, you will be blamed for breaking it.
  9. Already being sued... by RDW · · Score: 1

    ...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

  10. Smallpox, anyone? by sehlat · · Score: 1

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

  11. any one got some dino DNA? by Joe_Dragon · · Score: 0

    any one got some dino DNA?

    I need backers to fund a zoo.

    1. Re:any one got some dino DNA? by geekoid · · Score: 1

      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.

      --
      The Kruger Dunning explains most post on /. http://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect
    2. Re:any one got some dino DNA? by marcosdumay · · Score: 1

      any one got some dino DNA?

      Try asking some birds.

  12. 3dPrint: "Goodbye, World" by ankhank · · Score: 1

    ... achoo ...

  13. Next phase of career? by DontLickJesus · · Score: 2

    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
    1. Re:Next phase of career? by Anonymous Coward · · Score: 0

      Modifications in DNA either translate to modifications in proteins or in how DNA interacts with them. All the proteins in a cell are complex moving parts in a gargantuan machine, the complexity of which surpasses anything humanity has ever made by orders of magnitude. Predicting the effect of a modification can roughly be done in 2 ways:

      (1) by extrapolating from experimentally known effects of very similar modifications

      (2) by keeping supercomputers busy for months in order to get a glimpse of how the interaction of the protein/moving part with another moving part is affected by the modification, and combining these insights with experimentally known effects of similar changes in interaction. The advantage here is that "experimental results of a similar change in interaction" are much easier to come by in the scientific literature than "experimental results of a very similar modification"; it's a much looser criterion.

      The runtime environment you're talking about exists. It's named "physical reality at molecular scale". Its mechanics are more complex than the mechanics of commonly encountered machines in daily life. My day job is to simulate these processes. Our field was born in the mid-1970s, and since then, we've come to know very well on a coarse level which shortcuts, abstractions and simplifications we can introduce in our models without them diverging too far from reality. On a finer level, we're continuously pushing the boundaries. It's fascinating work, and by all means, you're welcome to join us, but don't think you'll turn the whole field upside-down with your leet skillz. Naive software developers are a dime a dozen. 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.

    2. Re:Next phase of career? by DontLickJesus · · Score: 1

      "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.

      --
      Where genius and insanity become confused true wisdom is found
  14. Protein expression? by h8sg8s · · Score: 1

    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..
    1. Re:Protein expression? by CanHasDIY · · Score: 3, Funny

      Wonder what the output device will look like?

      Genitalia.

      --
      An enigma, wrapped in a riddle, shrouded in bacon and cheese
  15. Non-news by Anonymous Coward · · Score: 0

    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.

  16. BSGtruth by Korruptionen · · Score: 1

    Nuoh my god we're cylons.

  17. Not the same as metal by Anonymous Coward · · Score: 0

    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).

  18. Sussman: Emacs mode to edit genome by ODBOL · · Score: 4, Interesting

    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.

    --
    Mike O'Donnell http://people.cs.uchicago.edu/~odonnell/
    1. Re:Sussman: Emacs mode to edit genome by RDW · · Score: 2

      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

    2. Re:Sussman: Emacs mode to edit genome by ColdWetDog · · Score: 2

      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.

      --
      Faster! Faster! Faster would be better!
    3. Re:Sussman: Emacs mode to edit genome by Daniel+Dvorkin · · Score: 1

      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."

      --
      The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
    4. Re:Sussman: Emacs mode to edit genome by Bob+the+Super+Hamste · · Score: 1

      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?

      --
      Time to offend someone
    5. Re:Sussman: Emacs mode to edit genome by brausch · · Score: 1

      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.

      --
      "Almost every wise saying has an opposite one, no less wise, to balance it." - George Santayana
    6. Re:Sussman: Emacs mode to edit genome by mdielmann · · Score: 1

      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.

      --
      Sure I'm paranoid, but am I paranoid enough?
    7. Re:Sussman: Emacs mode to edit genome by Luyseyal · · Score: 1

      Ha! Thanks for making my day.

      -l

      --
      Help cure AIDS, cancer, and more. Donate your unused computer time to worldcommunitygrid.org. Join Team Slashdot!
  19. Goldilocke's Zone by Anonymous Coward · · Score: 0

    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.

    1. Re:Goldilocke's Zone by Raenex · · Score: 1

      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.

  20. epigenetics? by DdJ · · Score: 3, Insightful

    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.

    1. Re:epigenetics? by Anonymous Coward · · Score: 1

      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.

    2. Re:epigenetics? by Anonymous Coward · · Score: 1

      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.

    3. Re:epigenetics? by kwyjibo87 · · Score: 1

      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.

  21. Hey GNU by Anonymous Coward · · Score: 0

    How long until we see a GCC release implementing this?

  22. Point and Click by ThatsNotPudding · · Score: 1

    Bioweapons.

    Careful what you wish for.

  23. Pet Dragons, Griffins, and REAL MERMAIDS! by Anonymous Coward · · Score: 0

    Just a wish list...
    Kinda like ponies, rainbows and sparkly vampires

    1. Re:Pet Dragons, Griffins, and REAL MERMAIDS! by bobthesungeek76036 · · Score: 1

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

      --
      Karma: Bad
    2. Re:Pet Dragons, Griffins, and REAL MERMAIDS! by dkleinsc · · Score: 2

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

      --
      I am officially gone from /. Long live http://www.soylentnews.com/
  24. The tools would come anyway. by Anonymous Coward · · Score: 0

    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.

  25. Sims... by bobthesungeek76036 · · Score: 2

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

    --
    Karma: Bad
  26. Welcome... by Anonymous Coward · · Score: 0

    ....to Jurassic Park!

  27. Aww.... by sabt-pestnu · · Score: 1

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

  28. Scare Quotes Not Needed by me01chanl · · Score: 4, Insightful

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

  29. Re:3dPrint: "Goodbye, World" by Anonymous Coward · · Score: 0

    We can print a new one.

  30. Bioinformatics by Anonymous Coward · · Score: 0

    why the fuck would you put bioinformatics in quotes?

  31. are the dna synthesisers regulated? by bityz · · Score: 1
    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.

    1. Re:are the dna synthesisers regulated? by Anonymous Coward · · Score: 0

      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.

      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.

      I have designed multiple high throughput DNA synthesizers, some of the output being sold as unlabeled oligos being sold to the molecular biology market. Trust me, the ethical purveyors or DNA sequences screen the incoming sequence requests against references databases holding known, dangerous viral gene data.

  32. It's an evolved programming language with variatio by ODBOL · · Score: 1

    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.

    --
    Mike O'Donnell http://people.cs.uchicago.edu/~odonnell/
  33. not so ubiquitous by pepty · · Score: 3, Informative
    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.

    1. Re:not so ubiquitous by Genda · · Score: 1

      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!

  34. I have this horrible vision... by dlingman · · Score: 2

    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?"

  35. Dodo by ChrisMaple · · Score: 1

    Carrier pigeon. Carolina Parakeet. Mastodon. Elephant bird.

    --
    Contribute to civilization: ari.aynrand.org/donate
  36. drugs by Anonymous Coward · · Score: 0

    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!

  37. Just a new skin for existing technology by Anonymous Coward · · Score: 0

    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.

  38. How does this work with Circular RNA? by WillAffleckUW · · Score: 2

    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! --
  39. No money to be made. by Dcnjoe60 · · Score: 1

    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.

  40. There's more to the problem than duplicating genes by dtjohnson · · Score: 1

    '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.

  41. Vindaloo Monster by deek · · Score: 2

      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?!

  42. Bioinformatics does not need single quotes by damn_registrars · · Score: 1

    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.
  43. Entirely Overstated Article by DeathByLlama · · Score: 0

    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.

  44. WHY was this moderated up? by damn_registrars · · Score: 1

    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.
  45. Re:So -- the Davros wins in the end by Anonymous Coward · · Score: 0

    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!

  46. Re:There's more to the problem than duplicating ge by whovian · · Score: 1

    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.
  47. Genome Compiler Corp will never fly by Anonymous Coward · · Score: 0

    gcc is already taken

  48. EA got to this already... by The_Star_Child · · Score: 1

    Spore