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Software Lets Scientists Assemble DNA

Soulskill posted about a year and a half ago | from the replicating-functionality dept.

Biotech 149

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.'"

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hear (-1)

Anonymous Coward | about a year and a half ago | (#43027011)

If you like humping your mommy
And getting caught by your dad
If you're not into poota
If you have half a tes'ticle
If you'd like humping butts at midnight
In the smooth anal gape
Then I'm the love that you've looked for
Write to me and assrape.

So -- the terrorists win in the end (1, Interesting)

Rudisaurus (675580) | about a year and a half ago | (#43027025)

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 (1, Insightful)

emagery (914122) | about a year and a half ago | (#43027067)

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 (4, Funny)

ArcadeMan (2766669) | about a year and a half ago | (#43027195)

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

Re:So -- the terrorists win in the end (2)

cheater512 (783349) | about a year and a half ago | (#43027367)

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 (1)

CanHasDIY (1672858) | about a year and a half ago | (#43027441)

What makes you think they don't already?

Re:So -- the terrorists win in the end (0)

Anonymous Coward | about a year and a half ago | (#43027595)

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.

Re:So -- the terrorists win in the end (1)

nbauman (624611) | about a year and a half ago | (#43028415)

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 [wikipedia.org] and Pakistan hasn't.

Re:So -- the terrorists win in the end (2)

Grayhand (2610049) | about a year and a half ago | (#43027197)

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 (1)

spxZA (996757) | about a year and a half ago | (#43027427)

Here's a man that managed to infect Madagascar.

Re:So -- the terrorists win in the end (2)

ceoyoyo (59147) | about a year and a half ago | (#43027249)

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 (2)

Alopex (1973486) | about a year and a half ago | (#43027459)

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 (1)

ShanghaiBill (739463) | about a year and a half ago | (#43027523)

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 (1)

Anonymous Coward | about a year and a half ago | (#43027283)

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

Re: So -- the terrorists win in the end (0)

Anonymous Coward | about a year and a half ago | (#43027377)

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.

Re: So -- the terrorists win in the end (0)

Anonymous Coward | about a year and a half ago | (#43027517)

Open your closed mind it is pretty clear he means humans

Re: So -- the terrorists win in the end (0)

Anonymous Coward | about a year and a half ago | (#43027997)

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.

Re:So -- the terrorists win in the end (1)

tibman (623933) | about a year and a half ago | (#43027465)

oh, but this will be intelligently designed : P

Re:So -- the terrorists win in the end (1)

StripedCow (776465) | about a year and a half ago | (#43027297)

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 (0)

Anonymous Coward | about a year and a half ago | (#43027783)

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.

Re:So -- the terrorists win in the end (0)

Anonymous Coward | about a year and a half ago | (#43027309)

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

Re:So -- the terrorists win in the end (5, Insightful)

micromoog (206608) | about a year and a half ago | (#43027311)

QUICK, STOP ALL SCIENCE

Re:So -- the terrorists win in the end (1)

bdwebb (985489) | about a year and a half ago | (#43028421)

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

Re:So -- the terrorists win in the end (3, Insightful)

Baloroth (2370816) | about a year and a half ago | (#43027319)

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 (2)

DragonWriter (970822) | about a year and a half ago | (#43028267)

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 (1)

Alopex (1973486) | about a year and a half ago | (#43027389)

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 (2)

fast turtle (1118037) | about a year and a half ago | (#43027401)

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 (0)

Anonymous Coward | about a year and a half ago | (#43028023)

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!

Re:So -- the terrorists win in the end (0)

Anonymous Coward | about a year and a half ago | (#43028307)

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)

Goldilocke's Zone (0)

Anonymous Coward | about a year and a half ago | (#43027419)

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.

Re:So -- the terrorists win in the end (1)

CanHasDIY (1672858) | about a year and a half ago | (#43027423)

If you knew anything about the American government's historic propensity for secretly testing dangerous chemicals and weapons [cbsnews.com] on their own populace, [knoxnews.com] 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 (2)

pesho (843750) | about a year and a half ago | (#43027455)

This was published couple of years ago by Gibson and Venter. You can even buy a kit [neb.com] 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 (4, Insightful)

ultranova (717540) | about a year and a half ago | (#43027501)

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 (1)

Anonymous Coward | about a year and a half ago | (#43027677)

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.

The tools would come anyway. (0)

Anonymous Coward | about a year and a half ago | (#43027671)

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.

Re:So -- the terrorists win in the end (1)

loufoque (1400831) | about a year and a half ago | (#43027937)

People need to be educated to use this..

Re:So -- the terrorists win in the end (1)

dkleinsc (563838) | about a year and a half ago | (#43027991)

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.

Think I've played this game already (4, Funny)

dywolf (2673597) | about a year and a half ago | (#43027033)

It was called Spore.

Re:Think I've played this game already (1)

Anonymous Coward | about a year and a half ago | (#43027127)

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

Re:Think I've played this game already (2, Funny)

Anonymous Coward | about a year and a half ago | (#43027155)

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

Re:Think I've played this game already (1)

drinkypoo (153816) | about a year and a half ago | (#43027647)

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 (2)

wanzeo (1800058) | about a year and a half ago | (#43027701)

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 [ox.ac.uk] .

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

Sounds great (3, Interesting)

emagery (914122) | about a year and a half ago | (#43027047)

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 (2)

ArcadeMan (2766669) | about a year and a half ago | (#43027183)

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

Re: Sounds great (1)

Anonymous Coward | about a year and a half ago | (#43027539)

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

Re:Sounds great (2, Informative)

geekoid (135745) | about a year and a half ago | (#43027189)

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 (0)

Anonymous Coward | about a year and a half ago | (#43027239)

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".

Re:Sounds great (0)

Anonymous Coward | about a year and a half ago | (#43027251)

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

Re:Sounds great (1)

maxwell demon (590494) | about a year and a half ago | (#43027425)

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 (1)

loufoque (1400831) | about a year and a half ago | (#43027949)

Programming language: The computer executes a sequence of commands.

That only covers the imperative paradigm.

Re:Sounds great (1)

GodfatherofSoul (174979) | about a year and a half ago | (#43027375)

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 (2)

Anne Thwacks (531696) | about a year and a half ago | (#43028161)

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

"a bacteria" (1)

Anonymous Coward | about a year and a half ago | (#43027051)

Not cool.

Re:"a bacteria" (1)

mark-t (151149) | about a year and a half ago | (#43027151)

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?"

Re:"a bacteria" (0)

Anonymous Coward | about a year and a half ago | (#43027661)

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

Undo? (4, Funny)

meta-monkey (321000) | about a year and a half ago | (#43027081)

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

Re:Undo? (1)

Rhacman (1528815) | about a year and a half ago | (#43027381)

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

Re:Undo? (1)

bobthesungeek76036 (2697689) | about a year and a half ago | (#43027629)

<quote><p>"Undo feature?" Shouldn't the command to eliminate your unwanted DNA creations be called "Abort?"</p></quote>

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

Re:Undo? (0)

Anonymous Coward | about a year and a half ago | (#43027889)

"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!

Why is bioinformatics in inverted commas? (1)

spxZA (996757) | about a year and a half ago | (#43027109)

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

Re:Why is bioinformatics in inverted commas? (1)

ceoyoyo (59147) | about a year and a half ago | (#43027267)

Because the submitter doesn't understand what it is.

Re:Why is bioinformatics in inverted commas? (0)

Anonymous Coward | about a year and a half ago | (#43027275)

Velcroman1 perhaps has a better "degree"

Misleading title (4, Informative)

subanark (937286) | about a year and a half ago | (#43027113)

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 [wikipedia.org]

Can't wait for... (1)

roc97007 (608802) | about a year and a half ago | (#43027115)

...the blue screen of giant grasshoppers.

Oh yeah, let this genie out of the bottle (1)

p51d007 (656414) | about a year and a half ago | (#43027133)

Of course...NO ONE would ever abuse that now would they LOL. Sometimes, I wish a giant meteor would just hit the planet and wipe us all out, with the stupidity of messing around with something like this. Yes, there are some great things that could be done, but, you know the idiots that want everyone living like it was 1590, would exploit this and use it as a weapon.

Smallpox, anyone? (1)

sehlat (180760) | about a year and a half ago | (#43027139)

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

any one got some dino DNA? (0)

Joe_Dragon (2206452) | about a year and a half ago | (#43027157)

any one got some dino DNA?

I need backers to fund a zoo.

Re:any one got some dino DNA? (1)

geekoid (135745) | about a year and a half ago | (#43027207)

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.

Re:any one got some dino DNA? (1)

marcosdumay (620877) | about a year and a half ago | (#43027477)

any one got some dino DNA?

Try asking some birds.

Pink (-1)

Anonymous Coward | about a year and a half ago | (#43027171)

Great, when can I order my cat-girl sex slave [wikipedia.org] ? (warning: cover art may be NSFW)

3dPrint: "Goodbye, World" (1)

ankhank (756164) | about a year and a half ago | (#43027175)

... achoo ...

Re:3dPrint: "Goodbye, World" (0)

Anonymous Coward | about a year and a half ago | (#43027893)

We can print a new one.

Next phase of career? (2)

DontLickJesus (1141027) | about a year and a half ago | (#43027221)

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".

Protein expression? (1)

h8sg8s (559966) | about a year and a half ago | (#43027235)

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? (3, Funny)

CanHasDIY (1672858) | about a year and a half ago | (#43027449)

Wonder what the output device will look like?

Genitalia.

Non-news (0)

Anonymous Coward | about a year and a half ago | (#43027271)

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.

BSGtruth (1)

Korruptionen (2647747) | about a year and a half ago | (#43027303)

Nuoh my god we're cylons.

Not the same as metal (0)

Anonymous Coward | about a year and a half ago | (#43027383)

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).

Sussman: Emacs mode to edit genome (4, Interesting)

ODBOL (197239) | about a year and a half ago | (#43027407)

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 (2)

RDW (41497) | about a year and a half ago | (#43027607)

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 [mahalito.net]

Re:Sussman: Emacs mode to edit genome (2)

ColdWetDog (752185) | about a year and a half ago | (#43027823)

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 (1)

Daniel Dvorkin (106857) | about a year and a half ago | (#43028033)

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 (1)

Bob the Super Hamste (1152367) | about a year and a half ago | (#43028337)

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?

It's an evolved programming language with variatio (1)

ODBOL (197239) | about a year and a half ago | (#43028341)

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.

epigenetics? (3, Insightful)

DdJ (10790) | about a year and a half ago | (#43027487)

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? (1)

Anonymous Coward | about a year and a half ago | (#43028095)

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? (1)

Anonymous Coward | about a year and a half ago | (#43028169)

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.

Hey GNU (0)

Anonymous Coward | about a year and a half ago | (#43027527)

How long until we see a GCC release implementing this?

Point and Click (1)

ThatsNotPudding (1045640) | about a year and a half ago | (#43027645)

Bioweapons.

Careful what you wish for.

Pet Dragons, Griffins, and REAL MERMAIDS! (0)

Anonymous Coward | about a year and a half ago | (#43027665)

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

Re:Pet Dragons, Griffins, and REAL MERMAIDS! (1)

bobthesungeek76036 (2697689) | about a year and a half ago | (#43027741)

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

Re:Pet Dragons, Griffins, and REAL MERMAIDS! (2)

dkleinsc (563838) | about a year and a half ago | (#43028029)

You don't want a real mermaid: Let Shel Silverstein [lyrics007.com] explain why.

Sims... (2)

bobthesungeek76036 (2697689) | about a year and a half ago | (#43027723)

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

Welcome... (0)

Anonymous Coward | about a year and a half ago | (#43027739)

....to Jurassic Park!

Aww.... (1)

sabt-pestnu (967671) | about a year and a half ago | (#43027747)

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

Scare Quotes Not Needed (4, Insightful)

me01chanl (553161) | about a year and a half ago | (#43027753)

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

Bioinformatics (0)

Anonymous Coward | about a year and a half ago | (#43027957)

why the fuck would you put bioinformatics in quotes?

are the dna synthesisers regulated? (1)

bityz (2011656) | about a year and a half ago | (#43028333)

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 [foxnews.com]

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.

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