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Writing Genetic Code

ScuttleMonkey posted more than 8 years ago | from the working-with-soylent-green dept.

Biotech 190

An anonymous reader writes "The Globe and Mail is reporting on another group of researchers delving into the field of 'synthetic biology.' The project stemming from the efforts of two biology labs in British Columbia and Maryland is attempting to create the first synthetic life form. From the article: 'The project is being spearheaded by U.S. scientist Craig Venter, who gained fame in his former job as head of Celera Genomics, which completed a privately-owned map of the human genome in 2000. Dr. Venter, 59, has since shifted his focus from determining the chemical sequences that encode life to trying to design and build it: "We're going from reading to writing the genetic code," he said in an interview.'" This is certainly not the first group to venture into this territory.

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190 comments

I for one... (4, Funny)

jpellino (202698) | more than 8 years ago | (#14338202)

... welcome our new two-codon overlords.

Synthetic Creatures (0)

loupgaroux (60976) | more than 8 years ago | (#14338206)

First creature!
Coded to get first Post!
*Muahahahahahahahaha!!!!*

Re:Synthetic Creatures (1)

cartel (845256) | more than 8 years ago | (#14338224)

...looks like there's a bug in the code.

Python vs Perl vs Ruby vs.. (5, Funny)

Anonymous Coward | more than 8 years ago | (#14338210)

There you go, no more bitching about which is the best coding language, now you can code in the most natural one.

Re:Python vs Perl vs Ruby vs.. (2, Funny)

aurb (674003) | more than 8 years ago | (#14338629)

Yes, but how many lines of genetic code would it take to do this:

print "Hello world!"

Compiler? (5, Funny)

r00t (33219) | more than 8 years ago | (#14338211)

I hope there is a gcc backend for this. I hate using Visual Studio to write my code.

Re:Compiler? (1, Redundant)

TubeSteak (669689) | more than 8 years ago | (#14338266)

Sorry, no gcc backend.
DNA comes in fours.

Maybe you can have a GCCC backend, to go with the rest of your DNA.

Re:Compiler? (0)

Anonymous Coward | more than 8 years ago | (#14338291)

I'd far prefer a GCTA front end. You know... one that uses all the amino acids.

Re:Compiler? (1)

Iron (III) Chloride (922186) | more than 8 years ago | (#14338554)

True, DNA comes in fours nucleotides, but codons are read in nucleotide triplets by RNA transcriptase, so it'll still be a GCC backend.

Re:Compiler? (-1, Offtopic)

Tablizer (95088) | more than 8 years ago | (#14338333)

Being a Microsoft Person(TM) is a pain. Right in the middle of a shit your ass locks up and turns blue. You have to ask the Janitor to reboot you, and then it takes another half hour to perform that system check scan. All that waiting on the crapper really makes for a sore ass. Goatse is rumored to be a Microsoft Person(TM).

And then all the viruses and spyware. One MS-Person told his boss to buy some Rogain and Viagra. Needless to say, he got fired.

Re:Compiler? (1)

Kafka_Canada (106443) | more than 8 years ago | (#14338451)

Also, don't forget to use mount -w with your biont.

Problems? (4, Insightful)

Renraku (518261) | more than 8 years ago | (#14338214)

Just wait until someone writes a piece of code that cures a genetic disease, but must be 'fed' with a certain medication. If not fed with said medication, it will do something real bad.

Re:Problems? (2, Insightful)

segment (695309) | more than 8 years ago | (#14338290)

This just reminded me of Genetic warfare amongst other things...

THE HAZARDS OF HUMAN DEVELOPMENTAL GENE MODIFICATION

...Attempts at developmental gene modification will certainly be subject to experimental error, but this is not the only source of potentially unfavorable consequences. Certain genes undergo a process of "imprinting" during development, in which the version of the gene inherited from the father or the mother is blocked from contributing to the individual's biological constitution. This phenomenon is part of a wider group of processes known as "allelic interaction" or "paramutation," in which the expression of one version, or "allele," of a gene is influenced by another allele. These phenomena are poorly understood, but it is clear that they are essential to healthy development. Failure of a certain gene to be correctly imprinted, for example, leads to Beckwith-Wiedemann syndrome, which is characterized by organ overgrowth and several different childhood cancers. Simply inserting a desired gene into the embryo in place of an undesired one does not ensure that allelic interaction will proceed appropriately, and experience with farm animal embryo manipulation suggests that it is readily disrupted and results in malformations.

Read the full document here [gene-watch.org] ...

It's rather scary to allow certain things from happening at least in my opinion. I'm all for stem cell research, just about anything to better man, but I don't see how attempting to create life from scratch is something worthwhile. Especially with all of the cons associated with it. What would happen on a worst case (Resident Evil) scenario. Its possible no one would be able to handle certain situations. Why bother putting us there. How does creating a "species" help us again?

With all of the balances and checks in this world (food chain on down), something like this has the capability of going completely wrong

Re:Problems? (0)

Anonymous Coward | more than 8 years ago | (#14338442)

As there are ways to test software before releasing it, so there should be ways to test the genetic code before releasing an organism.

Re:Problems? (1)

nurhussein (864532) | more than 8 years ago | (#14338406)

If not fed with said medication, it will do something real bad.
Yeah, it turns into the Fleshreaper [penny-arcade.com] . BTW, great business model for ambitious genetics companies that want to be the Microsoft of the biotech world.

Re:Problems? (1)

Velox_SwiftFox (57902) | more than 8 years ago | (#14338478)

Hey, whose fault is it if you don't read the EULA?

Re:Problems? (0)

Anonymous Coward | more than 8 years ago | (#14338423)

DNA codes are "open", sequencing such synthetic sequences is no more difficult than sequencing natural DNA. The reason it took so long to sequence human genome is because the genome is so damn big.

Even protein sequencing is possible, although more time consuming than DNA sequencing.

So unless such "feature" is an essential part of the function of the gene, it is unlikely to go unnoticed and unfixed.

Unless, of couse, they start using synthetic polymers, rather than the naturally occuring amino acids and nucleic acids.

In Soviet Russia.. (1, Funny)

Combas (776699) | more than 8 years ago | (#14338215)

...biology programs you!

Re:In Soviet Russia.. (1)

Carnage Pants (801975) | more than 8 years ago | (#14338331)

so... Soviet Russia=the natural world?

Unlikely, but exciting if they pull it off (4, Interesting)

yog (19073) | more than 8 years ago | (#14338216)

Bacteria are already used to synthesize organic materials by reprogramming their DNA. For example, some antivirals and antibiotics are manufactured this way; the desired pattern is injected into the bacteria's genome and it will then produce that pattern. Venter's project is really just an extension of that approach.

I have doubts as to the likelihood of success using present science; in twenty years, perhaps it will be possible, but today it's really casting about in the dark. Even something as elemental as a bacteria is an incredibly complex thing, with a sophisticated genome and complex organelles working in biochemical harmony to reproduce, to "mate" by conjoining with other bacteria, and to adapt and thrive in a very wide variety of conditions.

Bacteria have been around for billions of years and, as Stephen Jay Gould put it, we are living in the Age of Bacteria [stephenjaygould.org] . In a few short years it seems unlikely that even brilliant scientists can recreate these things. Modify some, yes, but completely create from scratch something that is going to be viable--well, that's going to be interesting to see.

That said, if they can pull it off the possibilities of its use, for good or evil, are endless. They can be encoded to synthesize all sorts of compounds, eat nasty pollutants, generate fossil fuels, attack disease microbes, or be diseases themselves. Luckily, the human body has a pretty comprehensive immune system that will adapt to just about anything except retroviruses like AIDS that reprogram the immune system itself.

Re:Unlikely, but exciting if they pull it off (1, Informative)

Anonymous Coward | more than 8 years ago | (#14338245)

I'm pretty sure that most bacteria reproduce Asexually. Therefore they do not mate. Also, I'm not sure that someone with a last name of 'Go[a]uld' has our best interests in mind!

Re:Unlikely, but exciting if they pull it off (2, Insightful)

Anonymous Coward | more than 8 years ago | (#14338345)

Bacteria don't have organelles; you're thinking of protists.

Another commenter mentioned that bacteria can't "mate". It was in quotes because its not really mating like we'd think of it; basically, some bacteria, when nearing death by starvation, will attach to another bacteria and inject its RNA or DNA strand into the other bacteria, producing an "offspring" that is a fusion of the two "parents" with the injector being the "male" and injectee the "female".

I'm not even a bio major, I'm an engineering major. They teach this stuff in Bio 1.

Re:Unlikely, but exciting if they pull it off (1)

Nyph2 (916653) | more than 8 years ago | (#14338489)

It's not really casting about in the dark, we've got plenty of organisms around to examine and reverse engineer. Sure, it took millions of years thru evolution, but that's not at all the approach they'll be taking. While they dont want to pull the basic stuff we've been doing with genetic splicing, I'm sure there will be sections of DNA from other organsims they use, and sections that are similar but different in some key way or another than existing organsims. The shortcuts we take often seem to get results much faster and cause side effects we didnt forsee. This compared to evolution is sort of a brute force method, but one which weeds out very detrimental side effects(or the side effects weed out other organsims), so the unforseen side effects on the scale of synthesized(sp?) items isnt there.

actually easy to pull off, but would you want to (0)

Anonymous Coward | more than 8 years ago | (#14338505)

using genetic algorithms you dont have to know how something works in order to get it to do something.

but considering the recent history of the human race, i think all "development" in this area should stop until the human animal can advance morally and ethically more than it is currently.

what you are talking about is far more deadly than any atomic weapon could ever be.

Genetic Engineering < Synthetic Biology (1, Insightful)

Anonymous Coward | more than 8 years ago | (#14338558)

Bacteria are already used to synthesize organic materials by reprogramming their DNA. For example, some antivirals and antibiotics are manufactured this way; the desired pattern is injected into the bacteria's genome and it will then produce that pattern. Venter's project is really just an extension of that approach.

That's the genetic engineering approach. Find a gene and splicing it into bacteria. That's like finding a chasm and splicing in the Empire State building to bridge it. It might work, but designing a bridge to span the chasm will probably work better. That's synthetic biology.

I have doubts as to the likelihood of success using present science; in twenty years, perhaps it will be possible, but today it's really casting about in the dark. Even something as elemental as a bacteria is an incredibly complex thing, with a sophisticated genome and complex organelles working in biochemical harmony to reproduce, to "mate" by conjoining with other bacteria, and to adapt and thrive in a very wide variety of conditions.

I'd be more inclined to think that cost is the restricting factor today. It costs a ton of money to have a gene sequence assembled, but the price to do so is dropping exponentially if what I read on the subject back in January was true.

'Generic' Code (1, Offtopic)

Alamei (781359) | more than 8 years ago | (#14338220)

I think I've had too much exposure to .NET recently. Did anyone else read that headline as "Writing Generic Code"?

Here comes the pain (4, Funny)

redthefed (713416) | more than 8 years ago | (#14338221)

I've seen WAY too many sci-fi movies to consider this a good scientific endeavor. If you need me, I'll be in my concrete bunker. :)

Re:Here comes the pain (0)

Anonymous Coward | more than 8 years ago | (#14338250)

Mmmmm, cat-girls

Writing Code, huh?? (0)

Anonymous Coward | more than 8 years ago | (#14338222)

from reading to writing code

Can't wait for what the Haxors come up with!

In Soviet Russia... (5, Funny)

Ruff_ilb (769396) | more than 8 years ago | (#14338228)

Genetics code YOU!

Oh wait... they do...

Carry on.

Re:In Soviet Russia... (-1, Flamebait)

Anonymous Coward | more than 8 years ago | (#14338516)

ENOUGH WITH THE GOD DAMN SOVIET RUSSIA JOKES ALREADY.
Jesus Christ people, why are these getting modded up to +5 all the time?
They aren't funny and they sure as hell don't contribute to the discussion.

Re:In Soviet Russia... (1, Funny)

Anonymous Coward | more than 8 years ago | (#14338564)

In Korea, only old people have genetic codes.

Recolada (3, Insightful)

Eli Gottlieb (917758) | more than 8 years ago | (#14338229)

Good to hear somebody is working on something important.

If God didn't mean us to create life he would smite these people straight out, so we can kill that objection, BTW.

The interesting part is going to be how they actually turn their new genome into a living bacteria. They're basically going to have to either assemble the first one from whole cloth or trick some other microbe into producing what they want.

And even if we can make these things perform useful functions, how to make sure they don't die out from lack of an evolutionary niche or mutate and become pathological?

Re:Recolada (2, Interesting)

Ruff_ilb (769396) | more than 8 years ago | (#14338244)

And even if we can make these things perform useful functions, how to make sure they don't die out from lack of an evolutionary niche or mutate and become pathological?
Simple.
If we know their genome, presumably we can kill them off pretty darn quickly.
In this case, design flaws ARE a feature.
Can't wait until Microsoft gets into this field. Those BSOD's must be nasty.

Re:Recolada (1)

B5Fan (639395) | more than 8 years ago | (#14338384)

If we know their genome, presumably we can kill them off pretty darn quickly.
In this case, design flaws ARE a feature.
Can't wait until Microsoft gets into this field. Those BSOD's must be nasty.

My first thought was: "Don't let Microsoft at it, whatever you produce will get a virus!".

I wonder if there's any organisation at all that would be able to create a design that could be trusted to be okay to release outside a lab.

Any organism that you create and release (outside controlled conditions) and that survives will probably mutate. That may make it be hard to kill off unless you've very carefully designed in a way to kill it that will still be there after it mutates. So you'd better be really sure you got it right the first time. You'll be releasing a version which has self-modifying code. It won't install a patch/update/service pack.

Re:Recolada (1)

Ruff_ilb (769396) | more than 8 years ago | (#14338537)

If you provide say, even TEN fail-safes that can mutate, what are the chances that ALL TEN will mutate and allow the organism to survive? What about 100 fail-safes?

Very, VERY small, I'd bet.

Re:Recolada (1)

cskrat (921721) | more than 8 years ago | (#14338283)

likely they'll design something that will take a very basic protein or nutrient and convert it into energy and proteins that it can use in it's own structure and then self replicate. It can then be tested in a solution of it's ideal diet in an otherwise sterile environment where it won't need to compete with bacteria that have the advantage of 3-4 billion years of evolution.

Once a basic structure is laid out, we can then start modifying it to serve specific purposes or we can try to piss it off by gradually changing it's environment and observing how it evolves to handle the new conditions.

But it will be quite a while before we artificially produce a single cell critter that can compete with native bacteria.

Re:Recolada (2, Insightful)

karmatic (776420) | more than 8 years ago | (#14338325)

> If God didn't mean us to create life he would smite these people straight out, so we can kill that objection, BTW.

If god didn't mean for people to lie, commit adultery, and murderer, he'd just smite them too, right?

That being said, genetics is a tool. Like any tool, it can be used for good purposes, or bad purposes (ok, almost any tool - it's kind of hard to abuse a Nerf bat - I know, I've tried).

Re:Recolada (0)

Anonymous Coward | more than 8 years ago | (#14338480)

it's kind of hard to abuse a Nerf bat - I know, I've tried

Did you try every orifice?

Re:Recolada (0)

Anonymous Coward | more than 8 years ago | (#14338591)

I said I'll ride with you if you can get me to the border
The sheriff's after me for what I did to his daughter
I did it like this, I did it like that, I did it with a...

...a whiffleball bat but I guess a Nerf bat could work too

A bit spongy perhaps?

Re:Recolada (1)

dourk (60585) | more than 8 years ago | (#14338506)

> If god didn't mean for people to lie, commit adultery, and murderer,
> he'd just smite them too, right?

Glad I don't believe in god.

Correct. (1)

Belial6 (794905) | more than 8 years ago | (#14338646)

"If god didn't mean for people to lie, commit adultery, and murderer, he'd just smite them too, right?"

Correct.

Re:Recolada (1)

zee-mich (933191) | more than 8 years ago | (#14338497)

If God didn't mean us to create life he would smite these people straight out, so we can kill that objection, BTW.
Along with any human with reproductive genes. :)

Re:Recolada (1)

ichigo 2.0 (900288) | more than 8 years ago | (#14338508)

or mutate and become pathological?

I don't think the chances for that are any larger than for natural bacteria. And if one of these mutated, then why would it necessarily be any deadlier than most of the deadly bacteria/viruses out there? I guess it would be pretty weird if it mutated into a pathogen that turns people into drugs or clean energy.

This research makes it a easier to make even more effective bioweapons though, and some governments will always be willing to build them. Even scarier is the thought of what will happen when it becomes feasible for private persons to afford to create their own species. But by the time that is possible, nanotech has hopefully developed to the level where everyone has a silicon based programmable immune system.

Whats the ethics of such a project (0)

Anonymous Coward | more than 8 years ago | (#14338231)

I bet there are a lot of naysaying protestors gearing up to disrupt this.

Re:Whats the ethics of such a project (1)

Ingolfke (515826) | more than 8 years ago | (#14338431)

I bet there are a lot of ignorant investors gearing up to pour money into this.

relevent quote (0)

Anonymous Coward | more than 8 years ago | (#14338237)

"It is the business of the future to be dangerous; and it is among the merits of science that it equips the future for its duties."
- Alfred North Whitehead

Re:relevent quote (0)

Anonymous Coward | more than 8 years ago | (#14338420)

"Science is for dumb motherfuckers who couldn't get laid in high school or college and yet the practicioners of this field are some of the most arrogant sons of bitches on the planet." - Lord Byron

Re:relevent quote (1)

Boronx (228853) | more than 8 years ago | (#14338681)

When asked why he was no longer so involved with Academic Philosphy, Bertrand Russell responded: "I discovered fucking."

relevant quote from einstein (0)

Anonymous Coward | more than 8 years ago | (#14338530)

"if i had known what my invention would be used for, i would have become a shoemaker"

Here's what we need... (2, Funny)

johansalk (818687) | more than 8 years ago | (#14338241)

Forget 'curing disease', that's not the future of the species, what we need are perfect blondes and supermodels.

Re:Here's what we need... (1)

Zantetsuken (935350) | more than 8 years ago | (#14338341)

I'm not sure if you're just joking, or if you genuinly can't comprehend that the technology being discussed in the post IS BEING DEVELOPED TO CURE DISEASE!

Re:Here's what we need... (0)

Anonymous Coward | more than 8 years ago | (#14338653)

But what happens when those "perfect" blondes and supermodels contract sexually transmitted diseases?

Is it Open Source? (5, Funny)

$0.02 (618911) | more than 8 years ago | (#14338242)

Seriously, are we going to have both propriatory as well as free genetic code organisms? What's the legal status of a living being that's a result/offspring of a crossing/mating between a propriatory and a GPL organism?

Re:Is it Open Source? (1)

castoridae (453809) | more than 8 years ago | (#14338461)

Well these "programs" are likely to reproduce by themselves, given that they are bacteria... what is the ownership of a (computer) virus? It reproduces itself - and if you're not careful, you might be running an unlicensed copy of that virus. Does that mean that you owe the virus writer a license fee?

It's late & I'm feeling pretty incoherent - does my analogy even make any sense? :-)

Re:Is it Open Source? (1)

zcat_NZ (267672) | more than 8 years ago | (#14338636)

ask monsanto [percyschmeiser.com] ?

genetic code? (3, Funny)

radicalnerd (930674) | more than 8 years ago | (#14338252)

how the @#$! are you going to debug it?

Re:genetic code? (1, Funny)

Anonymous Coward | more than 8 years ago | (#14338277)

With bug spray and/or a flyswatter.

Re:genetic code? (0)

Anonymous Coward | more than 8 years ago | (#14338464)

your post was probably meant to be humorous or flippant, but "debugging" artificial genes are in fact frequently performed in labs.

Recombinant proteins are not always designed properly, the most frequent problem is that too much hydrophobic surface is exposed which leads to insoluble protein. When expressed in E.Coli this forms an inclusion body, big insoluble pellet in the cells which is basically a big clump of insoluble proteins, other times the product can be toxic to the host cells.

So when such problems occur, researchers often have to redesign the constructs to remove or reduce such problems.

Re:genetic code? (1)

castoridae (453809) | more than 8 years ago | (#14338472)

Eventually, with software simulation tools. As soon as we either come up with hardware/algorithms that can perform protein folding and in-silico simulation in a reasonable amount of time, or understand protein functions better to the point that we can use algorithmic "tricks" to simulate it with present-day processing power.

Re:genetic code? (1)

oedneil (871555) | more than 8 years ago | (#14338602)

If there are holes, we can just replace them with frog DNA.

Mwahahahahah! (3, Funny)

Anonymous Coward | more than 8 years ago | (#14338267)

Remember all those stuffed suits who said that the GPL was viral? Just wait for their reaction when we prove them right!

"I'm sorry sir, but from now on your name ought to be GNU/Mr. Jones..."

Is it really that synthetic? (1, Insightful)

qw0ntum (831414) | more than 8 years ago | (#14338268)

I think the chicken/egg problem they talk about is a pretty interesting point.

The DNA is only a small portion of the cell. If they want to make a whole synthetic organism, they're going to have to make the other organelles and various membranes--a task I would imagine would be just as difficult as building the DNA.

Sure, this is a big deal. But I don't think you can call an organism synthetic if all you are doing is injecting synthetic DNA into a pre-existing organism.

Re:Is it really that synthetic? (3, Interesting)

castoridae (453809) | more than 8 years ago | (#14338482)

But I don't think you can call an organism synthetic if all you are doing is injecting synthetic DNA into a pre-existing organism.

Can you call a piece of (traditional computer) software your own (i.e. synthetic) if it mostly runs API functions provided by the (pre-existing) OS or a third-party library?

Re:Is it really that synthetic? (1)

zcat_NZ (267672) | more than 8 years ago | (#14338625)

More like how most compilers (eg GCC) are developed;

    First you write the compiler in it's own language, then you compile it using someone else's already-working compiler. With luck you'll then have a working compiler which can compile a fresh copy of itself.

Only a total masochist would try and hand-build the code themselves.

Answer: boot loader (1)

Impeesa (763920) | more than 8 years ago | (#14338490)

How long until someone comes up with the genetic equivalent of a bootstrap program? Some sequence of DNA that can be tacked on to the end of whatever their current project is, a sequence that will take raw biological material (amino acids? proteins? This is where I say "disclaimer: I am not a biologist") and construct a simple cell capable of then reading the actual organism DNA and replicating it.

One has to draw the line somewhere (2, Insightful)

ichigo 2.0 (900288) | more than 8 years ago | (#14338524)

In order to make an apple pie from scratch, you must first create the universe. - Carl Sagan

OMG (0)

Anonymous Coward | more than 8 years ago | (#14338296)

The bible thumpers are gonna freak when they hear about this.

Re:OMFSM (4, Funny)

AndroidCat (229562) | more than 8 years ago | (#14338606)

They're going to double freak when it's discovered that human genetics are made up of spagetti code!

ScuttleMonkey (0)

Anonymous Coward | more than 8 years ago | (#14338300)

There is a large, soft rectangular object upstairs calling you to it. Go to bed dude! I'm sure you made the record.

Re: ScuttleMonkey (1)

Tablizer (95088) | more than 8 years ago | (#14338358)

There is a large, soft rectangular object upstairs calling you to it.

Damn Jupiter monoliths go soft if you don't recharge them.
         

To mangle Ray Bradbury (1)

Tablizer (95088) | more than 8 years ago | (#14338303)

We *are* the I.D. now
     

Re:To mangle Ray Bradbury (1)

Busy (890287) | more than 8 years ago | (#14338491)

I know it's a joke, but if I had points I'd give you an insightful.

Personally, I'm of the opinion that writing code (I'm usually thinking computer code, but genetics works too) is about as close to playing god as mankind has come. I'm sure there's arguements against this, but for my world view, it fits.

OK, I'm done with my cheesy deep thought for the night.

Extremely interesting.... (5, Informative)

CupBeEmpty (720791) | more than 8 years ago | (#14338309)

This is something that is really, truly interesting. I am curious as to what they will consider a "human crafted" organism. I work in a virology lab and in the field there are often "frankenstein" viruses that are created to preform certain tasks. I know many people do not consider viruses to be living, but you are getting pretty darn close. Also, the viruses that are created (actually quite often) are usually combinations of parts of DNA sequence from a variety of viruses. Literally just last week I created an engineered virus that will insert the DNA that codes the protein USP18 [nih.gov] into human cell cultures (huh-7.5 cells... modified human hepatoma 7 cells). The goal is actually to support or detract from the conclusion of the linked paper. The virus in question is basically a highly modified form of HIV. It has certain elements that are exactly the same as HIV but there are large portions (the parts that make it really pathogenic) that are removed and other things are added (promoters and insertions sites to allow the USP18 -or whatever- to be inserted).

The long and short of it is. These "life forms" are significantly different from their naturally occuring cousins. They are this way by nature of human engineering. This argument can also be extended to bacteria that have been highly modified. There are laboratory strains of almost every bacteria that we know of that are significantly different from wild type bacteria. I am curious as to where they will draw the line. From the article is appears that they are paring down mycoplasma to the barest bones.

The other question is, once you have the DNA how do you kickstart the process. They appear to be inserting it into and E. coli with the nucleus removed. This means that the cellular machinery of the E. coli will be used to translate the DNA into protein and eventually a new synthetic cell. Does this mean that it is human created if we use naturally occuring cellular machinery?

I don't mean to detract from the research in any way because it is highly interesting and will tell us a lot about how life works on the most basic level, BUT there are a lot of questions out there and I hope that people keep them in mind as we see this field develop over the next several years.

Re:Extremely interesting.... (2, Insightful)

rale, the (659351) | more than 8 years ago | (#14338398)

The other question is, once you have the DNA how do you kickstart the process. They appear to be inserting it into and E. coli with the nucleus removed. This means that the cellular machinery of the E. coli will be used to translate the DNA into protein and eventually a new synthetic cell. Does this mean that it is human created if we use naturally occuring cellular machinery?


The way I see it, the existing bacteria is just a DNA-compiler.

If I write a C-compiler in C, I need to use an existing C-compiler to build it. The old compiler, like the bacteria, is just a tool used in the process - no one would claim I didn't really write my compiler just because I had to bootstrap it off an existing one.

On the other hand, if I just took gcc and modified it extensively, I couldn't claim that I created it myself.

Re:Extremely interesting.... (1)

castoridae (453809) | more than 8 years ago | (#14338439)

The way I see it, the existing bacteria is just a DNA-compiler.

Specifically, I think the ribosome corresponds nicely to the compiler - it translates the RNA into the final protein product by performing mappings of codons (DNA/RNA triplets) into the amino acids that make up the proteins. I'd think of the bacteria as a whole more as the operating environment - different systems states, etc.

Now what would be interesting is to re-engineer the ribosome to compile DNA/RNA differently. Check out this [harmantechnologies.com] blog entry on the subject.

Re:Extremely interesting.... (1)

CupBeEmpty (720791) | more than 8 years ago | (#14338549)

This is an interesting analogy but in this case it is not necessarily that useful. The problem is that if a completely original and synthetic organism is made on a DNA level it means nothing unless it can be "compiled" into a new organism. The problem arises because raw DNA even with exact translation means nothing. There is an entire process of post translational modification that occurs to proteins. One single DNA sequence can produce more than one protein based on the activity of the rest of cellular machinery. There is also an ENORMOUS amount of regulation that occurs before RNA is even made into protein. This regulation is completely dependent on the native cellular machinery.

The point I am making is this: The output of the DNA genome is protein, BUT the output of one sequence of DNA can be wildly different depending on the cellular machinery. The same DNA sequence in humans can produce different proteins in bacteria (in some but not all cases). So if you are truly "synthesizing life" but are still dependent on existing cellular machinery (in this case E. coli) are you really synthesizing life? It is more something to think about than a truly practical consideration.

Re:Extremely interesting.... (1)

CupBeEmpty (720791) | more than 8 years ago | (#14338519)

Right so the real question (in the terms of this metaphor) is how did that compiler get coded without a compiler? The chicken/egg problem is that if DNA codes the machinery that allows DNA to code any machinery then how did that process actually occur naturally. It is one thing to use existing machinery to create modified proteins using synthesized DNA (this occurs constantly in biology) but it is another to "create life." This is one of the important questions in this field. These scientists will almost certainly be sucessful in coopting E. coli cellular machinery to create a "synthetic" organism but it is hardly completely original in an evolutionary sense. This is not to be taken as an attack on the science because this will no doubt yield good results if successful, but is it truly "synthesizing life?"

Re:Extremely interesting.... (1)

Dirtside (91468) | more than 8 years ago | (#14338635)

But someone had to write the first compiler, by hand, in machine code. The biological analogy is constructing the cellular machinery atom by atom until you've got something that can process DNA code.

I can see it now (2, Funny)

Tablizer (95088) | more than 8 years ago | (#14338343)

"Frankenstien XML on Rails 101 for Dummies, with MySql."

Re:I can see it now (2, Funny)

Mr. Vandemar (797798) | more than 8 years ago | (#14338416)

Elementary Frankenstein design with PHP and MySQL: Arms everywhere, all with a different number of incompatible joints that, if improperly attached, are vulnerable to injections which cause them to attack the body they're attached to. Oh, and it can sprint like the wind, but sometimes pieces fall off, and are replaced by slightly different pieces, but you can't tell until the arm gets caught in the meat grinder where the creature works since it's become too long.

Okay, I think I confused myself with that one...

In Soviet Russia.... (0)

Anonymous Coward | more than 8 years ago | (#14338396)

In Soviet Russia, there's code in your bugs.

Re:In Soviet Russia.... (1)

Busy (890287) | more than 8 years ago | (#14338503)

Not bad, but I think it would have been funnier without the Soviet Russia angle ;)

Typo (2, Funny)

zephc (225327) | more than 8 years ago | (#14338404)

You misspelled "Dr. Venture"

"Why is it every time I need to get somewhere, we get waylaid by jackassery?"

Building with DNA (4, Insightful)

castoridae (453809) | more than 8 years ago | (#14338413)

I think one of the biggest challenges isn't in synthesizing strings of DNA, per se - it's in knowing what DNA to synthesize. The real holy grail of synthetic biology is to engineer genetic functions to accomplish a particular goal - design to spec. From the average /. POV, this means "programming" genes in some high-level language (C++ DNA lib, anyone?). Take a look at The Registry of Standard Biological Parts [mit.edu] for a first library of genetic "functions".

As I understand it, the current state-of-the-art in terms of programming DNA is basic logic gates that still tend to lose coherence when connected together. Once this is accomplished (best guess, 3-4 years from now to work out the basic science), all of the sophisticated tools and techniques developed by the IT community over the last decade(s) can be rapidly applied, and that goal of design/build to spec will become possible.

Re:Building with DNA (1)

user32.ExitWindowsEx (250475) | more than 8 years ago | (#14338433)

so within a decade we could see a DNA backend for GCC? or (*shudders*) one for Visual C++?

Re:Building with DNA (1)

castoridae (453809) | more than 8 years ago | (#14338494)

Yes, that's the idea. I think the challenge is finding an engineer with both the CS and the bio background to take advantage. This is an area that really interests me, and as I'm researching it I find that I have trouble really understanding the context and even the problems in biology that need to be solved at anything more than a layman's bird's-eye view.

Hopefully as these tools evolve, they'll do so in a way that helps to abstract the gory details of cellular biology in much the way that high-level programming languages abstract away the bits & registers inside your CPU.

Re:Building with DNA (1)

Hartree (191324) | more than 8 years ago | (#14338551)

I think the challenge is finding an engineer with both the CS and the bio background to take advantage

Aubrey DeGrey?

I know he's controversial, but that's exactly his background.

I'm sure he'd be enthusiastic.

I doubt (1)

Jotii (932365) | more than 8 years ago | (#14338428)

I doubt the DNA language is layout free: Back to the BASIC syntax.

Why bother? (1)

SHP (8391) | more than 8 years ago | (#14338449)

All the wonderful forms of life we now see arose without the input of a designer, so why would we try to one up nature now? Let's just go about randomly mutating DNA, and let natural selection take its course.

Re:Why bother? (1)

castoridae (453809) | more than 8 years ago | (#14338572)

If you've got another 4 billion years to wait around for your "product"...

Maybe... (2, Interesting)

rodm13 (870050) | more than 8 years ago | (#14338453)

God intends us to make lifeforms of our own. Just finished reading an interesting piece on a person's "Talk with God", here's a link. [Ragged Trousered Philosopher]

Just noticed that the site's bandwidth is out, here's the Internet Archive's Cache:

http://web.archive.org/web/20050312133142/http://w ww.fullmoon.nu/articles/art.php?id=tal [archive.org]

Even if it is fiction, it's an interesting idea nonetheless.

hehe (0, Insightful)

Anonymous Coward | more than 8 years ago | (#14338470)

hehe, bring on the catgirls! :)

OMG (1)

NixLuver (693391) | more than 8 years ago | (#14338475)

Oh, my god; they're treading on the holy ground of the Almighty, and he will smite them with Furious Vengeance. The Lord knows that we know not what we do, but sometimes we gotta pay anyway. Look for disasters of biblical proportions to follow this research.

If God had meant us to write the code of life, he'd have given us scanning electron microscopic eyes and nanomanipulator fingers, dammit!

Run away now, you righteous before God!

Soon... (1)

SnarfQuest (469614) | more than 8 years ago | (#14338499)

Soon we will be hiding in old malls, with infected humans running around saying "Brains...."

(Someone had to say it)

anyone else sense disaster? (3, Interesting)

SuperBanana (662181) | more than 8 years ago | (#14338515)

We're going from reading to writing the genetic code," he said in an interview.

We have a very bad track record when it comes to "our world" and "technology we invent".

Far as I'm concerned, "God" doesn't enter into it. I don't think we've developed nearly enough of an understanding about our world or microbiology...to even think about this. Our planet is a pretty complex machine, and we're stuck with it for the moment (and to all the escapists, no, I don't want to hear about your colonization ideas. Let's feed, clothe, and shelter our fellow humans before we send the most elite off to establish a "perfect" world...otherwise Earth becomes the home of the poor and disadvantaged.)

Call me crazy, but this sounds even worse than the whole nanomachine "grey goo" problem. "Grey goo" scenarios mostly revolved around incompetence (ie, we know how to design a perfect nanobot but someone skips "step number 54", or keys in an extra zero.) Here, we've got not only incompetence but also "we're not really sure how this all works." Oh, and to top it all off? The little buggers could just spontaneously mutate all on their own, because biology isn't a perfect machine. Lovely!

Just wait (1)

Fengpost (907072) | more than 8 years ago | (#14338528)

Just wait until some code engineered monster goes nuts and start killing people and we have to send in an unit of elite fighting unit to take them out.....

Wait, I am confusing my game play with reality.

Dear God... (1)

sd_diamond (839492) | more than 8 years ago | (#14338687)

Please, nobody tell Michael Crichton.

SF Antecedent (1)

CaptainCarrot (84625) | more than 8 years ago | (#14338698)

Years ago Omni published a story by Alfred Bester called "Galatea Galante". The title character was genetically engineered from scratch, and her designer coded her genome using a language with a regular syntax similar to computer languages. Bester shows us a few lines of it before remarking in his narrative voice that it would be really, really boring to show any more of it. It might be of interest in this context if anyone could dig it up though.
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