Writing Genetic Code

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.

Comments

I for one...

[jpellino]

... welcome our new two-codon overlords.

Synthetic Creatures

[loupgaroux]

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

Re:Synthetic Creatures

[cartel]

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

Python vs Perl vs Ruby vs..

[Anonymous Coward]

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..

[aurb]

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

print "Hello world!"

Re:Python vs Perl vs Ruby vs..

[boaworm]

I think you missed a ";" in the end =)

And of course you have to think a bit deeper, DNA is "binary" so you have to compare it to machine code instead. You cannot simply compare base pairs with a "print" syntax.

When coding genetically, you have the four bases A, C, T and G, so it's not really binary either.

Re:Python vs Perl vs Ruby vs..

[aurb]

So, it would be something like this then?

push G
xor G, G
mov A, 09h
mov C, msg
mov T, C
int 21h
pop G
ret

msg db "Hello, world!", 10, 13, 36

PS. that previous code was in Python -- ';' is not needed.

Re:Python vs Perl vs Ruby vs..

[Anonymous Coward]

Perl uses the semi-colon as a statement seperator, not a statement
terminator. So the final semi-colon in a scope is not enforced:

{
        print "Hello "
}

print "World\n"

Is perfectly valid Perl!

Python allows newlines to terminate statements, so the
semi-colon is not required either.

Re:Python vs Perl vs Ruby vs..

[TapeCutter]

"...now you can code in the most natural one."

Someone told me non-nerds have been doing that for a while, phfff, what would they know.

Re:Python vs Perl vs Ruby vs..

[killerkalamari]

Unfortunately Microsoft messed up MS-DOS and that code no longer works (except under emulation, even in XP). But thanks... I still have fond memories of writing TSR's on our old XT. And MS-DOS runs great under qemu :)

Re:Python vs Perl vs Ruby vs..

[Decaff]

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

print "Hello world!"

Assuming you are a human poster... about 3 billion

Compiler?

[r00t]

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

Re:Compiler?

[TubeSteak]

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?

[Anonymous Coward]

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

Re:Compiler?

[Kafka_Canada]

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

Re:Compiler?

[Iron (III) Chloride]

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?

[CarpetShark]

Actually, it's implemented on .NET, and it's patented, along with the rest of the Earth's genomes.

Re:Compiler?

[anubi]

GCC? It codes for Alanine.

Re:Compiler?

[TubeSteak]

nevermind, that's what i get for trying to be witty amongst slashnerds.

A good joke is funnier if it's true, but God help you if you make shit up and the details are off.

Problems?

[Renraku]

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?

[segment]

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...

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?

[nurhussein]

If not fed with said medication, it will do something real bad.

Yeah, it turns into the Fleshreaper. BTW, great business model for ambitious genetics companies that want to be the Microsoft of the biotech world.

Re:Problems?

[Anonymous Coward]

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.

Re:Problems?

[Anonymous Coward]

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?

[Velox_SwiftFox]

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

Re:Problems?

[DigitalReality]

How does creating a "species" help us again?

Their goal with that is probably to create "lifeless" shells to produce organs and stem-cells with. Or at least something to that effect. But I agree. What happens when we create some super-bacteria by accident, and we have no way of stopping it?

Re:Problems?

[TapeCutter]

"Its possible no one would be able to handle certain situations."

I am not advocating bio-weapons but the Universe itself is a situation no one can handle (eg: Bird Flu, Aids).

"How does creating a "species" help us again?"

A species that inhales CO2, exhales H2 and tastes like steak when cooked on a standard BBQ would be handy. Existing benefits can be seen in just about every domesticated species of plant, animal or fungus. Eg: The modern dairy cow, maybe not an entirely new species but they certainly give way more milk than when humans first trained them to stand still. I imagine milking a wild cow could be described as a situation no one (at the time) knew how to handle.

Re:Problems?

[ceoyoyo]

Fantastic. I'm going to steal a little bit of it and reverse engineer it so it doesn't need the medication any more. THEN I'll inject it. What, you want a copy too? Hm... well, I suppose I could upload it to Basetorrent.

In Soviet Russia..

[Combas]

...biology programs you!

Re:In Soviet Russia..

[Carnage Pants]

so... Soviet Russia=the natural world?

Unlikely, but exciting if they pull it off

[yog]

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. 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

[Anonymous Coward]

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

[Anonymous Coward]

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

[Nyph2]

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.

Re:Unlikely, but exciting if they pull it off

[SpaceballsTheUserNam]

"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."

Eventually AIDS, if for some reason we Never find a cure, will probably just run its course. Humans would adapt or AIDS would evolve to be non-lethal, like in chimps. Or it will at least level off.

Re:Unlikely, but exciting if they pull it off

[alicenextdoor]

Well, they teach it wrong, then. Bacterial 'sex' involves the transfer of extrachromosomal loops of DNA called plasmids, via a sex pillus also coded by a plasmid. Plasmids can carry, amongst other things, a casette of genes for antibiotic resistance, which is one of the reasons why resistance can spread so rapidly. It has little or nothing to do with near death experiences, and no 'offspring' is created; it's just a transfer of genes.

Re:Unlikely, but exciting if they pull it off

[adolfojp]

The only way to have the technology to be able to do this in twenty years is to start making the technology today ;-)

Re:Unlikely, but exciting if they pull it off

[Salis]

Well, they know the sequence of many different bacterium. What happens if they were to synthesize the entire DNA chromosome for one of those bacteria and inject it into an plasma membrane whose DNA was removed? Would you call that synthetically creating a bacteria or just synthetically creating all of the programming of the bacteria?

Now, what happens if you decide to change parts of the DNA chromosome by inserting your own genes or entire pathways that perform interesting and useful functions? If you do the same procedure you will have created something which does not exist in nature (that we of know of). So once the procedure is practiced it can be used to generate entirely novel bacterium.

I think that's where the excitement comes from. Our ability to create arbitrary DNA sequences will make it a lot easier to engineer bacteria.

And this isn't BS....there are numerous DNA synthesis companies who will sell by the base pair (around $1/bp). Typical bacterial chromosomes are ~1 million bp and I believe a few of the synthesis companies have actually produced contiguous strands of DNA of that length or greater. So it's happening and it's real! (But still too expensive for my budget!)

'Generic' Code

[Alamei]

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

[redthefed]

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

[Anonymous Coward]

Mmmmm, cat-girls

Re:Here comes the pain

[Cyno01]

With any luck they'll be creating a concrete eating microbe. Sucker.

Writing Code, huh??

[Anonymous Coward]

from reading to writing code

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

In Soviet Russia...

[Ruff_ilb]

Genetics code YOU!

Oh wait... they do...

Carry on.

Re:In Soviet Russia...

[Anonymous Coward]

In Korea, only old people have genetic codes.

Re:In Soviet Russia...

[DigitalReality]

I thought it was pretty funny.

Re:In Soviet Russia...

[gkhan1]

I agree, it was a reinvention of the Soviet Russia jokes.

Recolada

[Eli Gottlieb]

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

[Ruff_ilb]

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

[cskrat]

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

[karmatic]

> 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

[B5Fan]

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

[Anonymous Coward]

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

Did you try every orifice?

Re:Recolada

[zee-mich]

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

[dourk]

> 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.

Re:Recolada

[ichigo 2.0]

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.

Re:Recolada

[Ruff_ilb]

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

[Anonymous Coward]

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

[Anonymous Coward]

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

Yup, if he existed.

Re:Recolada

[AsparagusChallenge]

Actually, no. If God didn't didn't mean us to create life he would let us do it, and then we would smite ourselves with our little new toys :)

Re:Recolada

[physick]

Perhaps not. They mutate quickly. Selection pressure will ensure that if you only kill 99% the other 1% will find a way to mutate around the mechanism that is supposed to kill them. Then you need a new mechanism to kill the mutated ones, and if 1% of them survive.....

You can't predict which mutationswill occur, so you can't guarantee that you can completely eliminate an organism once it is released/escapes into the wild. Even if you put "self-destruct" genes into it so that you can turn them on to cause it to kill itself, those genes may be suppressed in later generations. I would expect them to be so, as apoptosis is very tightly regulated in cells and there is no selection pressure to keep around some genese whose only function is to kill you. But there will be strong pressure to eliminate such genes.

Re:Recolada

[Zakabog]

(ok, almost any tool - it's kind of hard to abuse a Nerf bat - I know, I've tried).

Obviously you didn't take off the soft foam and beat a person with the hard plastic inside. And if it doesn't come off, just turn the bat around. The handle, even though it's usually covered in foam, is very solid.

Re:Recolada

[ceoyoyo]

But don't worry, he'll save the faithful. So really, if you believe, you should be encouraging this. Fewer scientists to argue with!

Whats the ethics of such a project

[Anonymous Coward]

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

Re:Whats the ethics of such a project

[Ingolfke]

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

Not New News, if you've been keeping up

[Maverick TimeSurfer]

The article does not seem to contain mention of just when this all started. The Globe & Mail is a bit behind- Discover magazine reported on the project in 2001: http://www.discover.com/issues/apr-01/features/fea tsimple/

relevent quote

[Anonymous Coward]

"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

[Anonymous Coward]

"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

[Boronx]

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

Re:relevent quote

[narcc]

This troll is particularly funny if you consider Lord Byrons' daughter was spending an awful lot of time with Charles Babbage.

Here's what we need...

[johansalk]

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...

[Zantetsuken]

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...

[Anonymous Coward]

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

Re:Here's what we need...

[Anonymous Coward]

I'm pretty sure he was joking. I mean... c'mon. You'ld have to be a moron to not realize he was joking.

-Q

Re:Here's what we need...

[Anonymous Coward]

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

Well, then, they wouldn't be perfect, would they?

A perfect supermodel must have all of the following characteristics:

• Has perfect skin, eyes, figure, etc.
• Doesn't age, get sick, or have periods.
• Is not a disease carrier.
• Does not get jealous or have any other personality defects.
• Is willing (even eager) to perform any act, no matter how perverse, at any time, with any persons, entities, or objects, for my sexual gratification.
• Is willing (even eager) to have any act, no metter how perverse, performed on her, at any time, with any persons, entities, or objects, for my sexual gratification. And, most importantly,
• Does not require payment for any of the above.

Now, that's not asking too much, is it?

Is it Open Source?

[$0.02]

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?

[castoridae]

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?

[zcat_NZ]

ask monsanto?

Re:Is it Open Source?

[Anonymous Coward]

Considering Celera filed quite a few patents on genes, I doubt they'll give away anything useful they might engineer for free.

Re:Is it Open Source?

[marcosdumay]

Biotech patents are on a much worse situation than software ones. At least, on software we can still do basic research without paying taxes^W roalties to some company.

That is the real problem, since life seems to not be covered by copyrights. At least until some realy clever lawer get on the way.

genetic code?

[radicalnerd]

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

Re:genetic code?

[Anonymous Coward]

With bug spray and/or a flyswatter.

Re:genetic code?

[Anonymous Coward]

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?

[castoridae]

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?

[oedneil]

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

Re:genetic code?

[mark-t]

Probably we would have to let it debug itself... much as we try to do for ourselves.

Of course, debugging it would take many hundreds or thousands of generations, but if evolution works, it should happen.

Mwahahahahah!

[Anonymous Coward]

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?

[qw0ntum]

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?

[castoridae]

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?

[zcat_NZ]

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.

Re:Is it really that synthetic?

[Anonymous Coward]

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?

Yes, but you can't then say you created your own computer.

OMG

[Anonymous Coward]

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

ScuttleMonkey

[Anonymous Coward]

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

[Tablizer]

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

[Tablizer]

We *are* the I.D. now

Re:To mangle Ray Bradbury

[Busy]

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....

[CupBeEmpty]

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 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....

[rale, the]

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....

[castoridae]

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 blog entry on the subject.

Re:Extremely interesting....

[CupBeEmpty]

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....

[CupBeEmpty]

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....

[Dirtside]

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.

Re:Extremely interesting....

[Anonymous Coward]

So you're basically saying that the compiler takes some command-line args?

Thanks. I'll be here all day...

Re:Extremely interesting....

[ceoyoyo]

Ah, you have to write your first compiler in assembly. Of course, you need an assembler. You write that in machine code, by punching holes in little cards or flipping switches if you have to.

Life probably did it the same way. First you had some chemicals that happened to form up into useful structures spontaneously. Then there was one of these structures that would behave differently if a certain other structure were present. And so on, building structures that can then be leveraged to build something even more complex.

I can see it now

[Tablizer]

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

Re:I can see it now

[Mr. Vandemar]

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....

[Anonymous Coward]

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

Re:In Soviet Russia....

[Busy]

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

Typo

[zephc]

You misspelled "Dr. Venture"

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

Building with DNA

[castoridae]

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 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

[user32.ExitWindowsEx]

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

Re:Building with DNA

[castoridae]

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

[Hartree]

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.

Re:Building with DNA

[Pavan_Gupta]

And this is one of the reasons why Biomedical Engineering is the hot, up and coming field of the 21st century. Cheers =)

Re:Building with DNA

[Salis]

I agree that the major challenge is to figure out what DNA to synthesize. And we need some procedural method to explicitly determine the DNA sequence that performs some specific function. Although, I don't know if thinking about these systems as modular electronics is the best way. These systems certainly are modular, but the fact that there are no wires and no clear separation between modular devices means that a full modularization of the entire system into separate parts is a real challenge. It can probably be achieved, but it requires a lot of engineering of the individual parts.

But, even after that, I think the techniques in building organisms will be very different from building electronics. Even simple bacteria use regulatory mechanisms acting on multiple different layers: transcriptional, translational, post-translational. The code itself (the DNA) can get cut, reversed, and reinserted to generate "dynamic coding". And then there's diffusion, signal tranduction, active transport, etc that are all completely foreign to the design of electronic chips or "programming".

So maybe thinking as an electrical engineer or computer scientist will help in the beginning, but by the end a new type of engineering has to be created. I'm a chemical engineer myself so it's natural to think of these systems as small chemical reactors, engaging in numerous biochemical reactions with extremely dilute concentrations. So maybe I'm biased in that regard. I describe these systems using chemical kinetics and the answers often match experimental data. It's probably possible to use a detailed kinetic model of a "part" to fully characterize its modular behavior. And then use that information to better stitch together multiple parts. But, who knows, the field is young and we will eventually figure out the best ways of doing things.

Re:Building with DNA

[Anonymous Coward]

"I think one of the biggest challenges isn't in synthesizing strings of DNA, per se - it's in knowing what DNA to synthesize."

To paraphrase Albert Einstein: "Duh".

I doubt

[Jotii]

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

Why bother?

[SHP]

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?

[castoridae]

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

Re:Why bother?

[Anonymous Coward]

It would work of course, but it would take too much time. I wonder what scientist would be willing to wait 5 million years, especially when he would be dead after 120 years max.

Re:Why bother?

[Anonymous Coward]

It's called mutagenesis
and is cheap and effective when you know exactly which bits you want to change. If you're just changing things at random in a 3-billion basepair genome, you have to wait billions of years and use planetary-scale populations to get useful results.

Maybe...

[rodm13]

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

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

hehe

[Anonymous Coward]

hehe, bring on the catgirls! :)

OMG

[NixLuver]

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!

Answer: boot loader

[Impeesa]

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.

Soon...

[SnarfQuest]

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

(Someone had to say it)

actually easy to pull off, but would you want to

[Anonymous Coward]

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.

anyone else sense disaster?

[SuperBanana]

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!

Re:anyone else sense disaster?

[Liam Slider]

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.)

Actually, "grey goo" would have to be designed. A self replicating nanomachine that can survive in shirtsleeve environmental conditions, scrounge all the resources it needs to replicate itself from the surrounding environment and process them all into the desired forms, with the programming to carry all this out? You think something like that could happen because of a coding error?

Re:anyone else sense disaster?

[marcosdumay]

Oh yes, it could. It could happen even by not checking the replicated bots apropriately, getting random errors on the code.

All you need to have for a grey goo situation is an imperfect self replicating being capable of doing that outdoors. And this will probably be the goal of any nanobots project. The only part missing is to replicate without control.

Re:anyone else sense disaster?

[Ullric]

mod parent up!,he's right.this only shows the collosal arrogance some of our scientists have.to assume that they can create life,when they are unable to treat some diseases,when they do not understand how life works or is created,it is like trying to write an OS,when all you know is how to write a simple HELLO WORLD program.

Re:anyone else sense disaster?

[Sarlacc83]

I don't sense an impending disaster for one simple reason.

I really don't think they're going to be able to pull this venture off. It sounds like a neat idea, but in the end, the objections about how little we know of life will probably spell the death of this type of experiment pretty quickly. Unless one knows the origin of life and how it came to be, how can we expect to replicate it?

One has to draw the line somewhere

[ichigo 2.0]

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

Just wait

[Fengpost]

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.

relevant quote from einstein

[Anonymous Coward]

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

Genetic Engineering < Synthetic Biology

[Anonymous Coward]

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.

Re:OMFSM

[AndroidCat]

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

Correct.

[Belial6]

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

Correct.

Re:Correct.

[Anonymous Coward]

I think, perhaps, the grandparent poster was being ironic.

That is, just because god allows things to happen, doesn't mean that he _means_ for them to happen, only that he tolerates them because of some presumably higher purpose that humans do not currently understand.

Or are you of the mindset that we now know everything there is to possibly know already, and that everything is exactly the way we think it is?

Anyways, I do not wish to enter into a debate on whether or not God exists. I'm only pointing out that you completely failed to recognized sarcasm where it was clearly intended.

Dear God...

[sd_diamond]

Please, nobody tell Michael Crichton.

SF Antecedent

[CaptainCarrot]

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.

quit yer bitchin

[Anonymous Coward]

Chicken and egg science is going to be like that.

Re:OMFSM

[Hektor_Troy]

Of course human genetics are made up of spaghetti code! We were all created by the Flying Spaghetti Monster!

How to debug genetic code?

[RedLaggedTeut]

In Soviet Russia, genetic code debugs you!

Re:Python vs Perl vs Ruby vs ((Lisp?))

[Anonymous Coward]

According to at least one guy, Lisp is DNA.

The result: Lisp is pure DNA. You can build anything with it, and you always have the ability to evolve even large existing systems in new directions. And that's exactly what you need, because your problem domain is unique.

Hopefully...

[ShaunC1000]

they'll release their genetic code under the GPL, I'd really hate it if went all commercial.

Just a hunch...

[eremitic]

Something tells me this code will be very vulnerable to viruses.

So you can code your own organisms...

[zopf]

but can you run linux on them? You could probably set up some serious clusters...

Interesting Issue with DNA as code

[ndansmith]

"Code" is an interesting word to use when talking about DNA. I think it was first termed as such since it seems to be an obvious descriptor of DNA: Information which is stored by the DNA molecule can be interpreted by the living organism as instructions for various proceses. There is obviously information there, and it does require interpretation, so it is "encoded."

Normally, when I talk about code, I understand that an agent, some sort of intelligent being, has put the information into code. If there is a code, it must have been encoded by someone, and non-intelligent phenomena do not produce encoded information (as far as I can reason). This sounds like a perfect solution for ID adherents, but must be troubling for evolutionists. Is "code" the correct terminology for talking about DNA? How does science explain the fact that all this information came to be encoded and stored in a DNA molecule by the process of natural selection (an unintelligent phenomenon despite the term "selection") such that living tissues can interpret it and put it into action? This issue is primary over natural selection itself, since the ability to pass information to offspring is a necessary condition for natural selection.

I am simply asking because the issue of humans writing their own custom DNA begs the question about how information came to be encoded in DNA in the first place. I never took biology, so I am quite ignorant and curious about this issue.

Re:Interesting Issue with DNA as code

[AsparagusChallenge]

That's similar to what I've been thinking. If it's possible to trace back every piece of DNA through evolution to a piece of code, then that original DNA, having such properties as to evolve into either a cockroach or a dinosaur, should have been somewhat hard to appear from thin air assembled that way.

I mean, even with evolution making sense one has first to set initial conditions. It's kind of fuzzy once we get to that point; evolution doesn't explain everything, just pushes the nasty and hard to explain parts into another field.

Re:Interesting Issue with DNA as code

[aonic]

DNA is "code" because each set of three (or is it four) nucleotides forms a codon. When a strand of DNA is transcribed to RNA, and then processed by an enzyme (transcriptase or something? it's been years since i took bio), protiens with one end that fits with that codon hook up to the RNA strand. the other end of that protien carries an amino acid (the components that form proteins), and so each codon gets "decoded" into an amino acid -- chains of which form proteins.

the information came to be "encoded" because that's probably the best way to pass on protein information. the double-helix of DNA allows it to be error-resistant (think bit flips), and makes it easy to replicate. and the encoding isn't really that complicated, but allows for many combinations from only 4 DNA molecules.

on the article itself, i belive what they're trying to do is put combinations of codons together to create a protein. so far, all we've done is take existing DNA strands that call for certain proteins and mix them around, adding insulin-producing DNA to e-coli, for example.

as for the dangers, i'm less worried about viral strains of mutant human-designed bacteria running around infecting everyone, as much as i'm worried about mutant proteins that we've never seen before. mad cow disease, anyone?

Re:Interesting Issue with DNA as code

[aonic]

think back a little. the first primordial pools of goo. random organic molecules assembled into amino acids, lipids, etc.

why are these traits still prevalent in life today? not because god decided to put a bunch of different nucleotides together and call it DNA. the protieins hooked together and it happened to survive and easily replicated itsself. a single strand of DNA floating there in the goo, complement proteins stick to the exposed nucleotides, form their own strand, and float away. the process repeats, and you have DNA.

things that replicate easy and survive to replicate tend to win out in the evolutionary war. DNA tends to survive better if it's surrounded by a lipid membrane, so that's what happened. then came the bacteria, then came the multi-celled life. millions of years later you have dinosaurs and cockroaches, plants, humans, etc.

Re:Interesting Issue with DNA as code

[AsparagusChallenge]

Right; still, it's not the point.

It's still missing why did that molecules took that particular configuration; once there one has two choices: "sheer luck" and "induced by something else". None of those choices has a real advantage over the other one right now.

"Sheer luck" sends us back to a realm similar to spontaneous generation (everything in science has to have an origin, right? Saying "It just happened" is ugly-ish) and "Something else made it" creates the trouble of this "something" needing to be created first. One way or another we have something that can't be quite fully explained from a pure and formal scientific POV.

Re:Interesting Issue with DNA as code

[aonic]

Unfortunately, "sheer luck" is the best answer you're gonna get for now.

Why did the big bang happen? Well in a timeless universe (remember, time is a dimension created by the big bang) everything that has a nonzero probability of happening happens instantaneously. therefore the big bang, having a nonzero probability of happening (it did, didn't it?), happened.

the same thing applies to evolution. over millions of years, even things that have a very slim chance of happening (non-zero probability), such as organic molecules happening to form into something coherent, happen.

Re:Interesting Issue with DNA as code

[isthisnickinusetoo]

Well, the Miller-Urey experiments give us an answer to this.
They showed that organic molecules can be created by discharging electric sparks in boiling water, methane, hydrogen and ammonia, which happens to reproduce quite well the conditions that prevailed on the early Earth.
He showed that this could produce aminoacids, sugars, lipids, nucleic acid bases. There are your basic building blocks.

Re:Interesting Issue with DNA as code

[AsparagusChallenge]

Errr... "things that have a very slim chance of happening" includes "some entity bootstrapping itself and creating this universe from scratch" too. That's why saying "just happens" is quite ugly viewed scientifically.

Re:Interesting Issue with DNA as code

[Genlochlee]

And of course you know that the "inteligent" agent behind developing our code are super transdimensional beings whose protrusion into our own dimension are little white mice. And furthermore you must know that these particular beings designed our world as the greatest computer ever made to answer the ultimate question. So technically our being "coded" is very reasonable and easily answerable. If you wish to worship your lab mice overlords who are only using you to solve their own problems be my guest. :)

Re:Interesting Issue with DNA as code

[EternityInterface]

I figure it as: the universe dies by collapsing in a black hole. (Which would be true if it's one of those 3 shapes?) When the collapse is complete, when all matter is at the same spot, we get divide by zero, and all the matter explodes. Then everything happens again, aka eternal return.

What constiutes a new life form?

[kweg]

Many new life forms have already been made by some definitions, just swap one gene for another and you have something different.
How do they decide when what they make is an *new* lifeform?

In Korea...

[Anonymous Coward]

In Korea, only old people write DNA.

No more syntax errors!

[cciRRus]

With just "G", "T", "A" and "C" as keywords, it is very unlikely to make syntax errors. Cool...

Re:No more syntax errors!

[danielmsantana]

indeed... just stack overflows errors resulting mutants... the x-men are coming...

Golf...

[dodobh]

And you thought Perl was unreadable?

Old your code are belong to me

[ytr]

I have written a C program to produce a patent submission which includes sequences of all combinations of the letters c, g, a and t.

And prior art does not count, I believe.

Re:Old your code are belong to me ....

[ytr]

Followed by a program in C to produce the previously mentioned program.

ID anyone?

[adolfojp]

If this project is successfull... whe can only hope...

I wonder if in a couple of years the result will start debating about its origins with theories like evolution vs. intelligent design. :-P

Reminds me Asimov too...

[DrYak]

(...specially the The last Question. Albeit that one is on a much more philosophical level)

We *are* the I.D. now

Human designing synthetical life :
Yeah that's the proof of I.D. !!!
See ?
Life must be created by someone !
Life cannot be explained by science, only an Architect could have done it !
It is such much complex in its "irreductible complexity" that we humans will never be able to study it and understa... Oh, wait...

"trying to design and build it"

[endoplasmicMessenger]

Did he say "design"? Obviously, this belongs in the philosophy classroom!

Re:Writing Code, huh??

[grimJester]

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

It's funny. Laugh.

And, speaking of C++...

[Chemisor]

Well, as a C++ programmer, I am quite used to hearing how C++ is evil because of all the things it can do. Therefore, I am as justified as they are in saying that C++ is better than genetic code for the following reasons:

Genetic code is too low-level. While C++ comes with a standard library defining containers, iterators, and common algorithms, in genetic code you have to do everything from scratch. In quaternary. With 3D objects. Talk about a learning curve!

Genetic code has no garbage collector, and not even a simple malloc. In fact, you have to write self-modifying code to avoid memory leaks or dangling references. This makes it very difficult for the beginning programmer to write good code, and encourages bad practices.

Genetic code is not object oriented. You have to do horrible hacks to encapsulate private information or define interfaces to it. Most programmers just use a "signals-and-slots" method to pass messages, resulting in spaghetti code rivaling the worst abuses of goto.

Genetic code is too flexible. If you thought bad C++ code was hard to understand due to operator overloading, wait 'till you see the things a bad programmer can do with genetics! And, while in C++ the worst that can happen is a crash, bad genetic code could eat you.

Genetic code takes longer to develop for. You have to write lots and lots of code to duplicate even the simplest C++ line. Furthermore, compilation times totally suck, approaching twenty years for complex programs!

Genetic code has an arcane syntax, leftover from the early days of evolution. Just imagine, we're still using constructs nearly three billion years old! If you thought having some C in C++ was bad, wait 'till you see the archean leftovers you are forced to use in your eukaryotic cells!

Genetic code is dynamically typed and favors the "duck typing" philosophy. This creates an enormous amount of security holes, where special ducks ("poisons") with appropriate appearance but malicious behaviour could be introduced into the system.

Genetic code is hard to debug. Having no debugger, one has to rely on contrived printf-like trace statements. Unlike printf, the genetic equivalents are limited in number and expressiveness, sometimes making it impossible to figure out what is wrong.

Genetic code is a bloated pig. Just imagine, you need trillions of bits to define a simple organism, while in C++ I can code NPCs in under a hundred lines of code.

Genetic code VM is slow. Perhaps not as slow as Java, but it still takes milliseconds to do even simple operations. We could all think so much faster if we were written in C++.

Not ready yet

[richcoder]

Seems to me the steps are
1. Reading
2. Understanding
3. Writing

It makes sense to finish #2 first donchathink?

Re:OMFSM

[Zen Punk]

Thank you for making the object of the joke clear and understandable for all of us. You see, I have a genetic disorder which unfortunately prevents me from understanding subtle humor. This means I have to rely on the generosity of upstanding citizens such as yourself to explain these frustratingly opaque yarns. Someday I hope science will find a way to cure congenital defects like mine, so that such services will no longer be required. A man can dream...

Someone is dreaming

[jandersen]

Life is unbelievably complex, and for all our recent results and new insights in biology and genetics, we are still only just scratching the surface. A living organism, even the simplest prokaryote, isn't just a set of genes. The truth is, we only have a very rough idea about what genes go into any organism; on top of that we don't know what the functions are of the supposedly non-coding parts of the DNA, we hardly know anything yet about the epi-genetics side of things, and we have no idea about how to set up eg. a cell that would actually function even if we had all the necessary knowledge about which genes are necessary.

All we will be able to do in any foreseable future is try to synthesize a new gene, insert it into a cell and see if we can get it to work. I think the ability to build a cell from acratch is at the very least a thousand years away. It's the beginning of these things that is difficult - if you look at the timeline of life it seems that the very first stages of life, the first necessary molecules, were created even before Earth was formed 4 or 5 billion years ago; from this beginning it took something like 4 billion years for the first living cells to emerge, and only in the last 500 million years (since the Cambrian explosion) have we had life more complex than prokaryotes. This ought to tell everybody that we are not at all likely to be able to 'create life' in the near future.

Re:Someone is dreaming

[Anonymous Coward]

It's SO HARD to do that it MUST have been done by an intelligent designer!

Andromeda Strain

[mosel-saar-ruwer]

Call me a luddite, but you youngstahs should bone up on your classic SciFi* before you start joking about this shiznat.

Hell, if it were up to me, that damned comet debris wouldn't be allowed within a parsec of our atmosphere - unless the intention were to incinerate it.

*Cf the work of Vincent Price and Charlton Heston.

Too late.

[dpiven]

http://www.michaelcrichton.com/prey/index.html

ok i can do this

[Anonymous Coward]

cut n' paste

God Sues British Columbia and Maryland Scientists

[majikfox]

Some time in the future: Micro-time-warner-comcast-wal-mart-soft News reports today that God has brought a lawsuit against scientists from BC and Maryland for devloping beings who look exactly like, act exactly like and perform the exact same functions as humans. God claims that because these beings are essentially the same product, they must contain genetic code from humans. God is now demanding licensing fees for these new beings and has brought lawsuits against the original designers of the new beings, called Linmens. Scientists who developed the 'original' genetic code for the new beings claim that the work is entirely original and that if it walks like a duck and quacks like a duck, it may be a platypus.

NO BIOLOGY???

[dave1g]

How on earth did you get through school without a biology class????

Even in my 9th grade biology we learned the basics of how DNA information is transfered to offspring, and in cell division, the imperfect copies that lead to mutations, etc.

Re:OMFSM

[Anonymous Coward]

Oh My Flying Spaghetti Monster!

Hello World?

[4D6963]

What will the genetic Hello World! be like?

Re: We Are God! We are God!

[some guy I know]

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.

Well, humans have a way to go...

• Let there be light? Yep, electric lights were done over a century ago, light from fusion (like the Sun) about fifty years ago.
• Creating the Heavens and Earth? No, humans haven't done that yet, but humans have started research into terraforming (creating Earth-like environments on other worlds).
• Creating plants and animals from scratch? Well, that's what humans are working on now. However humans have created subspecies through selective breeding, etc.
• Taking part of some dude's body (Adam's rib) and making a whole other organism (Eve) from it? Well, with recent developments in stem-cell research, humans are getting close. Humans have also cloned various organisms, but there is a difference between making a twin of something and manipulating it to make what you want.
• Resting? Yeah, well, humans are experts at that.
• Destroying cities full of sinners? Oh, we can do that, too.
• Sending people to Hell? DMV and IRS.

So, we're on our way, but still have a ways to go.

Re: The First Compiler

[some guy I know]

someone had to write the first compiler, by hand, in machine code.

My guess is that the first compiler was written in assembly language.
The first assembler was probably written in machine code, or, more accurately, was probably written in assembly language, and then hand-translated into machine code.

Just dont let it out of the box

[Anonymous Coward]

Conciosness is The start of life, not just an option.One Specie toxic waiste is another specie gold mine.Life on this planet is a 4 billion year procces still in progress.It would be easier to make a house have a conciose mind than trying to use DNA.Crick should have told him.

I wished to see The Globes article

[jln_d]

The Globe wants a credit card number to see their article. Could somebody, please, provide one?

Youngsters?

[jpellino]

You're preaching to the choir - in 1970 I was 12 years old and the Andromeda Strain came out in paperback. I read - and reread it until it literally fell apart. I have never not had a copy at hand. There has not been a year in my teaching career that I have not used one of its lessons, from the use of sentinel values 'fail-safe' systems to the fluidity of evolution to the magnification of the problem caused by a stray shred of paper...

It was a joke, but we do need to remember the amazing efficiency of simple organisms. E.g., there's a circular plasmd - I believe it's for SV40 but it's been a while - where one side of the gene sequence codes for some useful protein in one part of the virus - and the remaining half of the helix - usually considered simply the logical compliment of the useful code - ALSO codes for other parts of the virus. Amazing.

God is not a teamplayer :-)

[gd23ka]

You're right. They wont pull something off as complex as a natural organismus...
But who in his right mind would want to construct somehting like that, taking it to
the programming paradigm: a code replete with hundreds of thousand dead ends and
blind alleys nobody knows that they're good for?? (HE is A TOTAL NIGHTMARE, HE doesn't
document, HE keeps the sources to himself, HE doesn't take dead code out...)

What we need is the _simplest_ organism we can create. I think we are going to have a
lot of fun coding with carbon, phosphorus, iron and oxygen and the way I see it
this will definitely take us into this next century we just started.

A New Kind of Science

[cr0sh]

You might want to read Stephen Wolfram's book, "A New Kind of Science", which explores the idea of complexity arising from very simple sets of rules (The Principle of Computational Equivalence). In this book (which, while long, is not too difficult to read - although the appendices will probably leave you scratching your head), he details a very simple set of 6 rules, which he utilizes to show how such simple rules, being used in a 2D cellular automata, can easily give rise to many complex patterns, including that of a UTM (Universal Turing Machine). While it isn't discussed in extreme depth, the topic of DNA is explored, how it may have come to be, etc. No, it doesn't require "magical" thinking, either...