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Hacking Biology

michael posted more than 13 years ago | from the tools-for-a-new-generation dept.

Science 72

taatacgactc writes: "DARPA (DoD) is now supporting the development of a SPICE equivalent for biological circuits (aka BioSPICE). Best of all, it's to be "open source". Given the hyperexponential improvement in biological technology and the bioengineering efforts getting off the ground, fun stuff should be happening. Of course, there is the "dark side"." More information here. The submitter may be overstating the bit about "open source": the proposal says "All software developed as a part of the program will be open, in the sense that program performers and other DARPA authorized users will have the right to view, use, modify, and distribute code within the program authorized community. All derived works including revision, enhancement, modification, translation, abridgement and expansion of code will also remain open in this sense. ... The DARPA Director reserves the right to approve and exercise licensing arrangements depending on the context and the relevance to national security."

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Next (1)

Anonymous Coward | more than 13 years ago | (#344645)

The five assed monkey.

Re:Biology is not just DNA (2)

Ian Bicking (980) | more than 13 years ago | (#344646)

Unlike your analogy, many aspects of DNA are not seperable. There isn't necessarily a sequence of DNA that accounts for every feature (most features?) that we may want. Anything as complicated as DNA is non-linear -- small changes in source can result in large changes in result, and we cannot necessarily deduce from a fixed number of known source->result mappings what all combinations of source will do.

Only with models of what DNA actually does could we (maybe) figure this out. Right now the theory is mostly experimental -- knowledge that when people have done one thing, something else has occured. That's very crude.

An historical analogy might be with semiconductors. Semiconductors are not very complicated -- you add some cyanide to silicon, I believe, and you have a semiconductor that can act as a transistor. But no one thought to do this until their was a model (with quantum mechanics) that would imply that such a combination would have useful behavior. There's no quantum-level manipulation involved in making semiconductors, only quantum-level understanding.

In the same way, we may be able to do nearly everything we'd want to just by manipulating DNA. But we have to understand more than DNA to accomplish what we want.

Hmmm... to explain the nonlinear part: say we have an original DNA sequence of AA (this is entirely abstract). Once you find out what BA and AB do, you may still have no idea what BB does. Understanding what each isolated change does may not give you any understanding of what changes do in combination. To figure out what A and B mean is in many ways simply to figure out how to predict what they will do in combination. And DNA has so many possible combinations...

Re:Sounds like! (1)

Delphis (11548) | more than 13 years ago | (#344647)

And if it breaks and leaks everywher you have to sort it out ... gives a whole new meaning to the word 'patch'.


--
Delphis

Re:Making up words (2)

Dr.Dubious DDQ (11968) | more than 13 years ago | (#344648)

"hyperexponential"?

For that matter, is "dynamical" even a real word? (Check the title of the page on the "BioSPICE" link above - "Arkin Laboratory for Dynamical Genomics"...)

Here's a real word for these people - "Neologism."...


---
"They have strategic air commands, nuclear submarines, and John Wayne. We have this"

Re:Biology is not just DNA (2)

Dr.Dubious DDQ (11968) | more than 13 years ago | (#344649)

The tools of biotech are very crude, like chopping away with bronze axes. It's not possible to modify organisms by mixing and matching the parts we understand in UNIX-style.

I don't know about that, necessarily, depends how you look at it:
grep fluorescent_green_protein_gene JellyFish >> bunnygenes; cat bunnygenes > bunny_egg_cell; cat bunny_egg_cell | mama_bunny > glowing_baby_bunny. [ekac.org]

Like the "core" Unix tools, our existing biotech tools ARE very "low-level", as you point out. We're certainly quite some way from the biotech equivalent of "higher-level" mix-and-match projects like php-gtk, but we've got some very useful building blocks to work with...including the project that is the subject of this article, which appears to be intended for building simulations of larger biochemical pathways...the next stage of biotechnology which we can't yet do much of, as you say. Sadly, this means I'm still probably at least a decade away from taking over the world with an army of Atomic Mutant Zombie Clones®

Incidentally, I'd be willing to bet that a determined and/or skilled individual can do a LOT with a bronze axe...but I think one level of analogy is plenty, so I'll avoid belaboring the point. Besides, I understand what you mean: Hype bad. Results good. :-) .


---
"They have strategic air commands, nuclear submarines, and John Wayne. We have this"

Re:Biology is not just DNA (2)

Dr.Dubious DDQ (11968) | more than 13 years ago | (#344650)

Anything as complicated as DNA is non-linear -- small changes in source can result in large changes in result, and we cannot necessarily deduce from a fixed number of known source->result mappings what all combinations of source will do.[...]Only with models of what DNA actually does could we (maybe) figure this out.

I'm not quite sure what you're getting at here. If you mean we don't have more than a blurry understanding of chemistry involved in the proteins that are encoded in the DNA, you're absolutely right. It almost sounds as though you're implying that we don't know what DNA "does" at all, though, which is obviously not true. We know EXACTLY what expressed DNA "does" - it codes for proteins. We also know exactly what the translation of DNA-base-pair-triplets to amino acids is. Noncoding sections of DNA are obviously trickier, but some of them are reasonably well understood now as well (e.g. promotor sequences, binding sites for repressor proteins, etc.).

To figure out what A and B mean is in many ways simply to figure out how to predict what they will do in combination. And DNA has so many possible combinations...

I can hear the original poster hopping up and down with agitation at the DNA-centric message here even as we type :-)
The original poster's central [and correct!] point was that from a "functional" point of view, protein chemistry is more important than raw DNA, which I THINK is what you're getting at (if "A" and "B" in your example represent sequences coding for two separate proteins [or parts of one protein complex, like hemoglobin])

To clarify my analogy, I'm thinking of DNA as the "at, tr, grep, and cat" (ATGC, get it? Sorry, couldn't help myself. Watson and Crick made me do it...) of biology, compared to protein chemistry's "Xfree86, Mozilla, Sendmail, and Koffice". My point was just that while the tiny utilities are just a meager bit of the more broadly useful and complex applications, they are still extremely useful themselves, just as the DNA data available is itself of great (but very focussed) usefulness, even before we have better knowledge of the protein chemistry later. (we don't understand the source code well enough to sit down and rewrite XFree86 from scratch, but have a pretty good understanding of many of the little subroutines and how they might be put together into new "proglets"...)


---
"They have strategic air commands, nuclear submarines, and John Wayne. We have this"

Re:Biology is not just DNA (5)

Dr.Dubious DDQ (11968) | more than 13 years ago | (#344651)

Rating the advances in biotechnology simply by looking at DNA sequencing improvements is not very smart..

Definitely a good point, but I wouldn't underestimate the usefulness of simply being able to sequence better.

DNA Sequences alone can be/are useful for a lot of different research. Archaeologists and Anthropologists can use DNA sequences to help determine, for example, the relationship of one population to another and/or help trace migration of a population. Medical types can not only check for genetic diseases, but could also use DNA sequences to quickly check the identity of a pathogenic organism, if the sequencing technology becomes readily available enough. (Running a few PCR cycles is still much faster than trying to isolate and culture a pathogen from a swab). Zoologists and Paleontologists can use DNA sequences for similar purposes to what I mentioned for anthropologists and archaeologists, and can be handy for environmental research.

Until we understand the *function* of the proteins that are derived from these genes, all biotechnology can do is recombine the already existing technologies.

Again, this is true...but don't forget that "recombining already existing technologies" can be pretty powerful and useful all by itself. (Heck, "recombining existing technologies" is, basically, a fundamental design principle of Unix-based systems, isn't it? I know MY Unix-based systems are extremely useful... I love my "|" key...)

I'm confident we'll be getting plenty of use out of DNA while we work on the harder problems of protein functions and chemistry

P.S. Thanks for reminding me...I've been meaning to download the folding@home [stanford.edu] client and throw some of my meager computing resources at helping out...


---
"They have strategic air commands, nuclear submarines, and John Wayne. We have this"

Lanier: life != digital (3)

peter303 (12292) | more than 13 years ago | (#344652)

I don't think it has been proven that knowing the
genome or pronome "code" allows to to manipulate
life to a serious degree.
Sure there have been results in some genetic
diseases, franken-food, and bio-identity.
But serious bio-hacking may require more than
just information sequences.

Jaron Lanier's recent "Half a manifesto" suggests
that information may not explain everything
and other aspects of reality may be acting there.
John Searle, the Berkeley philosopher has a similar
complaint toeards those who try to digitally emulate the mind.

Thinking that "information manipulation" explains
and controls everything may limit our understanding
of phenomena and ability to control it.
Don't get locked into this box.

Re:nanomachines (2)

The_Sock (17010) | more than 13 years ago | (#344653)

Any development, any invention, anything in existance can be used to destroy.

And please don't start on about creating something like a human life, because I'll throw my first born at you.

Re:Military (1)

gattaca (27954) | more than 13 years ago | (#344654)

Unfortunately, because the results of many pathogen sequencing projects, the human genome and various crops are open source, your favourite baddie is just as able to play around with the data as your favourite goodie. Working out what bad things can be done is a good idea if it gives you a handle on how to deal with the very real prospect of bioengineered weapons. I would agree if all military everywhere in the world were going to stay away from this kind of research, but I think that is a smidgen unlikely.

Seen that Honda walking robot? (1)

xtal (49134) | more than 13 years ago | (#344655)

You know the one that automatically learns itself how to walk, and looks wrong? Put a automatic rifle in it's hands, and you don't need any genetically modified soldiers :)

Re:Biology is not just DNA (1)

kovi (52074) | more than 13 years ago | (#344656)

Above is the only post worth reading so far. I am really surprised how bad the
knowledge of biology/biotech is among Slashdot readers (kinda feel my karma
going down). The amount of people wanting to clone Spice Girl(s) and such is
shocking too.
Anyway, skipping the part of proposal about so-called "DNA computing", which is
garbage and there are tons of such software around, the other section (Bio-Spice)
sounds interesting, although it's not written in very precise manner. I'd guess it's about
simulating metabolism and one does not really need Michaelis-Menten crap for that.
They should have check the research going on in their own country, specifically:

http://gcrg.ucsd.edu/

It's all about stoichiometry and linear programming and the __good__part__ is that,
although it can't really be used for cloning Spice Girls :-), it interfaces with genomic
data very nicely.
Regards,
kovi

Now, moderate me down.

Why is that not open enough? (1)

Lish (95509) | more than 13 years ago | (#344657)

I know I'm gonna get flamed here for not espousing the popular /. OpenSource view but....

Why isn't this a good enough definition of open source? True, not every Tom, Dick, and Sally can have the source. But everyone who uses the program has access to and can modify the source, and it stays open in that fashion. The only restriction is on who can use the software in the first place. And frankly, I wouldn't want just anyone to be using this program. In this situation, this is as open as the source can reasonably get.

Re:Military (4)

Daniel Dvorkin (106857) | more than 13 years ago | (#344658)

Remember, DARPA are the folks who came up with DARPANET, which begat the Internet, which begat the Web, which begat /. and many other wonderful things. Mindless paranoia just because the military is involved would mean turning our back on a whole lot of very cool things. And when it comes to biotech, it's not just cool; it may very well be the thing that saves your life somewhere down the line. (In a related vein, e.g., anyone who's been in a serious accident any time in the lastt few decades has the military to thank for their care, because the modern EMS system is the direct descendant of the military medevac system, which was first developed in its modern form in Korea and was perfected in Vietnam.) Yeah, it's perfectly reasonable about the government doing Eeevil Things with the knowledge -- but on the whole I'm a lot _more_ worried about cancer and diabetes and heart disease and AIDS and all the other killer diseases which may be cured with the knowledge this project creates.

Also, as a former military medic (and current biotech worker) I can tell you that the military is often _directly_ interested in doing good things for people, not just seeing spin-off benefits (e.g., the way the personal computer can trace its lineage directly back to NASA and the USAF.) The military population -- active duty, retirees, and family members -- constitutes a large, diverse patient population with health problems ranging from arthritis to (obviously) bullet wounds. DARPA, USUHS, and other military research institutions have a strong and legitimate interest in medical advances -- which will first help soldiers, and then their families, but which will inevitably propagate to civilian medicine as well.

... (1)

Erik Fish (106896) | more than 13 years ago | (#344659)

But how do you know it's really the DARPA Chief and not Decoy Octopus??

Making up words (2)

Richy_T (111409) | more than 13 years ago | (#344660)

Given the hyperexponential improvement in biological technology

"hyperexponential"? Michael, I think you are talking hyperbollocks.

Rich

This was played out in a video game (2)

Rurik (113882) | more than 13 years ago | (#344661)

If anyone has seen the Metal Gear: Solid Snake for Playstation, it revolved around this plot. Even had the DARPA Chief in it. Very interesting how fantasy and games now preceed real life by only a few years and months.

Re:Biology is not just DNA (1)

bonabo (120263) | more than 13 years ago | (#344662)

Again, this is true...but don't forget that "recombining already existing technologies" can be pretty powerful and useful all by itself. (Heck, "recombining existing technologies" is, basically, a fundamental design principle of Unix-based systems, isn't it? I know MY Unix-based systems are extremely useful... I love my "|" key...)

The analogy doesn't hold well. The tools of biotech are very crude, like chopping away with bronze axes. It's not possible to modify organisms by mixing and matching the parts we understand in UNIX-style. Only a few genes can be modified in an organism, easily in bacteria and yeast, with difficulty in rodents and domestic animals, and hardly at all in humans.

A better analogy for the current state of biotech would be we can see the source code (by sequencing), we only understand a bit of the language (sometimes we can't tell the comments from the code, like obfuscated C), and we have the technology to cut-and-paste a statement or two within and between programs (recombinant DNA technology).

Jim Lund jiml@stanford.edu

Re:Open Source Humans (1)

spiro_killglance (121572) | more than 13 years ago | (#344663)

Sadly, our orignal wetware is quite good at producing personnel hell on its own.

What the hell is this all about? (1)

SpanishInquisition (127269) | more than 13 years ago | (#344664)

They're trying to clone a Spice Girl?
I don't understand.

P.S. If the technology is available, can I have Mel C (even tough she is no longer a Spice Girl)?
--

What is a SPICE (3)

gutier (129597) | more than 13 years ago | (#344665)


Apparently many people are not familiar with electronics.

SPICE is a program used in electrical engineering to simulate electrical circuits. As with any other simulation, it can be used to evaluate correctness, find logical and physical failures, test performance, find bottlenecks, verify timing properties, and other things.

Open sure, but GPL? (1)

iainl (136759) | more than 13 years ago | (#344666)

So does this mean that my grandparents can demand the modifications between their source and mine be made public? :)

Re:I'm very leery of this wrt Second Amendment rig (1)

iainl (136759) | more than 13 years ago | (#344667)

disclaimer: funny joke, so I'm not being serious here.

Anyway...

How does the bullet resistance matter when only one side isn't allowed bombs? ;)

Re:I'm very leery of this wrt Second Amendment rig (2)

clary (141424) | more than 13 years ago | (#344668)

get a bazooka, silly yank. drive over'em in your little M1A tank. whatever. just keep your barbarism that side of the pond. Because that's how most european countries view your stance on guns. You probably also don't like the police wearing bullet-proof vests, or driving cars faster than your 4WD gasguzzling SUV (which you probably never even USE off the road..) As for natural, god-given right to guns.. well.. ever seen jesus sporting an AK47?
First, I hope you realize the the original "pro-gun" poster was clearly trolling, and does not represent the average supporter of the right to keep and bear arms in the USA.

Come to think of it, I guess you are trolling too, so I shouldn't be answering...but I can't resist. ;-)

Anyway, if you think that being willing to use force to defend innocent life is barbaric, I pity you. Human beings have a natural (or God-given, if that is how you look at it) right to life. The right to life implies a right to defend that life. The right to defend life implies the right to possess effective tools for defense. Firearms are very effective tools for personal defense.

BTW, police wearing bullet-proof vests is very cool. I have four cops in the family. I want them to have the best chance possible to stay alive. I also don't mind them having fast cars, as long as they use good judgement when deciding to continue a high-speed chase. (I don't own an SUV, but am considering buying one, if only to piss off the Sierra Club!)

Finally, with regard to your dim view of us yanks: Bite me.

To quote Penny Arcade: (1)

Rabenwolf (155378) | more than 13 years ago | (#344669)

The submitter may be overstating the bit about "open source"

Maybe he was having some kind of /. seizure [penny-arcade.com] .

Re:In the end, Infantry rules the battlefield (1)

schulzdogg (165637) | more than 13 years ago | (#344670)

The entire history of weapons development is predicated on being able to sit your soldier in a particular area and "own it". Witness Vietnam, witness The Battle of Britian.

Read through memiors of any armed conflict and one sentiment that pops up over and over again (besides not wanting to die questioning importance of all this) is how much destruction you can rain down on an enemy and they will still live and fight on.

It's easier to get troops in and win if the enemy has been shelled to the point of exhaustion, but it still has to be done.

Besides, in a civil insurrection bombs are useless. How do you decide what to blow up? Everything you destroy brings people into the fold against you.

If this gets real.. (1)

AltGrendel (175092) | more than 13 years ago | (#344671)

..I want a copy of Malfena from Outlaw Star [animefu.com] .

Along with the ship itself, of course.

Re:What is a SPICE (1)

gus2000 (177737) | more than 13 years ago | (#344672)

Of course, from reading the DARPA blurb it would appear that the only thing that bioSPICE will share with "normal" SPICE is the acronym...

Hmm... (2)

Sir_Real (179104) | more than 13 years ago | (#344673)

Couldn't any human being claim prior art if this were to be patented?

Re:Hmm... (2)

DeadVulcan (182139) | more than 13 years ago | (#344674)

Couldn't any human being claim prior art if this were to be patented?

Only if you are an existentialist, and you claim to have invented yourself.

--

Re:What the hell is this all about? (2)

Erasmus Darwin (183180) | more than 13 years ago | (#344675)

They're trying to clone a Spice Girl? I don't understand.

SPICE [penzar.com] is a circuit simulator used by the EE types to design circuits.

What this is all about (2)

kstantfw (187237) | more than 13 years ago | (#344676)

As someone who is reasonably well conversant with this field (I've read many of the biological modelling papers, and heard Adam Arkin speak twice), I thought I would try and explain what's going on here. The DARPA call for proposals seems to contain two items - one on DNA computing and one on BioSPICE. As far as I can tell, they are two separate things. BioSPICE is an attempt to make a piece of software to model biological systems. It has everything you would expect: synthesis of RNA from DNA, translation of RNA into protein, chemical reactions, interactions, and so on. The goal is to use this software to model biological systems. The benefit of this is two-fold: one, you can test an existing biological system to see if the model agrees with the data; two you can use it to design new systems. However, the technology is very primitive. The only system that's beem modelled with any confidence is a piece of the phage lambda decision making circuitry (phage lambda is a virus that infects E. coli). There has also been some modelling of the cell cycle (the timing of DNA replication and cell division, but that was done more phenomenologically). As far as building novel biological circuits, this is still in its infancy: the only two things that have been built (both in the last two years) have been a flip-flop and an oscillator. So biology has a long way to go before it even gets to where electronic circuits were in the 40's.

Not OS (5)

bluesninja (192161) | more than 13 years ago | (#344677)

The submitter may be overstating the bit about "open source": the proposal says "All software developed as a part of the program will be open, in the sense that program performers and other DARPA authorized users will have the right to view, use, modify, and distribute code within the program authorized community

Whew. The last thing we want is a bunch of B10-5kr1pt k1dd135 running around h4x0ring the neibourhood pets...

/bluesninja

Re:Let's trade: Britney for Spice Girls (1)

nekid_singularity (196486) | more than 13 years ago | (#344678)

You really belive she is a virgin?!?! Well, then are you interested in purchasing the moon? I can give you an excellent deal!

Re:Open Source Humans (1)

Vuarnet (207505) | more than 13 years ago | (#344679)

I know it's a worst case scenerio, but imagine a future where normal, unmodified humans are considered to be an inferior waste product of the technological revolution.

I thought we already had those... we call them lawyers.
Tongue-tied and twisted, just an earth-bound misfit, I

Not truely Open sourced then? (2)

QwkHyenA (207573) | more than 13 years ago | (#344680)

It seems to me that alot of organizations/corporations enjoy using the buzz word 'OpenSource' when, in fact, it isn't!

As this article states 'Authorized' and 'licensed' too many times for me!

I can see it now, Microsoft has just now 'OpenSourced' Windows 2000. But only if you're stamped, approved, authorized, certified and licensed?

Reboot... (1)

fleeb_fantastique (208912) | more than 13 years ago | (#344681)

I'm having this uncomfortable feeling of Microsoft getting involved in some way.

"Abort, Retry, Fail..."

Gives 'Blue Screen Of Death' quite a different perspective, eh?

Re:Great. . . (1)

praedor (218403) | more than 13 years ago | (#344682)

I don't know what process is being used in the systems you mention but it is hardly necessary to destroy any DNA (or RNA for that matter) to get its information. There are several ways, off the top of my head, that information can be pulled from DNA without harming it: 1) plain, old sequencing. Been done for years. 2) Newer tech - DNA chip arrays. Analyze the florescence on the DNA chip vs your test DNA or RNA and you know its information content - no destruction necessary.

Beyond that, it is incredibly simple to produce limitless copies of any DNA or RNA you are interested in (PCR/RT-PCR, subcloning).

In any case, what does it matter if the nucleic acid is destroyed. Once you know its content, you can generate it again easily enough, though...what's the point of that?

I love PSPICE. (2)

AFCArchvile (221494) | more than 13 years ago | (#344683)

It saves so much time in calculating the voltages and currents in circuits. Also, you can make perfect circuit diagrams. The Windows demo of DesignLab (which uses SPICE) is here [bucknell.edu] ; it's limited to 50 components, but that's enough to make simple circuits. I don't know if there's a Linux version of the GUI though.

Sounds like! (1)

WinterSolstice (223271) | more than 13 years ago | (#344684)

This sure sounded like a cool way of moving forward with bio-computing. From the people who brought you the world's best 24 hour porn delivery system. (Just kidding)

I wonder if we will get plastic computers, biological computers, and organic displays that run Winblows? Will Windows 2098 (released, of course, in 2100) require a 3 liter PC to run? Will the install be done with a hypo? Coooool...

-WS

Re:Sounds like! (1)

WinterSolstice (223271) | more than 13 years ago | (#344685)

Best yet, when you get a virus, it actually requires Penicillin...

-WS

Wet-wired WAR! (1)

B14ckH013Sur4 (234255) | more than 13 years ago | (#344686)

So, when I get that PHAT new augmentation to my brain, with P2P and Tivo(TM) built in...
I'm running GNOME on it, cuz KDE sucks! I don't want to find out that Trolltech has changed back to proprietary control over Qt and owns my thoughts and memories!

Spice? (1)

Conspiracy_Of_Doves (236787) | more than 13 years ago | (#344687)

They're trying to genetically engineer drug-addicted starship navigators?
----------

Seen in Slashdot 2025... (1)

Seinfeld (243496) | more than 13 years ago | (#344688)

Features: The Open-Source Master Race
Posted by JonKatz [mailto] on Friday March 7, @09:12AM from the I'm-still-alive-and-ranting-dept.

All hail the race of geeks created through open-source BioTech! This new paradigm-shifting race of uber-geeks has blown the doors off our current mind-framework of what we thought humans were capable of...
(note from future- this article goes on for another 4200 words, basically saying that the world will be radically changed by biotech-made people who pretty much can't do anything else but play video games 30% better than non-biotech people. I'd post it all, but, you know, read one Katz article, you've read them all...)
-----------

Re:Hmm... (1)

Rosonowski (250492) | more than 13 years ago | (#344689)

Patents...Yeah.

They're great, but I don't think that the DoD will be getting one

This is something that the DoD is working on.

Karma...Police...
Arrest this man...
He talks in maths,
He buzzes like a fridge..

biological computers? (1)

SGDarkKnight (253157) | more than 13 years ago | (#344690)

i quickly skimmed over the story link and it seems that they are trying to develop a method of making a bio-computer (so to speak). -- " 1. Scalable DNA Computing 2. Compact, content addressable storage 3. Programmable, self-assembled 2-D and 3-D DNA nano-structures 4. Implementing computational elements and circuits that use in-vitro transcription and/or translation, and application demonstrations 5. Other related ideas with revolutionary promise" -- and not only a computer but an atrifically intelligent one at that -- "Second, the program aims to develop computational models, techniques, and tools, for in-silico analysis, capable of predicting cellular processes and their spatio-temporal behavior, which can also assist in developing control strategies. These include rapid prediction of the impact of external agents and environmental factors, and quick identification of targets and design of intervention mechanisms." -- now does this sound much like the human brain?

Nothing too earthshattering here.. (1)

Mercaptan (257186) | more than 13 years ago | (#344691)

It's just about the advances in DNA computing and a bunch of related cellular process simulation which accompanies it. Certainly having detailed cellular process simulators would be extremely useful in other branches of biology too. But this describes a computer that's made from biological compounds and has little to do with engineering existing organisms or animals.

Certainly the language describing biological components as computing hardware is fascinating. It leaves a lot of room to speculate about a cross-over between actual organisms and powerful DNA computing systems.

Re:What this is all about (1)

pabs3 (259410) | more than 13 years ago | (#344692)

>an attempt to make a piece of software to model biological systems
See bioinformatics.org (they use sourceforge) for more.
E-CELL is one http://bioinformatics.org/e-cell/

Close, but Jesus was Jewish (1)

typical geek (261980) | more than 13 years ago | (#344693)

Jesus prefers something more compact, like an Uzi or a Tek-9. ;P~

So he'd support the home team, and get an Isreali made weapon.

Galil for field work, an Uzi for urban work.

I don't know if he'd wear a T-shirt that sez

"Kill'em all and let me sort them out"

though.

In the end, Infantry rules the battlefield (1)

typical geek (261980) | more than 13 years ago | (#344694)

How does the bullet resistance matter when only one side isn't allowed bombs? ;)

Typical geek response, it sort of worked in a flat desert (Iraq), it's failing in Kosovo, and failed miserably in Vietnam.

In the end, it's the lowly infantryman with his or her rifle who controls the battlefield. You can bomb a country back to the stone age, but until you're willing to commit men to go into the rubble, you don't control the ground.

Replicants, anyone? (1)

gentlewizard (300741) | more than 13 years ago | (#344695)

This reminds me of my favorite scene in Blade Runner -- Harrison Ford is talking to a little old Chinese woman in Chinatown, who just happens to be operating a scanning electron microscope. So instead of the Playstation IX, will we all have hot biotech gear in our garages?

Re:Uggh, do American's want this? (1)

Bobo the Space Chimp (304349) | more than 13 years ago | (#344696)

At least this explains why we don't receive signals from other worlds. Everyone is biocomputerized and lives forever in a virtual world much more interesting than the real world, AND they don't want to contact any primitives until the primitives get to a virtual stage and won't try to do any silly adventuring.

Re:I'm very leery of this wrt Second Amendment rig (1)

Bobo the Space Chimp (304349) | more than 13 years ago | (#344697)

> But, if DARPA genetically engineers soldiers who are resistant to bullets

Ehh, that Soldier movie with Kurt Russel isn't looking like such a terrible movie anymore, is it? Huh? Huh?

Re:Making up words (1)

Bobo the Space Chimp (304349) | more than 13 years ago | (#344698)

"Hyperexponential"?

Dang, that's two levels above The Incredible Hulk's geometrically increasing strength when angry.

Re:Open Source Humans (1)

Bobo the Space Chimp (304349) | more than 13 years ago | (#344699)

> I know it's a worst case scenerio, but imagine a
> future where normal, unmodified humans are
> considered to be an inferior waste product

When? It's inevitable.

Cyberpunk novels make guesses about the technologies that will be out there, but even that's short-term, near-future (a few hunderd years or a few thousand at most.)

Expect to see "people", that is, "minds", existing completely independent of a physical body, and heavily modified with various database storage and auxiliary thinking modules, whatever.

No one will exist in a human-style body in a thousand years or less; it may end up being a nothing more than a quaint way to take a vacation from time to time. Even then, probably not, as things like sex could be much more erotic with all your relevent brain locations fired up to 100%. Heck, if they can lick the study of the subjective perceptual experience, imagine living in a virtual world where they multiply the feelings by 10, 100, 1000 times what is theoretically possible in a "real" body.

Would YOU want to go back to the real world?

We just have to make sure purely artificial thinking devices with no subjective perceptual experience are ever let loose to manage things with human goals in their minds.

Re:Open Source Humans (1)

Bobo the Space Chimp (304349) | more than 13 years ago | (#344700)

Anybody who doesn't want to live that way can continue in their current, vastly limited form. I have no problem with that; that is their business. I am no democrat, republican, or religious believer; I wouldn't force my views on them. Would you?

Re:I'm very leery of this wrt Second Amendment rig (1)

Glanz (306204) | more than 13 years ago | (#344701)

Try revolting with a pen instead of an AK47. And when the big THEY come to censor you, stick the pen in one of their all-seeing eyes. Yes dear macho gun tottin revolurevolutionary, you too can become one of the select few who simply drop out. When there's no-one left to participate in the madness, there will be no-one there to revolt against.... (I love prepositions at the end of sentences, a viable alternative to bullets at the end of lives)...

But will bio-computers run DOOM? (1)

Savage-Rabbit (308260) | more than 13 years ago | (#344702)

So in 30 years time when I visit my grandkids my grandson will drag me up to his room show me a cube full of green sludge and go:

See grandad that's my new PC! "Virtual Reality Doom 7" kicks ass on this baby! Lets do a deathmantch, Huh grandad! Pleeeease

Re:This was played out in a video game (1)

symplegades (310676) | more than 13 years ago | (#344703)

I don't remember the plot of Metal Gear Solid having anything to do with DNA-computing or modeling cellular processes. The soldiers, protagonist, and antagonist were the products of genetic-engineering... Engineering entire organisms and DNA computing/cellular modeling seem rather different to me, but I know very little about these things.

rene

Biology is not just DNA (4)

Ubi_NL (313657) | more than 13 years ago | (#344704)

just for your information
Rating the advances in biotechnology simply by looking at DNA sequencing improvements is not very smart..
We will not advance in understanding biology by simply looking at genes. That is like deciphering german ENIGMA codes, only to find out that you don't speak german. At the moment the advances are made in protein function (very difficult, and relatively slow progression).
Until we understand the *function* of the proteins that are derived from these genes, all biotechnology can do is recombine the already existing technologies.

Military (1)

lordmacmoose (319187) | more than 13 years ago | (#344705)

The fact that they are trying to do this is just a little disturbing. Maybe i'm just being paranoid, but i don't want ANYONE, much less anyone involved in our miltary, which serves as a model for narrow-mindednes and hypocrisy everywhere, playing with my biometrics the way i play with pcbs. Who do they think they are to be playing with biocircuitry?

Re:Open Source Humans (1)

UltraBot2K1 (320256) | more than 13 years ago | (#344706)

I don't think this is a good idea for mankind.

Humans have evolved into what we are over hundreds of millennia, and artificially tampering evolution could have potentially catastrophic consequences.

I know it's a worst case scenerio, but imagine a future where normal, unmodified humans are considered to be an inferior waste product of the technological revolution. Imagine a world where the richest members of society are genetically modified with superior DNA and circuitry, while those of us who choose to keep our existing god-given bodies are reviled and treated as second class citizens. Adolph Hitler experimented with similar body modifications in his quest for racial purity and superiority, and we all know the results of that little endeavor.

I think that technology is wonderful for the advancement of humanity, but it needs to be kept seperate from biology. We need to keep our bodies the way God and nature intended them to be, and cease this senseless quest for an Arian race. If we do not, the consequences could be catastrophic.

Re:I'm very leery of this wrt Second Amendment rig (1)

Chakat (320875) | more than 13 years ago | (#344707)

Relax, this is open source genome hacking. You simply take their modifications, add a few of your own tweaks to make your own super soldiers. Maybe give them some of those funky regenerative characteristics of a starfish so when they get blown apart they regenerate themselves, or the hearing capabilities of a dog so you can speak with at a frequency higher than the hearing range of "normal" humans. Or even make them hermaphrodites so you don't need to make two different types to have a sustainable population.

Of course, you do the last suggestion, I'm not responsible if you make them overly horny and have them take over humanity thanks to their exponential birth rates.

Re:Open Source Humans (1)

Chakat (320875) | more than 13 years ago | (#344708)

Hrmm...the millions of years of evolution that created human beings also caused species to become extinct. Think of the Neanderthal, Australopithicus, Smilodon, all of which once represented the pinnacle of evolution, and all of which became extinct. What makes you think humans are all that much different?

Biotechnnoloy ---OKAY (1)

Plasmagrid (322106) | more than 13 years ago | (#344709)

I was thinking of all this bio tech. and came to a conclusion. When your working at home for some major corporation and all of sudden your computer gets sick, Does the company hold you responsible. After all one would think Bio tech would be subceptible to virii as humans are. Any one have any thoughts about this.

DeCSS and my bodily fluids? (3)

carlcmc (322350) | more than 13 years ago | (#344710)

Just wait till you get sued by the RIAA et all for having a program in your bodily fluids that extracts and decrypts DVDs .... **** Court: You are hereby ordered to cease and desist any and all Semen production. Failure to do so will result ...

nanomachines (1)

secondharmonic (325641) | more than 13 years ago | (#344711)

Think about it. With this sort of development you can use the programs to deliver target drugs to specific areas in the body with accuracy. But it can also be used to program billions of little machines to destroy DNA. It is unfortunate that developments that can benefit mankind can also be used to attack it.

great understanding (1)

peaceofinfinite (411113) | more than 13 years ago | (#344712)

read How the Leopard Got its Spots - the author details this beautifully (chaos theory and biology hand in hand) when they start understanding and utilizing protein sequencing techniques, then we should be Gattaca-paranoid.

Mr. T can hack humans! (1)

MrsMcCheese (411321) | more than 13 years ago | (#344713)

I was having a little jibba-jabba with Mr. T the other day. He said, "Oh, I hack humans with the best of 'em! And I pity the fool who don't!" JIBBBBBBBAAA-JABBBBBBBBBA Lovingly yours, Mrs. McCheese

Re:Mr. T can hack humans! (1)

MrsMcCheese (411321) | more than 13 years ago | (#344714)

This gal knows what she's talking about! If I wasn't the same person who posted, I'd say it was monkey trash but since I am, I love it! Sincerly your, Mr. T

Re:What this is all about (1)

NearTheSea (411461) | more than 13 years ago | (#344715)

When you say "the only system that's been modeled with any confidence", I'll assume you are talking about Arkin's work. There's a good bit of work going on this area. And not all of it is academic. There are companies building systems to model cells, tissues, diseases, etc. The goal is to help pharma companies come up with better drugs and spend less money doing it (e.g., fewer failed drugs, dead ends).

Re:Close, but Jesus was Jewish (1)

bnUW (411498) | more than 13 years ago | (#344716)

"Oh God, please protect me from your followers... amen"
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