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Photoshop for DNA
pafischer writes "Forbes is reporting on a Biotech startup company trying to make DNA manipulation as easy as Photoshop. From the article: 'The goal is to move from having to merely tweak the proteins that are used as biotech drugs to being able to design them, even taking material from multiple organisms and using them to create new, functional genes.'"
Judging from the quality of some of the Photoshopped images I've seen out there, I really don't want to see what people will create with this...
I'll turn into a supernova and burn up everything. Well I'll turn into a black little hole and you'll turn into string.
if this is true then they're probably gonna need this neat photoshop plugin i just found...
s hop_Tutorials&file=dna
Plugin name: DNA (deoxyribose nucleic acid): "The genetic material of inheritance, undoubtedly has the most well-known molecular structure of all time. This tutorial describes how to make it."
http://www.nextdesigns.net/modules.php?name=Photo
I say genetics -- just like typography -- should be left for those to do who know what they're doing.
Sorry ... sorry ...
I'm thinking about it, therefore I might be.
Ultra-Sharp-Teeth Plugin
Breathe Underwater Plugin
Bigger Breasts Plugin
Jolyon
Please read my Canon EOS tech blog at http://www.everyothershot.com
that those tards at fark don't get ahold of this program.
Since when?
Mark me as a FOB (Fan of Bill), but kudos to him and his foundation for their contribution to science....
They do compare the advance in genetic manipulation to the difference between editing with Wite-Out and editing with a word processor, but that's what we call an analogy. They're not claiming that producing genes would be something anyone with no training can do with their home computer.
Don't blame me; I'm never given mod points.
That'd be even worse -- MSPaint for DNA... *shudder*
I'll turn into a supernova and burn up everything. Well I'll turn into a black little hole and you'll turn into string.
So this is how they framed OJ with all that DNA "evidence".
I thought, "what do multiple orgasms have to do with DNA research?"
sigs, as if you care.
How about making it as easy as Gimp instead. I like the interface better.
*Ducks*
I wonder what happens when you put a LENS FLARE in the genes of a dog... or a LENS FLARE in the genes of a camel... or a LENS FLARE...
We'll make a GIMP for DNA, and rule the world! It'll run on more platforms too: all variants of primates, birds, farm animals, and Slashdot nerds. :)
"multiple organisms"
I almost had a blockbusters moment there...
What a suprise they removed the dumbass human-check. a-holes. Finished reading "Dumb ideas for dummies" have you?
#hostfile 0.0.0.0 primidi.com 0.0.0.0 www.primidi.com 0.0.0.0 radio.weblogs.com
designer genes.
try { do() || do_not(); } catch (JediException err) { yoda(err); }
DNA manipulation as easy as Photoshop Have these peoples even tried Photoshop recently?
Mark me as a FOB (Fan of Bill), but kudos to him and his foundation for their contribution to science...
Of course, he has a motive. He's donating money to help develop a user-friendly gene manipulation tool in hopes that it will cut into the market of the Open Source gene manipulation. Then, when people become dependent on the new gene manipulation, Microsoft will buy the company and merge it with their next version of windows, leaving geeks as the only ones doing gene manipulation the old way (by hand at the console). It always the same with that guy.
The previous comment is purposely vague and generalized, but all of the facts are completely true.
Silly, everyone know DNA can't be created, it has to evolve. Otherwise we would have proof of organisms with intelligent design.
Torres was trying to remove the brow ridges from her fetus using something like that.
Um, let me get this straight... Bigger Breasts and Sharper teeth? What were you thinking?!?!
If they come up with Frontpage for DNA, I just might become an investor. I'm also moving to another planet just to be safe. What is the DNA equivalent to the blink tag?
now every person, animal, and plant will have a lens flare
They are writing a program to compute the results of manipulating genes. How does that relate to photoshop, other than there will probably be a picture you edit using your mouse. That is like saying Autocad and Photoshop are the same since you are creating pretty pictures in both.
If they pull this off, it has way more to do with biology and math than the interface they use. Not to mention that even if this application simulates gene manipulation, they will still have to do the same thing by hand to test it. It's not like it can remove the actual testing of the end result.
/. ++
I can't begin to imagine the DNAShop contests that will happen on Fark or Something Awful...
Trolls lurk everywhere. Mod them down.
onslaught of fake nude DNA ensues.
:::: the insomniac's digest
...Imagine if you could photochop your DNA.
X-ray vision here I come!!!
And as OS races to catch up with this new Photoshop feature can you imagine some of the freaks that will be created at people struggle with the GIMPs interface. Now I understand why they called it gimp.
Do not try to read the dupe, thats impossible. Instead, only try to realize the truth
What truth?
There is no dupe
I thought, "what do multiple orgasms have to do with DNA research?"
Oh that's easy.
Every woman will have not one G-spot but four, one of which will be at the back of the throat.
Every man will have a unit built from horse DNA.
And don't forget, everyone will be multi orgasmic!
Reinforced back muscles to support the standard DD chest. (That's the small model)
And of course, everyone will have a FANTASTIC rump.
And then King George W Bush will get wind of this and have everyone's DNA rewritten to be more moral. All pleasure will be taken out of sex, women will be programmed to be subservient to their husbands and submission to authority will be enhanced to the point where average citizens will shoot themselves in the head if anyone in uniform asks them to do so.
And the Conservative Christian utopia will come to be.
"Live Free or Die." Don't like it? Then keep out of the USA
Wake me when they've got it so it's as easy as Blender.
Pulp Audio Weekly - Geek News and Reviews
For all Microsoft's unethical business behaviour, that foundation does a hell of a lot of good, and Bill should be given credit for it. He's far more generous than a lot of the super-rich.
Me (Blog)
A lot of people have photoshop... doesn't mean they know how to use it properly!
Designing DNA to create a given protein is no big deal. The hardest problem is figuring out how the new gene/protein will act inside the organism. Biological systems don't have a nice layered OSI model for what connects to what -- its like nearly everything is a global-accessible variable so side-effects are a real problem. New drugs require huge amounts of R&D in the testing phase, not the synthesis phase.
I'd be more impressed if someone created an accurate in silico system for testing new drugs, rather than just designing new DNA sequences that MIGHT make useful new proteins that MIGHT make a useful new drug.
Two wrongs don't make a right, but three lefts do.
D is for DNA.
Pig and Elephant DNA just won't splice.
Other than being a computer application in which you can "do things" the choice of Photoshop as the analogous software tool seems to be picked entirely at random, and a lazy choice.
A more appropriate pick would probably been from under the CAD umbrella, or string manipulation tools like lex.
Hell, maybe even:
vi dna.txt
I don't mean the shape and colour, but the ability to grow lost tooth over and over again...
When I asked about this idea my dentist, he did not think that it would be such a good idea... for him, personally - of course.
Is editing genes something we want to make easier? I shudder to think of do-it-yourself genetic engineering kits.
DNA is a linear arramgnement of 4 letters - the bases A T G C. A molecule of DNA has some particular arrangement of the letters. E.g., an "8mer" molecule would be AGCTTCGC (there are 8^4 possible 8mers)
typically you need ~ 1,000 - 100,000 letters in a molecule to get bio function
right now, conventional synthesis, completely in vitro, from many companies (eg, www.idtdna.com; www.biosearchtech.com, etc) will make molecules with up to ~ 100 bases, so you need some subsequent set of (tedious manual) operations to put the "100 mers" together into bio active 1,000 mers.
So, if you could synthesize in vitro a 1,000 mer direrctly, you would save some time.
Very similar to being able to put results from multiple programs into a layout program - the ability to do a lot of things in a uniform enviroment saves tedious manual layout, where you have to manually assemble the word processor output with the pictures and graphics.
The market for synthetic DNA is known, so this is really an engineering problem, how to automate and roboticize a known chemical engineering process.
NOthing whatsoever to do with software, and the photoshop analogy sucks
Gals, with GTA:DNA, you can walk up to a sexy celebrity starlet and, well, actually, all you can do is find out what they really look like under all that make up, plastic surgery, silicone, botox and advanced composite materials. Sorry.
Reserve your copy now! Will be available sometime after Longhorn is released.
I'll wait for the "Easy as GNU/Gimp or GNU/KolourPaint".
Flexible bare-metal recovery for Linux/UNIX
I agree that genes should be left for geneticists, but when your compiler, debugger, and emmulator/simulator check for bad or even icky results, it might actually be fun to toy with genes, in an neat visual way.
At least, I have fantasies about modifying vegetables, fruits, and bugs. I expect that wasps can be reengineered to produce complete reams of laser printer paper, even with a sealed paper wrapper. I expect that ants or cockroaches could be modified to clean your house, better than they do. I expect bacteria or other small folded shapes can be reengineered to spit-out carbon nanotubes, construct simple buildings, or eat trash and grow fuel-cell cartridges.
All this hinges on us being able to effectively "file/print" DNA molecules. It's fun to watch technology accelerate, I am one excited geek.
Zhrodague.net - I do projects and stuff too.
In fact, a friend of mine did two major variants just this quarter at the Baker labs down the hall, one with a luminescent rocker switch and one with a ligand-activated toggle.
Just making it all pretty doesn't mean you know what it will do. It's more important to understand how it will work and how the whole chain will be impacted than it does being able to just visualize it.
-- Tigger warning: This post may contain tiggers! --
but would it be able to create a droplet for star destroyers or death stars?
Hate to say it, but this sounds like a pipedream. They want to 'take the proteins and tweak them' an dthen have a computer program spit out the DNA required to make that protein.
Well whoop-de-do. I'd like to make a computer that can generate wormholes. Doesn't mean it's going to happen.
Firstly, protein modelling is notoriously complex. Remember folding@home? http://folding.stanford.edu/
That's right - hundreds of thousands of computers cracking the problem of 12 amino acid chains. That's an oligopeptide, sort of like a 'protein lite'. Real proteins are hundreds to thousands of amino acids long.
IBM's Blue Gene supercomputers were even specifically designed with protein folding simulations in mind - read http://www.research.ibm.com/bluegene/.
So this company seems to be doing the following
1 Come up with nifty, but blindingly obvious, idea
2 Crack the age-old problem of accurately simulating protein folding
3 Profit!!!
It's just that step one is literally so obvious that you could ask a kid. And step 2 is so notoriously complex that I don't expect this company to amount to anything more than a plughole for research grants.
-Nano.
There is a better parallel with CAD programs than, with art design tools like Photoshop.
A better even better parallel could be with languages and toolkits.
Consider DNA as a binary code
Consider RNA memory access lines
Consider Ribosomes as the processing units.
Let"s add a DNA code assembler and a high level language to design the DNA code, access protocols and interactions vith chemicals input / output.
Use real cells as factory or use nanotechnology.
Léa Gris
Microsoft DNA editor.
Brrrrrr..... So scarry... All these blue creatures.
I see no possible way how this could lead to trouble. Michael Chrichton will get three or four books outta this one!
the preceding comment is my own and in no way reflects the opinion of the Joint Chiefs of Staff
Mark me as a FOB (Fan of Bill)
Usually people say "Friend of Bill".
Are you kidding? This has been shipping with the default load of MovieOS for YEARS!
Bill Gates uses "charity" donations as a marketing tool.
Remember those "computer for classroooms" "charity" writeoffs?
If the average Joe tried to "give" money to an organization that turned around and gave it back to him and then he wrote it off as charity, then he'd be in a federal "pound them in the ass" prison.
Taxes truly are for the little people.
He's dead man, what an insensitive gift. He needs like, reanimator, or something.
OSGGFG - Open Source Gamers Guide to Free Games
...I get to make that chrome-effect frog I've always wanted. Cool!!!
I own the rights to the "forever-perky breasts" gene sequence. In lieu of a cash royalties, I am willing to negotiate other forms of payment from all persons posessing this gene.
I don't know...a lot of the super-super rich are very generous.
It's been that way since the first super-super rich.
Ever heard of Carnagie Melon university? Or Carnagie hall? Vanderbilt? And yet these men were called robber barons.
The list of generous donations goes on and on for the super-rich.
It's still not as big a sacrifice as me donating $5 to a local charity.
Also, does the good they do outweigh the harm they do to society? Doubtful. It's equally doubtful for most super-rich men. I think it's a way to ease their conscience about all the horrible things they've done.
Mod me down and I will become more powerful than you can possibly imagine!
Now I can photoshop my dreamgirl *for real*
I think we can keep recursing like this until someone returns 1
...not PhotoShop for DNA.
We must be alert to the danger that public policy could become captive to a scientific-technological elite. - Eisenhower
"I don't know what it is, but it's DNA spells out my name."
You can MAKE the celbrity yourself! For your very own :)
Also, does the good they do outweigh the harm they do to society? Doubtful. It's equally doubtful for most super-rich men. I think it's a way to ease their conscience about all the horrible things they've done.
I'd be interested to hear how you think Microsoft's antitrust violations are more significant than the hundreds of millions of dollars the B&M Gates foundation donates to AIDS research, education, health initiatives, and technology.
I mean, I'm sure you hate Bill with a passion, but the causes that he donates to are FAR more important than some piddling software rivalries.
Also, it concerns me when people who donate are accused of "just easing their conscience". We should be grateful for every dollar donated to these causes. Attributing generosity to ulterior motives simply adds another barrier to future donations. We should encourage philanthropy, not punish it with unsubstantiated accusations of emotional instability.
I hope no one gets blurred...
Being funny is my sig nature.
in the hands of the wrong person, this allows any idiot to design a better plague. Why do people always see these things in the light of how it will be GOOD and never the downside. Do we really need easier bioterrorism?
Also, it concerns me when people who donate are accused of "just easing their conscience". We should be grateful for every dollar donated to these causes. Attributing generosity to ulterior motives simply adds another barrier to future donations. We should encourage philanthropy, not punish it with unsubstantiated accusations of emotional instability.
====
In that case, I wouldnt venture out in the real world if I was you. Most business magazines always cover topics such as how to maximize your generosity so as to better reflect on your organization and the first rule is kids and the infirm. Old people give the least value for the buck because no one cares if an old person is sick and in pain. It doesnt maximize enough publicity.
Its a business decision pure and simple. It depends on people like you saying "Well, Mikey D cant be that bad, they do have the Ronald Manor for kids."
Of course, believing PR is ingrained in the US psyche as any political campaign will prove.
Im pretty sure Georges Bush has given money for some sick orphans somewhere, so I guess it makes him alright.
and they keep trying to kill off BSD!
The first thing I thought of is how this might affect DNA used in criminal cases. If it becomes simple to manipulate DNA, would it be possible for a forensic analyst to, say, grease the wheels a bit on finding the "right" DNA on a particular item? It seems that if the DNA on an object were manipulated to mirror another's DNA, the switch wouldn't be so easily traceable. Then again, the analyist could always clean the item and tamper with it in a variety of other ways too.
Great, now I can be one of those deep-sea fangly fish with a party deck on the back ... or Sterance.
[Insert pithy quote here]
You're missing the point. A dollar to AIDS research is a dollar to AIDS research, *whatever* the reasons for donating. There is nothing to be gained by criticizing the wealthiest donors.
In the "real world", which you so kindly reminded me of, there is also such a concept as "pragmatism".
Well, so much for my webcomics character at other devices keeping above the curve of science....that software sounds very like the "lifeloom" described, or even the "metamother". Oh, well. It was inevitable that someone sooner or later would build an easier interface to do genetic manipulation.---Al
MINDMISTRESS ---the greatest super
I, for one, welcome our new bioengineered Pikachu Overlords!
The Island of Dr Moreau.... (ouch) http://www.imdb.com/title/tt0116654/
sig goes here!
Thank goodness for the Edit/Undo button.
Also, does the good they do outweigh the harm they do to society? Doubtful. It's equally doubtful for most super-rich men. I think it's a way to ease their conscience about all the horrible things they've done.
Yeah, because shady business practices are so much worse than fucking cancer.
You're being such a fucking child when you assume that a person has to do "horrible things" in order to get rich; that greed is the only motivator for wealth, and that guilt is the only motivator for charity.
Now we can look forward to FARK Gene Manipulation contests. How will they link the NSFW entries?
This could be interesting and scary at the same time.
But wait, we've already grafted human brain cells in to mice (Pinky & the Brain anyone?) and I have to wonder what new horrors this will bring up.
Sure, we've sequenced the genes but we don't know what a vast majority of them actually do. That actual process will take years.
But on the flip side - we've been hybridizing for hundreds of years. Just look what new and exciting fruits we've obtained through cross polenation.
Now imagine what new and exciting human fruits we'll creat.
Your honor, members of the jury. My client intends to prove that shortly after being conceived his father, client senior, willfully and and with maliciously intent applied the "smudge" and "fade" tools to various parts of my client's defenseless DNA. Client senior's lawyers will try to dazzle you with science and tell you that client senior used the "clone" tool to remove unsightly blemishes. It's a nice story, but there's no proof. In fact the only concrete evidence is the telltale watermarks left by the Genoshop software. Members of the jury, once you have reviewed the evidence I am certain you will find client senior guilty on all counts of first degree geomanipulation, unlicensed use of a Sony Mark III resequencer, and theft of two copies of Genoshop 4.1. Thank you."
...It's funny but I hope it gets modded insightful.
Hate to say it, but this sounds like a pipedream. They want to 'take the proteins and tweak them' an dthen have a computer program spit out the DNA required to make that protein.
Well whoop-de-do. I'd like to make a computer that can generate wormholes. Doesn't mean it's going to happen.
Can't promise much in the way of wormholes, but Homme Hellinga and David Baker's groups already make software for protein design.
Synthetic biology's been around for a while (see also e.g. Adam Arkin). This is just Drew's startup getting column inches in Forbes, and then getting eagerly lapped up by Zonk, as far as I can see.
We certainly don't call any of our clients 'The Meat', or 'Pork Chop #1'. That's just tabloid nonsense. And while we're skewering misconceptions, the job isn't as glamorous as you might think. Although I go to club and restaurant openings, film premières, first nights, fashion shows and stay in first-class hotels all around the world, I'm not there to enjoy myself. I'm there to prevent any live cells from my clients' bodies falling into the hands of meatleggers.
Currently, it's easy to 1) amplify large chunks of DNA verbatim and 2) change individual nucleotides. What is difficult is making large blocks of novel or heavily modified sequence, as it's expensive or impossible to synthesize them from nucleotides. Codon Devices seems to have a way to generate large chunks of customized sequence.
This is certainly on its way, whether from Codon Devices or elsewhere. See e.g. this paper by George Church et al on using microfluidics for DNA synthesis.
BTW, it's not currently impossible to synthesize DNA, just obscenely expensive at $1.45 per nucleotide.
--pete
Now can have real live Ackbar's running around yelling "It's a trap!"
DNAhack.Com is the website for amateur genetic engineering. This would be great for that!
"Michael Jackson is trying to look like a Mormon"
OK, I must have missed something here.
I've seen Jackson, and seen lots of Mormons (of various colors/races/countries/ages/languages), and don't see the connection.
Unless all they plan to produce is pretty pictures of DNA... I wonder if it will incorporate the physical and chemical properties of the agents or will they just be able to string together whatever sequences they want?
They also donate to Planned Parenthood (aka Ku Klux Klan).
Luke-Jr
nt
Perhaps the best euphemism since "left-handed mousing." ROFLMAO.
Welcome to the Panopticon. Used to be a prison, now it's your home.
Woman definately need an alpha channel that we can switch on and off!
This will greatly increase simple molecular cloning in the lab. My co-op student in a microbiology lab is currently spending weeks trying to do the PCR, subcloning, transformations, mutagenesis and sequencing before she can make her fusion protein. To custom order an expression vector with our choice of promoter, tags, selection marker etc would completely change basic scientific biological research. For example this would have impact on anyone who clones proteins (Biochemistry, Microbiology, Immunology, Molecular Biology, Genetics, Physiology and Cell Biology and there are probably more that I can't think of right now).
After simple cloning you can look at engineering metabolic pathways, engineering novel proteins, engineering protein expression networks. etc. etc. etc.
The difficulty right now is that we can synthesize DNA fragments easily up to about 100 nucleotides (and IANAS (I am not a synthesis person) so I am making what I think is an optimistic guess - ordering oligos up to 50 nucleotides is pretty standard). A current small expression vector is 2000 base pairs (pairs of nucelotides). I wonder what their technological leap is (or is going to be). The article is short on details and just says synthesis details are published in Nature (no reference).
It should have read:
Vapor: Fishing for Publicity
The grant from Gates was *not* given to the company mentioned in the article. It was to a different company (Amyris) that happens to share a founder. Amyris will use the money to try to develop a cheaper source of a naturally occurring antimalarial compound (artemisinin).
I use a 3,221,225,472 x 4 super-wide screen Trinitron when I'm editing my own DNA.
Blancmange
the goat man was created c. 1998, thanks to a top secret project just like this that went ary!
stop!!
You make toying with genes sound like fun. But this field is rife with potential for bad unforseen consequences.
Suppose somebody designs a breed of dog that can run twice as fast as a greyhound. Thousands of the cute critters are bred, but it turns out that this breed also invariably develops severe osteoarthritis at three years of age. A great deal of suffering has just resulted from somebody's "toying".
Things get worse when you start to mix in human genes. At what point should you start to accord human rights to the creature -- when its genome is 5% human? 50%? 90%? 95%?
What kind of suffering have you created when an organism that's 70% human wants to interact with us "real" humans and finds itself at a disadvantage...
Treated like a pariah by the pure humans.
Or confused by a hybrid sex drive.
Or cursed with a feline desire to kill smaller mammals.
Or endowed with slightly superhuman abilities like the ability to jump 30 feet, yet barred from the track meet.
Or reeking of skunk musk.
Or able to comprehend but not speak.
Or consumed by dark thoughts, because she's the only one of her kind.
That that is is that that that that is not is not.
It gives a whole new meaning to the term "to photoshop a moustache on a woman's face".
--
Mad science! Robots! Underwear! Cute girls! Full comic online! http://www.girlgeniusonline.com/
Like most advances in biotechnology, "any idiot" has no hope of using the technique (whatever the hell it actually is). Heck, half the molecular biologists out there will be incapable of using it properly if it's anything like other research tools.
And one more thing... this is all expensive. Very, very expensive. Even a basic (and I mean BASIC, as in you could maybe do three experiments) molecular bio lab starts at many tens of thousands of dollars. That's with teaching grade supplies and equipment, not real research quality stuff. Nobody's making the next plague in their basement even with this technique (whatever the hell it actually is).
Freedom: "I won't!"
Four quick comments:
(1) I don't think that we really know how to engineer biology yet. Progress at the moment is taking the form of adapting (stealing?) past lessons from other engineering disciplines, from when they got started back in the "good old days," and seeing if they are worth a damn in biology. Ideas like (i) standardization, (ii) abstraction, and (iii) decoupling. We've got a lot of work to do. Help. Check out the Registry of Standard Biological Parts as one place to get started.
(2) I'm really freaked out by the idea that we might see a "microsoft equivalent" developing in biological engineering. Imagine if our wheat in the year 2050 is running the equivalent of Windows95. That seems like a "bad idea." Please see comment (4) below.
(3) I'm also concerned by the possible, future mis-application of biological technology. But, I think that the only way to deal with this problem is to (i) expect that it will, at some point in time, happen, and (ii) make sure that there are many, many, many more people who understand what is going on and who can work together to fix the problems. Mitigation of future biological risk feels like solving problems related to the security of an open distributed network. Imagine if I told you that nobody was going to write computer viruses and not to worry about network security. The same thing is going to become true in biology, we just have to make sure that the numbers of folks who are disposed to cause harm are very small relative to the numbers of folks who are empowered and want to be constructive. See this PDF for more thoughts on this topic (apologies if it seems a bit abstract).
(4) We (some folks at MIT and all over) are starting a not-for-profit called the BioBricks Foundation (BBF) to help promote the development of open biotechnology. Here's the current plan (very early). Please help if you want (or by a T-shirt when they are ready)! I'm donating all stock/income that I might receive from working with Codon to the BBF.
Thanks/take it easy!
Drew
Prof. Church synthesizes long DNA sequences with remarkable fidelity by using parallel synthesis and amplification on a gene chip (ordered array of shorter DNA sequences). Paper.
Remember last year when researchers created polio virus from scratch? Paper. It took 3 years to make the 7500 bp genome -- this new technology would make this kind of project easier.
Your water is dangerous too! Do you have filters on your water tap? I drink straight from the tap.
Hell, if I could find out which GM foods were, I'd like to try 'em. Who cares if it's a bigger tomato, and is perhaps jucier and more tasty? I do, and that's what I think I want in a tomato, not a dinky little spotted nasty rotted thing -- which is what I see alot as an excuse for a natural tomato.
Selective breeding has been going on for longer than I care to speculate. And how bad is that? A bigger, tastier, insect-resistant tomato?
Zhrodague.net - I do projects and stuff too.