Slashdot Mirror
Online Artificial Gene Design
massivefoot writes to tell us New Scientist is reporting that researchers at Johns Hopkins University School of Medicine have released a new software suite, GeneDesign, that helps to simplify the steps in designing artificial DNA. From the article: "These key steps include translating proteins and amino acids - the building blocks which make proteins - backwards into a DNA sequence. Or the software can manipulate simulated DNA "codons" which can code for an amino acid. DNA codons are made of sets of three nucleotides - the fundamental molecules which link together to form a DNA chain."
SimGene?
So we put controls in place. That doesn't mean a rouge country with an axe to grind will. North Korean killer virus anyone? Replace "North Korean" with the rouge country of your choice.
Here is a link to GeneDesign: http://slam.bs.jhmi.edu/gd/
Now with animal hybrid OCX components.
I think you mean "rogue" countries ;-) "Rouge" is the red makeup women put on their cheeks. ("Whores use rouge. Ladies pinch...")
Does anyone know if they plan to release the source code? Indeed, it could prove to be a very useful resource to students studying bioinformatics, or other fields that combine biology and computer science.
Cyric Zndovzny at your service.
So who is going to sue me when I design a gene to make Avastin and Herceptin? This will be the real test of our obsolete intellectual property regime, when the medical establishment's equivalent of the RIAA/MPAA sues cancer patients for synthesizing their own drugs, like the music industry is now suing your neighbor's kids.
it's a blue bright blue Saturday hey hey
The article discusses how much of the software available today lacks safety checks on the DNA sequences that are produced.
That's really not much different than what we have with many programming langauges today. While most widely used C and C++ compilers today do offer numerous helpful compilation warnings, little is done to verify the safety of the emitted code. Many of the security problems we're dealing with today are due to buffer overflows, and other matters such as that.
It is often quite expensive to ensure software safety, be it when dealing with programming language compilers or DNA "compilers". Indeed, more study will be necessary to determine what a feasible trade off between the two is.
Cyric Zndovzny at your service.
Hmm, is that a serious threat though? You would need a quite competent biotech programme to produce biological weapons, and, frankly, with the state North Korea's in I doubt that they have such facilities.
Besides, with their current suspected nuclear capability, would biological weapons really be that great an advantage? Remember the DPRK regime's main concern is warding off an invasion by the US, and in such a situation a nuclear weapon is a far greater threat than any biological capability.
Ooo man the floppy drive is broken. No wait. The computer is just upside down.
North Korea's in I doubt that they have such facilities. Like I said, substitute your favorite rogue (how's that mrpeebles ^_^) nation. Any country that lacks the expertise but has the will will eventually obtain the tech. How about a biological AQ Kahn network?
The market will be overtaken by Microsoft Visual DNA++ in around five years.
With spending like this, exactly what are "conservatives" conserving?
Although it is mainly protein oriented, there are several molecular tools available at ExPASy that I use a lot.
Also, VectorNTI is now free if you join their user group. It's a really powerful suite for plasmid design and molecular analysis.
A small selection of my favourite rogue countries, in slightly random ascending order (just to build the suspense):
France
UK
Italy
China
Israel
Palestine
Nepal
USA
Iran
Syria
North Korea
Atlantis
...a simplified version of the human genome. Add encryption, data compression, and error correction, and it would be a good plot for a movie.
I suffer, i would say, from duchenne, the first decease dicovered by dna sequencing.
This causes muscle loss, and starts at early adolecence and ends in death between 20 an 30 years of age.
I'am currently 24 and hoping for a cure.
Keep going
What exactly is the exciting news here? This type of software has been around for many, many years. Analyzing a gene sequence to determine restriction enzyme sites, or optimizing codon usage for efficient heterologous expression is absolutely routine, and is performed even in undergraduate level molecular biology courses. It's laughable that the ability of this software to "...manipulate simulated DNA 'codons' which can code for an amino acid" is being touted as an advance.
I can't even believe that New Scientist is reporting this, let alone Slashdot. There must be at least 100 other tools which perform the same functions, many of which are free (both as in beer and source code).
rouge as in french for red? like urss, china and canada?
didnt know north korea was red too
What I don't understand is why everyone's making a big fuss over this... This kind of stuff is taught in HIGH SCHOOL. Only reason why I didn't make one myself is because I thought it was trivial otherwise.
I think the real thing that bothers me is, why is the biology field so devoid of computer people?! Btw, I am a Hopkins student who's doing Neuroscience major/CS minor.
Based on what I saw in the article, there's nothing this DNA does that hasn't been available in any number of DNA sequence manipulation suites for the last 10 years. 'Reverse translation', constructing a DNA sequence that could be transcribed and translated into actual protein is the sort of thing you might see in an undergraduate genetics homework assignment. Higher throughput versions, akin to what this article is describing, perhaps a masters level bioinformatics project. As to 'protecting' against potential evil-doers ordering proteins of mass destruction, viruses are quite a bit more complicated than proteins. Anyone who needs to order their custom gene from somebody else is not likely to be decades ahead of state of the art infectious disease researchers who, to the best of my knowledge, have been unable to generate a de novo infectious agent. Honestly, these algorithms have been around for quite some time.
At first blush, GeneDesign 2.0 offers nothing over the long-available, free, web-based or local-mirrorable Sequence Manipulation Suite 2 at http://bioinformatics.org/sms2/. When I start on a molecular bio project, I use a mix of SMS2, BLAST, NEB cutter, IDT's web-tools, and other free online tools to accomplish everything I need, and keep track of my thought process in a simple Word document. This suite adds no functionality I don't have free access to already elsewhere.
Not only is the innovation of the software insignificant, but the implementation is certainly lacking. It doesn't even do +1, +2, +3, -1, -2, -3 analysis for finding open reading frames.
This is non-news. And what's especially funny is that most of the commenters here on Slashdot have no idea what this software does, and they shoot their uneducated, ignorant opinions into the whole issue.
I am defenseless. Use your button. Mod me down with all of your hatred.
Frankenstein built via wiki-style callaboration. A troll adds two dicks, somebody removes one, but the troll adds it back again...
Table-ized A.I.
This is ok in it's limited way, but since it doesn't let you predict tertiary structure you can't use it to build anything cool, like a life form.
it is still beta.
There have been innumerable bioinformatics sites put up over the years by various institutions, but they've never been examples of refined usability. You could say that is because the focus has been on the underlying tools and not the interface.
Despite being highly educated and working alongside a great deal of computational effort, biologists in general are not anymore computer literate that your average office worker. Much of the computational side has been taken up by computer literate Mathematicians, Physicists and Comp. Scientists. Those that can bring together a multitude of tools (often rudimentary academia quality software) to solve a problem through programming, find many of their collegues cannot or will not do the same. The older generation directing the labs then ask those that can to design sites to provide tools for the illiterate but as is the case in research, these static tools generally do not provide the necessary power or flexibility. Many efforts end up being ignored in favour of simply casing down the programmer in question.
Ultimately, the best solution is to teach programming to biologists as a core subject. Our old categorization of the sciences is out-moded.
As far as I can tell from the description this application implements this piece of Haskell code:
/. and sell it for $20,000 a pop.
code [] = []
code ("Phe":s) = "UUU":code s
code ("Leu":s) = "UUA":code s
. . .
code ("Gly":s) = "GGU":code s
I've left out about 20 lines because I don't want to give it away when I could advertise in on
"The White House is not an intelligence-gathering agency," -- Scott McClellan, Whitehouse spokesman.
We all went about our business knowing the world was going to end some day but not really sure how or when. All the fear, the paranoia about nukes, religous zealots and in the end it was some grad student dicking around making protein sequences online. He designed a super virus, just to see if he could do it, not really intending to actually manufacture it. Then there was a mix up at the lab....
That's our life, the big wheel of shit. - The Fat Man, Blue Tango Salvage
c'mon everyone knows that robot love slaves are lower maintenance. and getting to pick the hardware out yourself is so much nicer than hoping a vat of tissue in an incubartor will not mutate on you, or develop free will.
They already have....
Ex nihilo nihil fit.
I'm somehow expecting Bush's next State of the Union address to mention how he's suing the creators of this for infringing the intellectual copyrights of God. I can imagine it now, the right rising up as 'Pro-Closed-Source'.
Of course, somebody will use it to design a virus.
I can't believe I was the first to say it.
I don't care if it was cheesy, I just couldn't resist.
Nam et ipsa scientia potestas est - Sir Francis Bacon
If you look at the link location, the "design a gene" link points to the "reverse translate" program. This could be why the program doesn't look that interesting. Anywone want to try finding the right program on their server?
-Aaron Redaphid
Well the parent did mention North Korea. That would be a communist country. Sounds pretty 'rouge' (red) to me.
I am not sure why simply because it is about one of many available tools, the post is out of place on Slashdot. I am not a member of a huge biochem or medical lab, but I am trying to learn and use biochemistry, so I can use every bit of help. My situation is also not unique - many researchers with background in "hard sciences" are now working with DNA in nanobiotechnology and biosensor projects. So user-friendly software that automates basic, routine calculations, and thus helps non-experts to avoid costly errors, is very welcome. Having many choices of such programs is great - just as it is great to have countless free and open-source replacements for Notepad. Since you apparently are quite familiar with other software for DNA design and analysis, perhaps you could share links to a few that you find particularly useful?
Of course the technology to sequence genes and deduce their protein counterparts has been around for a while. But as we know proteins are three-dimensional structures, with intricate folds and chemically active sites (think enzymes) that will partake in only specific reactions and ONLY in certain ways. They also operate in highly regulated environments. Heat the protein beyond a certain tolerance level, or substitute an innocent-looking peptide somewhere in the chain, and you end up with a malfunctioning protein no longer any good.
It would be interesting to correlate the nature of genetic mutation with potential biochemical ramifications (i.e. how does a point mutation in a particular exon translate into a polypeptide that cannot fold the correct way, thereby impairing certain biochemical pathways).
Have you even been to the site? Here it is:
http://slam.bs.jhmi.edu/gd/
Here's a little snippet from the manual if you are too dense to find it:
"GeneDesign will perform stepwise modifications to an amino acid sequence to produce a codon-optimized nucleotide sequence that codes for the specified protein. The modified nucleotide sequence can have dozens of customizations that will allow users to proceed to complex experimental work designed to quickly elucidate the structure and function of the gene in question. The final nucleotide sequence will be comprised of segments linked by restriction sites, allowing users to swap synthetic segments with native segments or to easily introduce mutations, in order to help determine which regions are necessary for the function of the gene. "
Considering you can't even understand what the site can do, how can you possibly make something equivalent to it? Cheeky bastard.
Even a drug with a simple-looking molecular structure, like aspirin, is the product of dozens of genes, each of which produces an enzyme with a specific catalytic activity. To enzymatically synthesize a drug in your basement, you'd have to 1) figure out the chemical steps needed to synthesize the drug, then 2) calculate the exact 3-dimensional protein structure needed to align the precursor molecules in the right way to catalyze each of those reactions, then 3) synthesize the DNA to make that protein, and then 4) produce that protein in a recombinant organism, and then 5) combine the raw material and all the enzymes in an environment where they would produce the drug. And THEN 6) purify the drug away from all the raw materials, many of which might be toxic.
With the structure of the drug in hand, A smart chemist could design a likely solution to step 1) on paper in an afternoon. But hundreds of the smartest molecular biochemists in the world haven't solved step 2) for all but a tiny subset of possible chemical reactions, even after decades of work. Synthesizing a gene to make a amino acid sequence is second year undergraduate work; figuring out exactly which particular amino acid sequence to make is the real rocket science.
You would be better off trying to synthesize the drug chemically, but without a PhD in chemistry, a well-trained staff and an expensive laboratory behind you, it might take you decades to figure out how. So I can safely say nobody is going to sue you for making an Avastin knock-off at home.
Where have you gone, K. Eric Drexler? Our nation turns its lonely eyes to you, woo woo woo
I have the software, its great. Alt-P will actually apply for a patent on the genes you 'discover'.
Wasn't this an episode of Battle Star Galactica this season?!?
...by BUILDING them! But it would save time if the site had templates based on famous models...
Unless you need no hightech equipment and knowledge to produce an atom bomb, your post is a contradiction in terminus.
To produce weapons grade uranium you need a massive enritchment factory, which costs a lot of money and hard to get materials.
Doing general genetic manipulation requires just a small lab and a (few) good scientist(s). The reagents and machines are not bulky or restricted and not hard to get in south korea. It wouldn't be too hard even to set up a company in a non-suspect country and do your research there. It is not that hard to disguise your research as having noble goals (like developing a vaccine against HIV or smallpox). The only difference might be that your 'vaccine' is a bit more lethal then intended. Then you ship it to the home country (terrible outbreak of HIV and smallpox to combat) and test it on some 'volunteers'.
So making the nasty stuff is not that hard, and a lot less hard then developing a nuclear bomb. The downside is, once you have demonstrated you have nuclear bombs, people accept that as a deterrent. Alternative weapons are not known at large, so their effect as deterrent are much less (if nobody knows you can kill everybody in a few seconds, nobody is going to be afraid).
This space is intentionally staring blankly at you
There have been significant roadblocks in the formation of genes. The first one, and most importantly, is that even if we could predict (and we currently cannot) what our desired protein or RNA would do, there is no guarantee that it would fold correctly. We could take elements of existing genes (motifs/domains) and fuse them together to interact with our proteins of interest, but when this has been tried in the past, the protein folds up on itself into a big gob of oil.
The second issue is that we are still many years from knowing whether we could just make this protein and have it work. In addition to folding, the addition of other modifications (like sugars, lipids, and other proteins) directly to our gene of interest, is a subtle change that highly regulates its activity. One may make a perfect protein only to find it functionally dead. We're just not there yet.
One could easily see the benefits to this technology: build a protein that stabilizes a tumor supressor, or construct a gene that confers highly specific affinity to degrade an over-active growth factor receptor (common in many cancers). But for the aforementioned reasons, scientists prefer to work with natural genes, constructing schematics of proteins and using only naturally-sourced DNA. Maybe in 20 years. Or 50. But not now.
I would definitely agree with you on that. Just look at the comments involving global warming. You would think that from reading their comments, that the world is going to end tomorrow.
I am defenseless. Use your button. Mod me down with all of your hatred.
DNAhack.com has a list of sites where you can order DNA synthesis and gene synthesis online. In gene synthesis, your DNA will be synthesized and inserted into an E. Coli plasmid so you can easilly insert it into your own E. Coli.
It is very simple: go to a web site, type in "ATCGCCGA..." and put in your credit card number, and the DNA or gene will come in the mail in a few days.
Its been easier to tie genetic diseases to heredity patterns, find the DNA, and reverse engineer the protein, rather than find the culprit protein directly. I believe this is how the bad Huntington's and Ty Sachs proteins were discovered.
These key steps include translating proteins and amino acids - the building blocks which make proteins - backwards into a DNA sequence.
My own GPL'd software can do this for a while now, to standard code or organism/mitochondria-specific.
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Thank you for the thoughtful answer - reading the posts today I'm glad that I've chosen this thread over the one where the debate has shifted to who is a bigger moron! I don't think that it is profitable to continue the debate on the merits of the post - perhaps the discussion is more important than the post itself, which is certainly not the first such case on Slashdot.
I looked at the suggested links, but I didn't quite see what I was looking for. I am interested in DNA structure, mostly that of oligos (less than 50 bases long) for surface-based applications. So actually a couple of the options on the GD site appear to suit my needs more than the full-blown genomics/proteomics resources that are indeed easy to find. The information that I need (Tm's, hairpins, construction of orthogonal oligo sets, maybe choosing a couple of restriction enzymes) is rather basic, but at the same time, most tools give different answers (e.g., for Tm's), and none are actually valid for the conditions (high-salt buffers) that I need to use.
It's basically the problem of being at the interface between two disciplines. The interface is considered as trivial by both of the parent fields, while neither of the two parent methodologies strictly apply. So yes, I have asked quite a few people, but so far have not found anything that fits my needs. But if you or others care to make any additional suggestions (either here or to biohack [at] nanowiz.mailshell.com), they will be appreciated!
I'm sure they're blushing at the thought.
Researchers also are experimenting with introducing a 47th (artificial human) chromosome into target cells. This chromosome would exist autonomously alongside the standard 46 --not affecting their workings or causing any mutations. It would be a large vector capable of carrying substantial amounts of genetic code, and scientists anticipate that, because of its construction and autonomy, the body's immune systems would not attack it. A problem with this potential method is the difficulty in delivering such a large molecule to the nucleus of a target cell. Some Questions to Consider... What is normal and what is a disability or disorder, and who decides? Are disabilities diseases? Do they need to be cured or prevented? Does searching for a cure demean the lives of individuals presently affected by disabilities? Is somatic gene therapy (which is done in the adult cells of persons known to have the disease) more or less ethical than germline gene therapy (which is done in egg and sperm cells and prevents the trait from being passed on to further generations)? In cases of somatic gene therapy, the procedure may have to be repeated in future generations. Preliminary attempts at gene therapy are exorbitantly expensive. Who will have access to these therapies? Who will pay for their use? Gene therapy is a technique for correcting defective genes responsible for disease development. Researchers may use one of several approaches for correcting faulty genes: