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One thing that interests me...

We went over PCR recently in a Biochemical Genetics lab. Apparently, the primer oligonucleotides can only be up to 3000 base pairs apart or so for the process to work effectively.

If this is the case, replicating the millions/billions of bases you'd have to recover to reconstruct the organism would surely be a daunting task.

Or are there any other PCR techniques more powerful than the standard 2nd year University ones we study? Would some Celera style shotgun approaches be applicable here?

I don't want to call bullshit on this one but I'm afraid I must. Sure, there are companies out there *cough* Celera *cough*who hoarded data and even used public data to advance their own research without then adding back to the public database. But to say that the public human (and mouse which is my specialty) genome project suffered because of private interference is karma whore bullshit.

If you remember correctly (which you apparently don't), the public and private human genome sequences were published on the exact same day, one in Science (Celera) and one in Nature (public). The data in the two sets is slightly different but essentially the same stuff. Interestingly though, the private data (to which I have some access) is almost completely undecipherable and full of restrictions on its use, whereas the public data is simple to get to, simple to understand and completely available for downstream academic use (and easily licensable for commercial use).

I do agree with you statement that many financial backers (including some who fund both public and private research) are ...
doing it "to make a crap load of money" but I think you ignore the fact that many of us in "public" research take advantage of the private money to advance the public interest. Yes, there are situations in which NDAs and similar documents are involved, but more often than not, the "private" money that I've been involved with in research has had no limits on publication or sharing of resources/reagents. DOD money on the other hand (I'm just getting started on a DOD funded collaboration) comes with so many strings attached that you feel like a freakin' puppet.

Whenever a scientist publishes, it IS open-sourced. But when Celera or some private company announces results, that's not same as publishing a paper in peer-reviewed journal. My comment wasn't about this case (go, Bo!), but about what I can tell of the process as a whole.

1- Most databases are publicly available.
2- Many bioinformatics groups DO cooperate
"Many and most" is not all. Is Celera really cooperating with the HGP? I know Celera has a Consensus Human Genome site, but that is that everything they know? How does that compare with the UCSC data? Is the patenting of gene sequences and techniques inhibiting research? I'm not asking these to troll, but simply because I'd like to know the answers. Unfortunately, everybody has a different view of what is a gene and how to find them. Probably in part because we don't know as much yet about genetics as we'd like to think. Is "junk DNA" just that? Or some subtle part of the design that we have yet to understand?

1- Most databases are publicly available.
2- Many bioinformatics groups DO cooperate
"Many and most" is not all. Is Celera really cooperating with the HGP? I know Celera has a Consensus Human Genome site, but that is that everything they know? How does that compare with the UCSC data? Is the patenting of gene sequences and techniques inhibiting research? I'm not asking these to troll, but simply because I'd like to know the answers. Unfortunately, everybody has a different view of what is a gene and how to find them. Probably in part because we don't know as much yet about genetics as we'd like to think. Is "junk DNA" just that? Or some subtle part of the design that we have yet to understand?

Sadly, given Celera's past history, it will almost certainly be proprietary. Although they have benefited immensely from government funded research and data collection, they have refused to make their sequence data publicly available in GenBank. Most journals require you to publish your sequence data in GenBank as a condition for publication of papers related to the sequence data. Celera was granted a special exemption to this policy by Science when they published their paper on the human genome recently and I anticipate a similar special exemption will be allowed for the mouse data as well, though I haven't closely followed what's going on with the mouse genome, since I work on Acetabularia Acetabulum (this is my professor's web page, not mine, the views expressed here are not ...and so on)

If you want to analyze publicly available gene sequence data, you can use GenBank at NCBI and software from Bioinformatics.org. There is also a great directory of online molecular biology tools and information here

... arti cles are belong to us.

____________________________
2*b || !(2*b) is a tautology

Personally, I am not so worried about the privacy aspect of these projects. It seems to me that both deCode and Uman Genomics work hard on solving that problem. More pressing to me is the kind of deals they are making. Is it really right for a society to favour one company before many others when the resources are actually public? This is an old problem in that countries has sold mining rights, fishing rights, and other natural resources for a long time, but we are not talking about a scarce resource here. This is information and it is not expensive or impossible to share that resource with others as long as they can pay.

And Celera has shown that it is certainly possible to have a business model an a truly open resource: The human genome. No one has exclusive rights to this data, and yet you can make a good business selling it.

Lars
__

This is not to say that I support gene patenting.. but I believe the reason for it is to provide an incentive for companies to research genes.

For inventions that require a lot of work up front (for example the internal combustion engine), patents work well because you know that after the patent is granted you can recoup (some of) your investment. The work required to apply for a gene patent is routine these days, which is why companies like Celera and Incyte can easily swamp the patent office with thousands of gene patent applications. A gene patent application will generally state what function the gene is thought to have, but normally that will be a computer prediction with no experimental backup. Once the patent is granted and if the company thinks there is a chance that the gene will make them money later the long and difficult laboratory work will start. The "if" in the last sentence is a big if.

If there was no such thing as a gene patent, then it would probably be much longer before we got a cure for cancer and whatever other genetic diseases there are.

Summary: Getting a patent on a gene is (relatively) easy, doing the laboratory work to develop a drug is (relatively) hard. Under the current system companies can get a patent before doing anything difficult. Meanwhile everyone else finds it more difficult to the challenging and expensive part because patents keep getting in the way.

It's not just shooting up mice and Mad Cow Disease- all those biotech people are clamoring for more computing power. But now that they've sequenced the whole human genome, does our pal J. Craig at Celera really know what to do with more computing power? I'd give dollars to donuts that he'd waste it on a UT server, while people like Stephen Mayo and his research group at CalTech are drooling over power like this.

Hot biotech now isn't about sequencing the genome, it's trying to decide what to do with the sequence now that there is a blueprint to work from. Thus companies like Incyte Genomics and Sangamo Biosciences are making money selling tools to build on or manipulate the structure we already have.

A machine running code that will reliably predict the actual folded tertiary structure of the unique protein that derives from any known sequence of DNA is the holy grail of biotech today. Maybe this IBM box (or should I call it a house?) is a step in that direction.

We'll finally have the script to our bodies. Whether you believe in God or Evolution or some combination thereof, this is a landmark event. For the first time, a species will have the ability to view and eventually change its own blueprint.

My fondest hope is that our society will be able to catch up enough with technology, so we can deal with this the Right Way(tm). I think Gattaca had some very relevant messages, that need to be discussed as we move into this technology. We the public need to be very aware right now of what is happening with the patenting of genes. There is a great potential for abuse.

I'm glad that both the public project and the private sector will be announcing this together. The Human Genome Project immediately publishes their data on every night. You can be sure that Celera's downloads it every morning. It would be an affront to the scientists who did so much work in the public project if Celera tried to steal all the credit.

Be sure to check out the Charlie Rose show this week on PBS. He has been running a week long special on all this. I highly recommend it.

Neither of them seems to have reported anything on the news conferences, though.

-hk

I am all for companies partnering up and moving forward like this. NASA has a joint venture thing going on with Dreamtime as discussed in last weeks slashback . Why shouldn't corporations do this to? If NASA's ever dwindling federal budget is preventing this type of lunar exploration then they will need to do commercially exploitive things like this as well. RadioShack partnering up with LunaCorp for this type of mission could be a great thing if handled correctly. Every program that NASA has put together has benefited us as a civilization directly and indirectly with new technologies. No need to list them here as most /.er's probably know of atleast 3 (not including TANG) off the top of thier heads. Unfortunately, i fear that this venture will lead to tons on IP trademarks/patents designed to benefit a select few pockets. I am not against making a buck or two but there has to be some benefit to all of US (read civilization as a whole not just the already deep pockets of corporations). I wonder what thier take on the technology involved is. Hopefully, the science aquired on this mission won't go the route of some of the companies involved in the human genome project. Commercial space ventures are an inevitable event that needs some form of government supervision/regulation before it gets out of hand. What bothers me about this venture is that a) LunaCorp is a privately owned corporation b) RadioShack is a publicly owned corporation c) Buzz Aldrin is now a (albeit heroic) civilian d) It would appear that NASA is out of the loop on this deal. I did not see a mention of NASA's involvement in this anywhere on the LunaCorp site even though there are several shameless plugs for Carnegie-Mellon. Rather conspicuous, no? If you are curious go check out The Artemis Project. The Artemis folks have carefully thought out most of the issues and thier plan seems cogent for the most part. IAAMOAC - so are you

I'm surprised I haven't seen any mention of this here yet. I submitted it as a story a bit ago but it got rejected (it's only marginally on-topic anyway).

Here's the gist: Celera is getting massively sued in at least three class-action suits. Shareholders claim that Celera has a bogus business plan and which "is dependent upon its ability to protect its database [of genomic] information through patent protection."

These upcoming lawsuits look ugly, and apparently the shareholders don't appear to think Celera is on the up-and-up with their claims of IP protection for the human genome.

Now dig this. The reason why the class-action litigants feel that Celera's business plan is flawed is that the Human Genome Project has already "open sourced" significant parts of the human genome.

Here is the full article from law.com.

Comparing this:- All in all, Celera plans to do the same process with four other people. to this: - The three million fly fragments are sampled from the gene-rich regions of the genome (about 120 million letters). For a simple genome there is a larger sampling, but for a more complex creature there is a smaller sampling. Doesn't this seem a bit of an oversight? OK, you might be able to improve your processes, but this doesn't seem to scale. Much like quickly typing nonsense in an attempt to grab that elusive first post...

"Gerald M. Rubin, head of the Berkeley Drosophila Genome Project and lead author of one of the Science papers, says, "about 60 percent or more genes are conserved between fly and human." In other words, nature practices the addage against reinventing the wheel. If you've got a core set of genes that work, why not use them over and over again in just subtly different ways."

So not only is there a law of conservation of matter and energy, there is also a law of conservation of genetic material. Now what were the drawbacks to Open Source?

Here is a much more detailed link of the story from Celera's site, talking about the similarities between our genes and the fruit fly's. (I've got a dollar that says their computers are all Celerons, ha ha ho ho.)

In many ways, this joint statement just states the obvious. The data from the publicly funded Human Genome Project is and always has been intended to be free and publicly available.

Celera is a competing private effort. I really do not believe that governments intend to expropriate Celera's database, which has been privately funded. However, Celera has made extensive use of the public data to augment its own. (The nature of their sequencing methods require many overlapping fragments and redundant coverage to ensure accuracy.) One way to pressure Celera to make its data freely available would be to license the public data under something like the GPL - to demand that any database products that use it or derive from it are made freely available.

Regardless, even if Celera does not share, the HGP will catch up within a few years.

TIGR != CELERA! TIGR is a non-profit research institute funded by grants TIGR CELERA is a for profit company funded by stock market and Perkin Elmer. CELERA
TIGR data is publicly and freely available, just go look at their website/ftp... tons of good stuff there.
Yes the head of TIGR went on to found celera but that hasn't changed TIGR. Except maybe that the scientists who remained at tigr when they likely were offered jobs at celera must be quite dedicated to doing non-profit public research

Anonymous Coward

Additionally Celera hasn't "beaten" the public effort except in their ability to issue press releases and it remains to be seen if they can assemble a final map without a BAC based mapped backbone to anchor it.
Still waiting for the fruitfly sequence celera announced was done in october...hrm, maybe they're having trouble putting it all together. And that's with a nicely mapped starting point they got by collaborating with berkeley
Anonymous Coward

Not much is more valuable than open-sourcing the human genome, especially with Celera attempting to patent genes! _Nobody_ should "own" human genetic sequences. The HGP gets my vote for certain.

Capital L

For an average researcher, having a complete set of clusers usually is irrelevant. (Of course, it may not always be; once cluster information is available, people will probably figure out ways to use it well.) All they want to know is how similar their gene(s) of interest is/are to other known genes. And there are plenty of tools that do that already, most notably the set at NCBI. DoubleTwist offers little of use there.

The interesting concept is that of "agents" who go out and look for your data for you. Agents aren't new, but they have not been used much in biological research thus far. Most of the relevant data is at a very small number of sites, so setting up an agent might not be much easier than going around yourself, but if agents become prevalent it will allow biological information to sprawl all over the place to a much greater extent. I wonder if this is a good thing? It is nice to have all your data found for you automatically, but if that's the only way to find anything it may get burdensome.

One point of concern: some of these agents will poll existing sites daily for new sequences. What happens if a hundred thousand researchers all ask for daily polling on ten or twenty genes? Suddenly NCBI will be getting a million extra hits a day and will be slowed to a crawl. I would feel a lot more comfortable if DoubleTwist did the searches on its own machines and only downloaded the new data once a day--but from the description, it sounds as though they plan on searching the public databases repeatedly. (And since it costs them nothing, if 50 people all request information on the same gene, they may not have an incentive to avoid making 50 separate search requests.)

I share the skepticism that anything *really* novel or useful will be greeted with a cheerful reminder that this is an "advanced" feature that requires payment. Further, I'd bet that Celera Genomics is paying close attention here...they are currently racing the NIH to sequence the human genome, and claim that their commercially-funded sequencing will be available for free. However, the advanced tools to search and understand the sequence will not. If Pangaea's attempt here goes badly, watch for Perkin-Elmer (the underwriters of Celera Genomics, who build DNA sequencers among other things) to make Celera back off on their openness statements and start getting really aggressive with patenting....

I've gone and checked out their site, and they don't mention patenting the genome sequences, but if you want to contact them, their contact page is at:

http://www.celera.com/Compan yInformation/Contacts.shtm


And, on a technical note: ".shtm"?! What the hell is that?! People started using .htm back when DOS/Windows could not handle more than 3-character extensions reliably, but this is just silliness! Sigh.

The problem I see would be that a lot of these really cool sorts of technologies are developed by private industry which means that private industry also gets first crack at them. It's also private industry who wants to random shotgun sequence the entire human genome and patent whatever they want (e.g. Craig Venter's Celera, who shows the most chance to do so).

I seriously wonder how the publicly funded labs can get this kind of stuff, since they're working entirely on government grants. Anyone care to build a GNU gene sequencer?