Yeah, I don't really like the idea of open-sourcing the genome. There is always the risk of a fork of the code base, and before you know it, we are two different species! Wouldn't you hate not being able to mix genes with everyone? Eh, I mean, like, 50% of everyone.
By de-emphasizing "CE," which never actually stood for anything anyway, [...]
Surely this is wrong? There must be some old meaning to CE!
I mean, NT used to stand for "New Technology", although Micros~1 newspeak nowadays denies that. I can't believe they use a name that do not have any connotation.
However, if standard medical law prevails, there's no way they can deny a person access to the information necessary to save that person's life or to prevent his/her disease if that person cannot afford to pay for the information. Basically, just like an emergency room can't turn away people who can't pay, how could a company that patented a human genome withold that information from people who can't afford to pay?
Hmm, sounds like a good point, but laywers have probably worked this out already. After all, you can patent compounds that are used for various treatments, and this has been going on since before the discovery of DNA.
I read in an text on patenting that you cannot for example patent a surgical method, but you can patent a device that is basically necessary for same surgical technique.
But is not the medical records anonymized before DeCode can make use of them? I guess it would be possible for them to deduce for whom the data is in some cases, since they have access to a near full family tree for icelanders, but it would in the end be quite obvious that they had done something illegal in that case, wouldn't you think?
The main problem in my mind is that they have been given exlusive rights to this data. That is really giving away a gold mine.
Ewan is a very informed and knowledgable guy at one of the key centers in HGP, so he needs more moderation. Hey Ewan, go get more karma!
This is only for the assembly and not for the analysis. With analysis you have a better data/cycles ratio. Assembly is done at the genome centres anyway...
Then I don't get it. The original submission was about trying "to match the bits up with other bits like a giant jigsaw puzzle". Clearly this is about the assembly problem, no?
Common successful distributed projects in cryptography rely on the fact that all you need on a client is the algorithm and a few keys to try. Therefore, clients are really cheap (resourcewise) to distribute and use.
In the case of the Human Genome Project, the situation is somewhat different. A well known analogy is the following: Take a few copies of a newspaper. Feed it through a shredder. Remove a handful or two of paper. Insert errors. Now, piece together one copy of the original newspaper.
In order to make a useful contribution, a client is going to need a lot of data. This means that it will be difficult to distribute (long downloading times for instance) and that few people will appreciate having the client on the machine because the client will be using a lot of memory and the machine might be a bit unresponsive (your HGP screensaver might flush all your apps to disk for instance).
Data Theft. An open source program could be modified by Big Bad Corporation Inc. to simply harvest raw data and feed it into their own computers, thereby gaining information they would otherwise have to find themselves. Granted, they won't have as much computing power, but when they have their own and the stolen data, they're still saving time. And I am not sure if enough data is produced to keep hundreds of thousands of computers occupied (see the problems SETI@Home had in the beginning).
The Human Genome Project is extremely open. They try to make all data public as soon as possible, making patents impossible. So data theft is not an issue here.
False results might be a problem, but I would expect it to be relatively cheap (computationally seen) to check a solution to see if it is valid.
A distributed (open source) effort will probably not happen because a computation like this is more difficult to distribute than trying crypto-keys et.c.
Are they simply going to make money off the support for "their" parts of the operating system? With hardware prices going down even for the fatter computers, they have to look for alterative sources of revenue. I just wonder what Sgi's perspective is going to look like...
Lower hardware prices translates to lower margins. If you want to increase revenue, you must then sell more computers. Presumably, SGI believes embracing and extending (in its honourable sense) Linux can make them sell more computers.
I know they try to appeal to the bioinformatics community by optimizing popular open source analysis software for their computers. It certainly seems to help them sell more computers.
Your first three points does not show that Mirabilis, AOL, et.c. have innovated, IMHO. They have done something that OSS traditionally is recongnized as strong at: Improving existing concepts.
I did not know about point 4, although I learned of ICQ by WofM myself. But how far did they come with WofM as marketing? I though instant messaging took off with programs bundled with Netscape and IE?
What do you mean with your point 5? If you are saying that OSS could not improve talk+finger because it was a broken concept, implying that OSS can only improve through evolution, then I disagree and again point at the WWW for a counter example. My guess at why the open software community did not improve instant messaging is that no one saw the need.
What I think he means is that open source projects don't tend to be radical new concepts/services, just free versions of a commercial product.
But commercial/closed source don't tend to be very innovating either. There have been loads of word processors and spreadsheet programs and DTP applications. Given how much resources that go into commercial software developing, the output is disappointing IMHO. Has anyone ever tried to justify these claims?
It is so easy, as you also point out, to give examples of revolutionary open source projects. What would the PC market look like had it not been for WWW browsers and servers from CERN and NCSA? Open source projects, from time to time, do outrageous things and MS will have to shell out more billions of dollars to mirror open source projects.
AOL is another annoying example. AOL rules their messaging protocol, and there is nothing we can do about it. It's our fault for not doing it first.
I think this is an example of something different. I was using finger and talk ten years ago for instant messaging. It worked excellent (finger was much more useful then than today and talk was simple and convenient on a text terminal) and surely it was open source? But commercial messaging systems has taken over because commercial companies rule the desktop market and probably also because of marketing. How much marketing does an initiative such as Gale get?
I believe the strength of commercial companies is in grabbing market share more than innovating. This may change with Red Hat et al. We'll see.
If everything were one technology, there'd be no competition.
This is not true. There is competition all over Europe. I think there is at least two competing companies in every large country. In Sweden we have three, and they all use the same technology. This is also good for the customer in that it is easy to change provider. You have your phone and it can be used in any of the available systems.
The Swedish companies also provide different call plans and different services. They have also competed on coverage, but I am not so sure that is important when you choose a provider any more simply because they all have good coverage now.
It's the only UI lib I know of that doesn't have problems with UI updates outside of the event thread. A multithreaded UI could be very cool, indeed.
You can have that UI lib today, care you use a somewhat non-standard programming language. Go look at Modula 3. I think it is an open source system, but I do not know to what extent it is compatible with the GPL.
Isn't there an add-on camera for Gameboy? If i remember correctly, it has really bad image quality, but has some means for sharing pics with your friends.
Now, this Kodak suddenly looks like the ultimate Gameboy killer, with both excellent image quality and excellent games!
I can't begin to describe my admiration for hacks like this!
As far as I'm considered, DNA is nothing more than the source code of life and should fall under the same catagory as algorithms when it comes to patents.
Now, patenting the effects of the new DNA is something entirely different. Should you be able to patent the method of replacing a specific sequence of old DNA with your particular new DNA sequences in order to change something, for example to change hair color in humans?
Right, that is what they do. They do not patent the actual DNA sequence, but simply an application of the gene.
One of the problems with the gene patents is quite analogous to software patents, in that they are so obvious. For instance, the protein leptin have been believed to regulate metabolism (or something like that) and could therefore be used as obesity-drug. So it was quickly patented and they have tried to make a drug out of it. (I think they basically have failed; It worked on mice but not on humans.)
Now that is a quite obvious application of leptin IMHO, and quite comparable to, say, using bitwise XOR for mouse pointers (AT&T patent for that expired not too long ago).
If it was methods in general, there could be a case for patents, but today they can basically patent information.
Patenting genes has gone on for a while, particularly in agricultural circles. If you patent a gene, nobody can USE the gene without a license. You buy a bag of genetically altered seed, part of what you are paying for is the license to use the patent on those genes. Here, they are making two big jumps from "mainstream" genetic patents: * it's human genes now * it's naturally occuring genes now
No, it is not a big jump that way, patenting human genes have been going on for quite some time now, and the genes have also often been naturally occuring. OK, in agricultural cases they move a gene from one organism to another, but it is usually a naturally occuring gene anyway (designed proteins have a long way before they are useful).
Here is an example. An Italian researcher found that people in a small village had very low frequences of chardiovascular diseases. He found that the gene for a protein had a mutation and patented this. Today that patent is held by Esperion, and they are working on makeing a drug out of this discovery.
The big change here is that Celera can patent 6000 genes. The reason they can (try) to do that is because they want to patent predicted function. There is no way they can have worked out 6000 drug targets without prediction. And therein also lays one of the problems the Wellcome trust have with these patents.
Lars
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Re:Support of many mailbox formats is nice
on
Mutt Hits 1.0
·
· Score: 1
Mutt seems to me to have the nicest of the text interfaces; it is somewhat unfortunate that it doesn't have huge support for the multiplicity of folders that a MH user grows to. (I've got 350 mail folders and 179MB of archived email, for instance.) For managing that, the user interface of EXMH combined with a variety of shell scripts are pretty much necessary.
Take a look at GNUS running in Xemacs (or alternatively FSF Emacs if you are a purist, but the user interface is not as good IMHO) for a great solution to handle large volumes of email! I can never go back. I used to be a MH user, but I grew tired of the user interfaces (console usage is tiring, really. And Athena widgets? No thank you.)
There is a quite a learning threshold to GNUS, but it is definately worth it. You can keep browsing your MH folders if you want to, and transfer them to any of several mail folder (there are tradeoffs such as one mail per file and one directory per folder or one file per folder) formats when you feel like it. And with a full programming language (emacs lisp) under the hood, there is no end to the customization.
Lars
(Inspired by your.sig, I feel it is appropriate to say "Those who do not understand emacs are condemned to reinvent it, poorly". Please don't mark this as flamebait!:-)
It is not as easy mitochondria float around happily in our cells and produce energy. I don't know mush about interactions cell--mitochondira, but I do know some things about state of the art research on them.
It is beleived that mitochodria started of as a parasite on our most pathetic and primitive ancestors. The relationship became symbiotic and we lived together forever after. But there is evidence that there are genes from the mitochondrial DNA (mtDNA) that have jumped over to the nuclear DNA. The system needs those genes, but it has turned out to be somewhat irrelevant as to where they are found. When these gene-jumps have occured I do not know and I am not sure about the state of research on that.
It will indeed be interesting to se how different the mtDNA:s are in related species! And if there are differences, will they matter?
Can you imagine the results of accidental cross-pollinization with 'Terminator' crops and regular??? (It's been proven to happen) It could've resulted in the accidental genocide of, say, corn.
I can't see how this would happen. If there would be a cross polination, and the terminator gene was transferred, well, then the product would not survive and the gene would not spread. To me it sounds like a terminator gene is much safer than any other kind of gene manipulation.
Lars Lars
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Re:One Time Pads and cypher technology
on
The Code Book
·
· Score: 1
It is true that a one time pad is perfectly secure; One can even prove it. Unfortunately, they are highly impractical simply because you may only use them once and you must use the right pad. So if you want to distribute a lot of data, and perhaps communicate with many different parties, the one time pad is not the way to go.
Andrew Leonard in Salon has a piece ('Open Source Journalism') too. He is more positive to the/. comment process and says "sites like Slashdot are pioneering new territory as they facilitate access to that knowledge, to the great and lasting benefit of us all".
That was a really bad article and I don't find the Nervana site that informative either, but my guess is that he wants to (or already has) put support for iterated function systems on the graphics card.
Use of IFS in computer graphics can hardly be regardes as news, but I guess putting it in hardware, making it possible to draw directly in video RAM, would make the technology usable also for games. This way you don't need that many polygons to draw an intricate structure.
Also, just out of curiosity, how exactly ARE Canadian residents going to be punished for late payments if the server goes down. Given the proper scenario (ie, server goes down for a week due to Hurricane Gates, and bill was sent online to begin with), then the user positively COULDN'T pay the bill on time, through no fault of their own. I dunno, just seems a little sketchy to me. Not enough paper trail for government work I guess.
You could ask the same questions about sending checks! What if the postperson drops your bill, or what if someone raids your mailbox, or what if the mail truck goes up in flames.
OK, so the paper system might be somewhat more tested, but computer downtime can be kept track of so people might actually be better guarded against unfortunate circumstances in an online system.
Slashdot Mirror
Yeah, I don't really like the idea of open-sourcing the genome. There is always the risk of a fork of the code base, and before you know it, we are two different species! Wouldn't you hate not being able to mix genes with everyone? Eh, I mean, like, 50% of everyone.
Lars
--
Surely this is wrong? There must be some old meaning to CE!
I mean, NT used to stand for "New Technology", although Micros~1 newspeak nowadays denies that. I can't believe they use a name that do not have any connotation.
Lars
--
Hmm, sounds like a good point, but laywers have probably worked this out already. After all, you can patent compounds that are used for various treatments, and this has been going on since before the discovery of DNA.
I read in an text on patenting that you cannot for example patent a surgical method, but you can patent a device that is basically necessary for same surgical technique.
Lars
--
But is not the medical records anonymized before DeCode can make use of them? I guess it would be possible for them to deduce for whom the data is in some cases, since they have access to a near full family tree for icelanders, but it would in the end be quite obvious that they had done something illegal in that case, wouldn't you think?
The main problem in my mind is that they have been given exlusive rights to this data. That is really giving away a gold mine.
Lars
--
Then I don't get it. The original submission was about trying "to match the bits up with other bits like a giant jigsaw puzzle". Clearly this is about the assembly problem, no?
What kind of analysis what this be?
Lars
--
Common successful distributed projects in cryptography rely on the fact that all you need on a client is the algorithm and a few keys to try. Therefore, clients are really cheap (resourcewise) to distribute and use.
In the case of the Human Genome Project, the situation is somewhat different. A well known analogy is the following: Take a few copies of a newspaper. Feed it through a shredder. Remove a handful or two of paper. Insert errors. Now, piece together one copy of the original newspaper.
In order to make a useful contribution, a client is going to need a lot of data. This means that it will be difficult to distribute (long downloading times for instance) and that few people will appreciate having the client on the machine because the client will be using a lot of memory and the machine might be a bit unresponsive (your HGP screensaver might flush all your apps to disk for instance).
Lars
--
The Human Genome Project is extremely open. They try to make all data public as soon as possible, making patents impossible. So data theft is not an issue here.
False results might be a problem, but I would expect it to be relatively cheap (computationally seen) to check a solution to see if it is valid.
A distributed (open source) effort will probably not happen because a computation like this is more difficult to distribute than trying crypto-keys et.c.
Lars
--
Lower hardware prices translates to lower margins. If you want to increase revenue, you must then sell more computers. Presumably, SGI believes embracing and extending (in its honourable sense) Linux can make them sell more computers.
I know they try to appeal to the bioinformatics community by optimizing popular open source analysis software for their computers. It certainly seems to help them sell more computers.
Lars
--
Your first three points does not show that Mirabilis, AOL, et.c. have innovated, IMHO. They have done something that OSS traditionally is recongnized as strong at: Improving existing concepts.
I did not know about point 4, although I learned of ICQ by WofM myself. But how far did they come with WofM as marketing? I though instant messaging took off with programs bundled with Netscape and IE?
What do you mean with your point 5? If you are saying that OSS could not improve talk+finger because it was a broken concept, implying that OSS can only improve through evolution, then I disagree and again point at the WWW for a counter example. My guess at why the open software community did not improve instant messaging is that no one saw the need.
Lars
--
It is so easy, as you also point out, to give examples of revolutionary open source projects. What would the PC market look like had it not been for WWW browsers and servers from CERN and NCSA?
Open source projects, from time to time, do outrageous things and MS will have to shell out more billions of dollars to mirror open source projects.
I think this is an example of something different. I was using finger and talk ten years ago for instant messaging. It worked excellent (finger was much more useful then than today and talk was simple and convenient on a text terminal) and surely it was open source? But commercial messaging systems has taken over because commercial companies rule the desktop market and probably also because of marketing. How much marketing does an initiative such as Gale get?
I believe the strength of commercial companies is in grabbing market share more than innovating. This may change with Red Hat et al. We'll see.
Lars
--
If everything were one technology, there'd be no competition.
This is not true. There is competition all over Europe. I think there is at least two competing companies in every large country. In Sweden we have three, and they all use the same technology. This is also good for the customer in that it is easy to change provider. You have your phone and it can be used in any of the available systems.
The Swedish companies also provide different call plans and different services. They have also competed on coverage, but I am not so sure that is important when you choose a provider any more simply because they all have good coverage now.
Lars
--
When I had read this far, I got the image that you want a car that run on decomposing bodies from people you had hit. Eeooooooww.
I am sorry. I should probably see someone about this.
Lars
--
It's the only UI lib I know of that doesn't have problems with UI updates outside of the event thread. A multithreaded UI could be very cool, indeed.
You can have that UI lib today, care you use a somewhat non-standard programming language. Go look at Modula 3. I think it is an open source system, but I do not know to what extent it is compatible with the GPL.
Lars
--
Isn't there an add-on camera for Gameboy? If i remember correctly, it has really bad image quality, but has some means for sharing pics with your friends.
Now, this Kodak suddenly looks like the ultimate Gameboy killer, with both excellent image quality and excellent games!
I can't begin to describe my admiration for hacks like this!
Lars
Lars
--
Right, that is what they do. They do not patent the actual DNA sequence, but simply an application of the gene.
One of the problems with the gene patents is quite analogous to software patents, in that they are so obvious. For instance, the protein leptin have been believed to regulate metabolism (or something like that) and could therefore be used as obesity-drug. So it was quickly patented and they have tried to make a drug out of it. (I think they basically have failed; It worked on mice but not on humans.)
Now that is a quite obvious application of leptin IMHO, and quite comparable to, say, using bitwise XOR for mouse pointers (AT&T patent for that expired not too long ago).
If it was methods in general, there could be a case for patents, but today they can basically patent information.
Lars
Lars
--
No, it is not a big jump that way, patenting human genes have been going on for quite some time now, and the genes have also often been naturally occuring. OK, in agricultural cases they move a gene from one organism to another, but it is usually a naturally occuring gene anyway (designed proteins have a long way before they are useful).
Here is an example. An Italian researcher found that people in a small village had very low frequences of chardiovascular diseases. He found that the gene for a protein had a mutation and patented this. Today that patent is held by Esperion, and they are working on makeing a drug out of this discovery.
The big change here is that Celera can patent 6000 genes. The reason they can (try) to do that is because they want to patent predicted function. There is no way they can have worked out 6000 drug targets without prediction. And therein also lays one of the problems the Wellcome trust have with these patents.
Lars
--
There is a quite a learning threshold to GNUS, but it is definately worth it. You can keep browsing your MH folders if you want to, and transfer them to any of several mail folder (there are tradeoffs such as one mail per file and one directory per folder or one file per folder) formats when you feel like it. And with a full programming language (emacs lisp) under the hood, there is no end to the customization.
Lars
(Inspired by your
Lars
--
It is not as easy mitochondria float around happily in our cells and produce energy. I don't know mush about interactions cell--mitochondira, but I do know some things about state of the art research on them.
It is beleived that mitochodria started of as a parasite on our most pathetic and primitive ancestors. The relationship became symbiotic and we lived together forever after. But there is evidence that there are genes from the mitochondrial DNA (mtDNA) that have jumped over to the nuclear DNA. The system needs those genes, but it has turned out to be somewhat irrelevant as to where they are found. When these gene-jumps have occured I do not know and I am not sure about the state of research on that.
It will indeed be interesting to se how different the mtDNA:s are in related species! And if there are differences, will they matter?
Lars
--
Let me make illustrate how a Swedish user interface could look like in your scheme. Guess what the English message was!
The list is endless!
Lars
--
Old Swedish saying: The sea sucks
Lars
--
I can't see how this would happen. If there would be a cross polination, and the terminator gene was transferred, well, then the product would not survive and the gene would not spread. To me it sounds like a terminator gene is much safer than any other kind of gene manipulation.
Lars
Lars
--
It is true that a one time pad is perfectly secure; One can even prove it. Unfortunately, they are highly impractical simply because you may only use them once and you must use the right pad. So if you want to distribute a lot of data, and perhaps communicate with many different parties, the one time pad is not the way to go.
Lars
Lars
--
Andrew Leonard in Salon has a piece ('Open Source Journalism') too. He is more positive to the /. comment process and says "sites like Slashdot are pioneering new territory as they facilitate access to that knowledge, to the great and lasting benefit of us all".
Lars
Lars
--
That was a really bad article and I don't find the Nervana site that informative either, but my guess is that he wants to (or already has) put support for iterated function systems on the graphics card.
Use of IFS in computer graphics can hardly be regardes as news, but I guess putting it in hardware, making it possible to draw directly in video RAM, would make the technology usable also for games. This way you don't need that many polygons to draw an intricate structure.
Lars
Lars
--
Well, Google has the same response for "the best internet company", so I won't draw any conclusions about Google's oraclian capabilities!
Lars
You could ask the same questions about sending checks! What if the postperson drops your bill, or what if someone raids your mailbox, or what if the mail truck goes up in flames.
OK, so the paper system might be somewhat more tested, but computer downtime can be kept track of so people might actually be better guarded against unfortunate circumstances in an online system.
Lars