What makes you think Windows is the best and most modern OS? My copy of windows sucks ass in terms of stability and configurability compared to my copy of Linux. It's less fun too:-)
I've got way better app support via apt-get (consistent updates, security fixes for all apps on my system), I don't have to reboot my system every time I make a network change, I don't have to reboot my system every time I load a new driver/module, and I've got the ability to boot multiple versions of my system with different features depending on what I need.
Oh yes, and I don't have such wonderful modern operating system type features such as Outlook and IE security holes.
Wow... my OS must be antiquated to allow such things and still not crash as much as my modern copy of windows. Personally, while Linux has a lot to learn from other systems, I think Windows has a long way to go to catch up to a ten year old clone of a thirty year old operating system.
Ok, this is just nuts, not insightful. I'm no kernel wizard either (far from it!) but I do know that integrating these things in to kernel space is just a bad idea. Preloading the mozilla libraries is something that can and possibly should be done at startup, although you don't want to integrate them in to the kernel by any means.
The reason you don't want them in kernel space is, should one crash, you'll take down the entire system. Not having protected memory for things like browsers and word processors is a very bad thing for any system. IE doesn't load anything into kernel space, and while IIS does apparently, you sacrifice stability and necessary reboots for the speed gain.
Konqueror does load up all its libs at KDE's startup making it a much faster start than Moz, although C++ has linking issues (see Waldo Bastian's paper on the subject).
And as for the assertion that taking MS's lead could lead Linux to desktop domination, then maybe you should read some of the other discussions on a KDE or Gnome story to get a better idea of what Linux does need to get on the desktop (this was a good one) and I can tell you it's not tying the browser to the kernel! Not having your system crash on you is a much better selling point than the slight speed gain from integration.
In conclusion: load libs at startup: good. Put apps in kernel space: bad.
Sure, but only if pulled off skillfully and effectively, which is a very difficult prospect. I don't think there's anything that's so compelling about the Yopy to make it worthy of snatching that opportunity. Maybe if they were to lower that price point or something.
Does anyone think that entering the PDA arena with what's been going on is such a good idea? Palm, the real leader, is in major trouble. Why would you want to enter the market now, especially with something targeted from $400 to $600, when anyone who's going to pay that probably already has a PDA? Crazy... don't be surprised to see this one fail, especially if they're hoping that the strength of linux alone will float it, because it didn't float indrema. Different sectors, granted, but linux alone does not a business plan make.
Ok, since you're obviously a mac apologist, then please tell me why they don't have the market that windows has? Not to say that OSX is a bad system (in fact, I think it's really damn impressive) but the fact that they've managed to nail all these things for years and they still haven't beaten windows (or DOS back when it was DOS) just goes to show that it takes more than the things you list.
Point 1: ease of use. Macs have had this down since day 1. MS has had the market.
Point 2: Games, Internet, Word Processing. Games, not the whole game market, but a lot of good titles made their way to the Mac in the past. Internet, always had decent stuff, especially with IE 5 for the Mac (great browser!). Word Processing. Can't beat MS Word.
Point 3: Make it pretty. Always was prettier than windows, and is now way way prettier. Still not beating MS. Granted, the interface is different now, but the consistent one over 15 years didn't save them before.
This whole post isn't to say that I don't like Macs (I used to love them actually, and I still work with them all the time) but the fact is that with a strong user base like Windows to take over you need a hell of a lot of factors, and the ones you list are only a few of the important ones. No one is going to even buy the system without a fairly consistent UI, among other things.
Personally, I think people would love a free system (free beer, although explaining how the speech thing will benefit them would be an extra bonus) and underestimating the factor of cost is making the exact same mistake that Apple themselves made for so many years. We just have to get Linux on to people's desktops pre-installed so they don't have to dick around so much.
I do this at work, although they're not diskless iMacs they do have preferences and such stored centrally. While it seems like a great solution it's really not because of the whole netboot thing. For some inexplicable reason, the iMacs have to constantly hit the network even for simple things like loading a webpage. We have a total of only four iMacs connected to the server, and not even stressing it much, but even browsing the internet slows the things to such a crawl that I get constant complaints about iMac speed. Open up a second or third browser window and the things become almost unusable.
Mac OSX isn't supported yet for netbooting or Macintosh Manager, so you can't get a modern OS running these things even though it would solve a lot (if not all) of the problems, although later in the year they should be there. But as it stands now, this is a really bad idea that I don't recommend it to anyone simply because it'll just piss off the users and make them hate Macs more. It's so bad that we're moving over to NFS for remote file access (also need to give PC's equal access via Samba) and doing all the multi-user stuff locally.
The success of a company may be judged on whether or not they hand on to the source, but you can also say that the quality of the product itself is reflective of the same. Buggy MS products, most notably IE, Outlook, and IIS, are a bane to the internet community as a whole, and it's a problem that could be solved by a true Open Source/Free Software philosophy.
MS chooses to be successful and make a buttload of money, and that's their choice, but in no small part their customers suffer because of shoddy products that are now a monopoly. Not that I necessarily think MS should open up their code, but you can't say the bugs and flaws wouldn't be helped tremendously by releasing it.
It comes down choice, as Mundie says, but what he's not saying is that his company is making the choice to protect its business interests well ahead of its customer interests.
Indeed! Why does it matter in reality if the average consumer is running free software on their box before it's ready? Free software is not ready to enter this arena by a long shot. We've got good libraries in Mesa and such, and some coming down the pipe, but we don't have the games yet, unless you count nethack and tuxracer (both cool, but they obviously aren't what we're talking about).
This is like saying that when people who bought Sparc's were using Solaris' compiler rather than the gcc in 1992 it was a major blow to free software. It wasn't, it's not, it didn't matter. The coders kept on coding. The software kept on flowing. Now we've got a whole damn system to use and we're working on making free software on the PC both powerful and friendly enough for the average frat boy. This is a huge task and it's going to take some more time, but we'll get there and then we can worry more about things like consoles (which may make more $, but aren't actually running anything of critical importance).
By then everyone will be replacing their X-boxes with something new and shiny with a brand new redesigned on button that they can press to run whatever. Consoles cycle completely, with a whole new system under the hood every five years, no ties to the old stuff. New games gives a whole new chance every five years for free software to be running that box full time. Linux does and will provide a way to run the console now as it will then. We will see consoles running some form of linux eventually, simply because it's too good a bargain not to use. But not until it's really ready. Until then, the people who load linux on their X-boxes will just have to be like those rogues who ran the early GNU tools as replacements for the ones that came with their version of UNIX. They may not be the mainstream, but don't count them out yet.
The modified BSD license is considered a free license by GNU standards too. Just because it doesn't mimic the GPL exactly doesn't mean it's not free. Next time you post a link to somewhere, be sure you've read what it's talking about.
"Goodbye ivy league" my ass. I hate that view because it's just not true. I have a friend who's at U. Penn in a special program doing a double science major in Biochemistry and Physics. In 9th grade he made a spectacle of himself by getting drunk before a school dance and wound up puking all over and getting his stomach pumped. Everyone at the school knew. People at other schools knew. And he was suspended for over a week and had to go to AA meetings and such. Despite this, he's still one of the brightest students in his college, and the entire ivy league system.
If you fuck up once or twice in high school you still have a chance to do very well, including getting in to ivy league schools (as though that's really the final measure of success anyway) and have a great life. And this kid was in middle school! The load kids like this have to bear doesn't get any easier with the idea that you can't recover from a fuck-up, and this is what's foisted on successful kids. The drive to constantly succeed doesn't allow any reprieve, and once you do mess up you really do feel like it's "goodbye ivy league" when that's just not the case. We need to teach kids that you've got to do your best, and if you fail or make a mistake then it's Ok. Pick yourself up. Dust yourself off. And go for it again. Just don't ever give up because that's when you've truly failed.
"I may not have morals, but I have standards."
Re:DNA isn't as hard as everyone says it is.
on
Bioinformatics
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· Score: 2
Yes and no. This is a decent idea for something like drosophila, where you can mutate the gene and see what happens, but there's no way this would work on humans. If you've got a phenotype, you've got to do massive forward (reverse? I always get them confused...) genetics to find your gene. Cystic Fibrosis took a decade or so.
If it's the other way around and you've just got a sequence then you've got some different work to do. What if multiple genes in a pathway are mutated? What if there are multiple pathways affected by this gene? What if there is no noticable phenotype for a mutated gene?
Sure, with a massive database, this could work (and I mean huge, like multi-century lineage-total-human-population huge) but realistically, linking DNA string object to phenotype object and expecting to elucidate a pathway is pretty insane, even for someone with your nick:-)
A better way is the genomics approach, where you sit down with the microarray and say "Ok, what's going on here?" The biological systems are too big for just a two variable approach.
The black box idea is a good one, but not the way you propose. If you use a black box to abstract away what's actually happening (i.e. ignore what you don't need in the microarray) without actually dumping any data (if you need it in the microarray, it's still there) then you have a feasible method. With the two variable approach, you force people to leave out so many variables that the system becomes just theoretical and pretty much impractical.
I couldn't find anything for ruby (either linked from bioperl, as those were, or on their own app list) but you can bet it's coming. I'd personally love to see it. But there's plenty of options for bioinformatics other than perl, although perl's excellent text handling makes it a very suitable choice.
One important thing to think about in terms of nanotech then, is that if biotechnology can go wrong with cancer, what happens when nanotech has its own cancer?
I think most/.'ers fail to understand how difficult a genome is, and how the software model tends to fail because of the complexity (not that it can't cope, but we've just never seen spaghetti code on this level, nor should we ever if we don't have to).
Well, you're right and you're wrong (like the other poster said). Granted, we have a long way to go, and all the wild claims of hearts in vats and the like are pretty unfounded, but we do have Gene Therapy already, which is the next big leap, and it'll have the largest immediate benefit. The stuff this article talked about, if it's coming at all (sounds kind of '50's vision of the future'-ish to me), is still decades off. But we've got gene therapy for Severe Combined Immunodeficiency (SCID) which works right now. It's a proof of concept, and it shows that there's more coming down the pipeline. The trick is not to get carried away with the hype, but also to keep in mind the amazing things we are capable of, and what we'll be capable of very soon.
College isn't so bad, it all depends on where you go. No one makes you live in the dorms at a public university (at least not a UC). I understand your problem with the casual interest vs. career, but you do have opportunities to learn outside. I'm taking a class in Roman History because it's required for me to graduate as a general requirement. Ancient history is something I'm fond of, but not something I'd major in. You do have the opportunities to look around though. I know tons of people who spend their first two years just looking around. Changing majors is a normal and constant thing. The goal of college isn't generally to trap you in to what you want to do, but let you feel around a bit (a lot more than in high school!) and finally pick a course. Even then there are options. I'm majoring in molecular biology, with a specialization in computing, and an English minor:-)
Your post put me very much in my place, and while I was aware that we don't have the multi-drug interactions down in the least (obviously due in large part to testing issues) that I wanted to inform the root post that there was some info on interactions available.
The real problem is the one you stated, that most seniors are on multiple meds at a time for about as many conditions. That is, quite simply, pumping the body with way too many chemicals to be safe, especically in people whose bodies are breaking down to begin with. These drug interactions are probably incredibly difficult to study, but I agree that it needs to be done. I also agree that we need some kind of mechanical checking via computer to eliminate a lot of the stupid errors. However, I think the real problem lies in the fact that we're pumping drugs in to people in ways that they just aren't capable of dealing with. We need better forms of treatment, and I think genetic therapies, as well as that critical yet neglected factor of prevention, are going to be key in the future. Healthy diet and exercise alone can help with a large number of ailments, thereby reducing the number, or at least dosage, of meds needed later on in life. And to prevent heart disease, rather than take the pill, introduce the healthy gene (I know it's not ready, but it is the future) and that's one less drug-drug interaction to worry about.
The other problem is that, in large part, we don't know what causes diseases really. Alzheimer's is getting closer, and the ulcer bacteria was just an absurd discovery in some ways. We need to understand the disease before we can treat it, and all these things have to play together. So while I fully agree with you, and apologize for oversimplifying, that we need to really study multi-drug interactions, I don't think that simply saying "well, we can treat you for heart disease or AIDS, but not both" (totally hypothetical example) is the answer. Prevention is key. Understanding the disease better is key. And, hopefully, gene therapy will ease the number of meds as well. We need to make use of all the things Molecular Biology has achieved and will achieve in the coming decades, rather than rely soley on the older method.
p.s. Thanks for teaching me something!
"I may not have morals, but I have standards."
Re:THANK YOU RUBY ADVOCATES!
on
Apocalypse 2
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· Score: 2
Hehe, I actually just sat down with Ruby and wrote a basic Hello World program with a class. I'm very impressed! The whole messaging idea (smalltalk, right?) is very very cool. I'm going to keep playing with it this weekend (or right now!!!! Hahahah!!!!) What kind of libraries does Ruby still need? It'd be nice to have it as feature complete as perl. I really like perl as a utility, and it's a fun language to hack, but I'm pretty impressed with Ruby as is.
Hehe, not to diminish what you did (very cool project that I thought about writing myself last year) but just that we're heading in to major league waters here, and it's pretty exciting. Punnet squares are an important part of genetics because of inheritance, but the stuff now is all gene expression and interaction. It's pretty terrifying, because that's where the real work is all going to be, but it's also incredibly exciting, because bio is going to be the science of this century.
If you're interested in slightly higher level concepts, I just found this website at my college's webserver (it's a class I had to take, intro to Molecular Bio) and it looks like it's got some good info through the flash animations. If you want the hardcore stuff, go to the NCBI site where you can browse the genome, search for proteins and genes, and do all the stuff real biologists do:-) If you're at a University that's paying online fees, you can read journal articles that they link to from University IP's as well.
Medicine Interaction related deaths are caused by either incompetent doctors, patients not disclosing medications fully, or foolish patients not reading warning labels. It's basically idiocy and carelessnes that causes this. When taking medication, remember that you are putting a chemical into your body, and we have a pretty good idea as to how they interact with other ones clinically, if not molecularly (experimenting with that's probably unethical anyhow). Medical interaction research isn't neglected, but is a standard and critical part of getting a drug approved for use. If you want to know more, go to www.fda.gov and look at their massive database on drugs. They've got info on interactions aplenty, particularly their medwatch database.
And as for why gene interaction is so hot, is that it's the real key to a lot problems. You thought that the human genome was it? No no no... that was only the beginning... it was the map for gene interactions. The genes are worthless if we can't figure out what they do and how they interact. I mean, we can't even tell you how an E. coli works even though we've got the genome. There will be a lot of profit out of finding protein interactions, sure, but it'll be to find cures. I work in a lab that's trying to figure out gene therapy in prostate cancer. We need to know the genetic mechanisms for therapy to be effective. Or don't you want cancer cured?
Yeah, a nice way to improve it would be to do something like a genscan search, where you take the raw protein sequence (or gene sequence) and look for conserved portions that are known to interact with other conserved portions (kinda like the zinc finger motif and such). Then go through the literature like this project has done, or a new kind of database of genechip-type data, showing which genes are expressed together, and correlate the data together. Then go from there with things like Chromatin Immunoprecipitation (ChIP) to find out what's really interacting. The future's looking good for us biologists!:-)
No offense, but this is really really different than an 8x8 punnet square (which isn't really that bad, I've done dozens of 'em by hand). This is hardcore datamining the scientific literature, involving lots and lots of parsing keywords and finding gene interactions. What I'd like to see is a tool to do this with raw gene and protein sequences (thinking... possible cool project for me!) Then a tool to combine those would be sweet! Mmmm... genes....
"I may not have morals, but I have standards."
Re:The Perl6 answer could be ... Ruby
on
Apocalypse 2
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· Score: 2
Ruby looks really cool to me too. I've just downloaded it and installed it, and I'm planning to write a few test scripts in it. Since our server doesn't have a heavy load, I'd rather have our CGI's readable, and Ruby seems to be a good way to do it. I just need the time to go through the tutorial...
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What makes you think Windows is the best and most modern OS? My copy of windows sucks ass in terms of stability and configurability compared to my copy of Linux. It's less fun too :-)
I've got way better app support via apt-get (consistent updates, security fixes for all apps on my system), I don't have to reboot my system every time I make a network change, I don't have to reboot my system every time I load a new driver/module, and I've got the ability to boot multiple versions of my system with different features depending on what I need.
Oh yes, and I don't have such wonderful modern operating system type features such as Outlook and IE security holes.
Wow... my OS must be antiquated to allow such things and still not crash as much as my modern copy of windows. Personally, while Linux has a lot to learn from other systems, I think Windows has a long way to go to catch up to a ten year old clone of a thirty year old operating system.
"I may not have morals, but I have standards."
Ok, this is just nuts, not insightful. I'm no kernel wizard either (far from it!) but I do know that integrating these things in to kernel space is just a bad idea. Preloading the mozilla libraries is something that can and possibly should be done at startup, although you don't want to integrate them in to the kernel by any means.
The reason you don't want them in kernel space is, should one crash, you'll take down the entire system. Not having protected memory for things like browsers and word processors is a very bad thing for any system. IE doesn't load anything into kernel space, and while IIS does apparently, you sacrifice stability and necessary reboots for the speed gain.
Konqueror does load up all its libs at KDE's startup making it a much faster start than Moz, although C++ has linking issues (see Waldo Bastian's paper on the subject).
And as for the assertion that taking MS's lead could lead Linux to desktop domination, then maybe you should read some of the other discussions on a KDE or Gnome story to get a better idea of what Linux does need to get on the desktop (this was a good one) and I can tell you it's not tying the browser to the kernel! Not having your system crash on you is a much better selling point than the slight speed gain from integration.
In conclusion: load libs at startup: good. Put apps in kernel space: bad.
"I may not have morals, but I have standards."
Sure, but only if pulled off skillfully and effectively, which is a very difficult prospect. I don't think there's anything that's so compelling about the Yopy to make it worthy of snatching that opportunity. Maybe if they were to lower that price point or something.
"I may not have morals, but I have standards."
Does anyone think that entering the PDA arena with what's been going on is such a good idea? Palm, the real leader, is in major trouble. Why would you want to enter the market now, especially with something targeted from $400 to $600, when anyone who's going to pay that probably already has a PDA? Crazy... don't be surprised to see this one fail, especially if they're hoping that the strength of linux alone will float it, because it didn't float indrema. Different sectors, granted, but linux alone does not a business plan make.
"I may not have morals, but I have standards."
Ok, since you're obviously a mac apologist, then please tell me why they don't have the market that windows has? Not to say that OSX is a bad system (in fact, I think it's really damn impressive) but the fact that they've managed to nail all these things for years and they still haven't beaten windows (or DOS back when it was DOS) just goes to show that it takes more than the things you list.
Point 1: ease of use. Macs have had this down since day 1. MS has had the market.
Point 2: Games, Internet, Word Processing. Games, not the whole game market, but a lot of good titles made their way to the Mac in the past. Internet, always had decent stuff, especially with IE 5 for the Mac (great browser!). Word Processing. Can't beat MS Word.
Point 3: Make it pretty. Always was prettier than windows, and is now way way prettier. Still not beating MS. Granted, the interface is different now, but the consistent one over 15 years didn't save them before.
This whole post isn't to say that I don't like Macs (I used to love them actually, and I still work with them all the time) but the fact is that with a strong user base like Windows to take over you need a hell of a lot of factors, and the ones you list are only a few of the important ones. No one is going to even buy the system without a fairly consistent UI, among other things.
Personally, I think people would love a free system (free beer, although explaining how the speech thing will benefit them would be an extra bonus) and underestimating the factor of cost is making the exact same mistake that Apple themselves made for so many years. We just have to get Linux on to people's desktops pre-installed so they don't have to dick around so much.
"I may not have morals, but I have standards."
I do this at work, although they're not diskless iMacs they do have preferences and such stored centrally. While it seems like a great solution it's really not because of the whole netboot thing. For some inexplicable reason, the iMacs have to constantly hit the network even for simple things like loading a webpage. We have a total of only four iMacs connected to the server, and not even stressing it much, but even browsing the internet slows the things to such a crawl that I get constant complaints about iMac speed. Open up a second or third browser window and the things become almost unusable.
Mac OSX isn't supported yet for netbooting or Macintosh Manager, so you can't get a modern OS running these things even though it would solve a lot (if not all) of the problems, although later in the year they should be there. But as it stands now, this is a really bad idea that I don't recommend it to anyone simply because it'll just piss off the users and make them hate Macs more. It's so bad that we're moving over to NFS for remote file access (also need to give PC's equal access via Samba) and doing all the multi-user stuff locally.
"I may not have morals, but I have standards."
And how do you know IBM was even responsible for this?
"I may not have morals, but I have standards."
The success of a company may be judged on whether or not they hand on to the source, but you can also say that the quality of the product itself is reflective of the same. Buggy MS products, most notably IE, Outlook, and IIS, are a bane to the internet community as a whole, and it's a problem that could be solved by a true Open Source/Free Software philosophy.
MS chooses to be successful and make a buttload of money, and that's their choice, but in no small part their customers suffer because of shoddy products that are now a monopoly. Not that I necessarily think MS should open up their code, but you can't say the bugs and flaws wouldn't be helped tremendously by releasing it.
It comes down choice, as Mundie says, but what he's not saying is that his company is making the choice to protect its business interests well ahead of its customer interests.
"I may not have morals, but I have standards."
Indeed! Why does it matter in reality if the average consumer is running free software on their box before it's ready? Free software is not ready to enter this arena by a long shot. We've got good libraries in Mesa and such, and some coming down the pipe, but we don't have the games yet, unless you count nethack and tuxracer (both cool, but they obviously aren't what we're talking about).
This is like saying that when people who bought Sparc's were using Solaris' compiler rather than the gcc in 1992 it was a major blow to free software. It wasn't, it's not, it didn't matter. The coders kept on coding. The software kept on flowing. Now we've got a whole damn system to use and we're working on making free software on the PC both powerful and friendly enough for the average frat boy. This is a huge task and it's going to take some more time, but we'll get there and then we can worry more about things like consoles (which may make more $, but aren't actually running anything of critical importance).
By then everyone will be replacing their X-boxes with something new and shiny with a brand new redesigned on button that they can press to run whatever. Consoles cycle completely, with a whole new system under the hood every five years, no ties to the old stuff. New games gives a whole new chance every five years for free software to be running that box full time. Linux does and will provide a way to run the console now as it will then. We will see consoles running some form of linux eventually, simply because it's too good a bargain not to use. But not until it's really ready. Until then, the people who load linux on their X-boxes will just have to be like those rogues who ran the early GNU tools as replacements for the ones that came with their version of UNIX. They may not be the mainstream, but don't count them out yet.
"I may not have morals, but I have standards."
The modified BSD license is considered a free license by GNU standards too. Just because it doesn't mimic the GPL exactly doesn't mean it's not free. Next time you post a link to somewhere, be sure you've read what it's talking about.
"I may not have morals, but I have standards."
"Goodbye ivy league" my ass. I hate that view because it's just not true. I have a friend who's at U. Penn in a special program doing a double science major in Biochemistry and Physics. In 9th grade he made a spectacle of himself by getting drunk before a school dance and wound up puking all over and getting his stomach pumped. Everyone at the school knew. People at other schools knew. And he was suspended for over a week and had to go to AA meetings and such. Despite this, he's still one of the brightest students in his college, and the entire ivy league system.
If you fuck up once or twice in high school you still have a chance to do very well, including getting in to ivy league schools (as though that's really the final measure of success anyway) and have a great life. And this kid was in middle school! The load kids like this have to bear doesn't get any easier with the idea that you can't recover from a fuck-up, and this is what's foisted on successful kids. The drive to constantly succeed doesn't allow any reprieve, and once you do mess up you really do feel like it's "goodbye ivy league" when that's just not the case. We need to teach kids that you've got to do your best, and if you fail or make a mistake then it's Ok. Pick yourself up. Dust yourself off. And go for it again. Just don't ever give up because that's when you've truly failed.
"I may not have morals, but I have standards."
Yes and no. This is a decent idea for something like drosophila, where you can mutate the gene and see what happens, but there's no way this would work on humans. If you've got a phenotype, you've got to do massive forward (reverse? I always get them confused...) genetics to find your gene. Cystic Fibrosis took a decade or so.
:-)
If it's the other way around and you've just got a sequence then you've got some different work to do. What if multiple genes in a pathway are mutated? What if there are multiple pathways affected by this gene? What if there is no noticable phenotype for a mutated gene?
Sure, with a massive database, this could work (and I mean huge, like multi-century lineage-total-human-population huge) but realistically, linking DNA string object to phenotype object and expecting to elucidate a pathway is pretty insane, even for someone with your nick
A better way is the genomics approach, where you sit down with the microarray and say "Ok, what's going on here?" The biological systems are too big for just a two variable approach.
The black box idea is a good one, but not the way you propose. If you use a black box to abstract away what's actually happening (i.e. ignore what you don't need in the microarray) without actually dumping any data (if you need it in the microarray, it's still there) then you have a feasible method. With the two variable approach, you force people to leave out so many variables that the system becomes just theoretical and pretty much impractical.
"I may not have morals, but I have standards."
Check this out:
Bioperl
Biopython
Biojava
BioXML
BioCORBA
I couldn't find anything for ruby (either linked from bioperl, as those were, or on their own app list) but you can bet it's coming. I'd personally love to see it. But there's plenty of options for bioinformatics other than perl, although perl's excellent text handling makes it a very suitable choice.
"I may not have morals, but I have standards."
Kinda like Samba? :-)
"I may not have morals, but I have standards."
One important thing to think about in terms of nanotech then, is that if biotechnology can go wrong with cancer, what happens when nanotech has its own cancer?
"I may not have morals, but I have standards."
Thank God for this post. Mod this baby up!!!
/.'ers fail to understand how difficult a genome is, and how the software model tends to fail because of the complexity (not that it can't cope, but we've just never seen spaghetti code on this level, nor should we ever if we don't have to).
I think most
"I may not have morals, but I have standards."
Well, you're right and you're wrong (like the other poster said). Granted, we have a long way to go, and all the wild claims of hearts in vats and the like are pretty unfounded, but we do have Gene Therapy already, which is the next big leap, and it'll have the largest immediate benefit. The stuff this article talked about, if it's coming at all (sounds kind of '50's vision of the future'-ish to me), is still decades off. But we've got gene therapy for Severe Combined Immunodeficiency (SCID) which works right now. It's a proof of concept, and it shows that there's more coming down the pipeline. The trick is not to get carried away with the hype, but also to keep in mind the amazing things we are capable of, and what we'll be capable of very soon.
"I may not have morals, but I have standards."
College isn't so bad, it all depends on where you go. No one makes you live in the dorms at a public university (at least not a UC). I understand your problem with the casual interest vs. career, but you do have opportunities to learn outside. I'm taking a class in Roman History because it's required for me to graduate as a general requirement. Ancient history is something I'm fond of, but not something I'd major in. You do have the opportunities to look around though. I know tons of people who spend their first two years just looking around. Changing majors is a normal and constant thing. The goal of college isn't generally to trap you in to what you want to do, but let you feel around a bit (a lot more than in high school!) and finally pick a course. Even then there are options. I'm majoring in molecular biology, with a specialization in computing, and an English minor :-)
"I may not have morals, but I have standards."
Your post put me very much in my place, and while I was aware that we don't have the multi-drug interactions down in the least (obviously due in large part to testing issues) that I wanted to inform the root post that there was some info on interactions available.
The real problem is the one you stated, that most seniors are on multiple meds at a time for about as many conditions. That is, quite simply, pumping the body with way too many chemicals to be safe, especically in people whose bodies are breaking down to begin with. These drug interactions are probably incredibly difficult to study, but I agree that it needs to be done. I also agree that we need some kind of mechanical checking via computer to eliminate a lot of the stupid errors. However, I think the real problem lies in the fact that we're pumping drugs in to people in ways that they just aren't capable of dealing with. We need better forms of treatment, and I think genetic therapies, as well as that critical yet neglected factor of prevention, are going to be key in the future. Healthy diet and exercise alone can help with a large number of ailments, thereby reducing the number, or at least dosage, of meds needed later on in life. And to prevent heart disease, rather than take the pill, introduce the healthy gene (I know it's not ready, but it is the future) and that's one less drug-drug interaction to worry about.
The other problem is that, in large part, we don't know what causes diseases really. Alzheimer's is getting closer, and the ulcer bacteria was just an absurd discovery in some ways. We need to understand the disease before we can treat it, and all these things have to play together. So while I fully agree with you, and apologize for oversimplifying, that we need to really study multi-drug interactions, I don't think that simply saying "well, we can treat you for heart disease or AIDS, but not both" (totally hypothetical example) is the answer. Prevention is key. Understanding the disease better is key. And, hopefully, gene therapy will ease the number of meds as well. We need to make use of all the things Molecular Biology has achieved and will achieve in the coming decades, rather than rely soley on the older method.
p.s. Thanks for teaching me something!
"I may not have morals, but I have standards."
Hehe, I actually just sat down with Ruby and wrote a basic Hello World program with a class. I'm very impressed! The whole messaging idea (smalltalk, right?) is very very cool. I'm going to keep playing with it this weekend (or right now!!!! Hahahah!!!!) What kind of libraries does Ruby still need? It'd be nice to have it as feature complete as perl. I really like perl as a utility, and it's a fun language to hack, but I'm pretty impressed with Ruby as is.
"I may not have morals, but I have standards."
Hehe, not to diminish what you did (very cool project that I thought about writing myself last year) but just that we're heading in to major league waters here, and it's pretty exciting. Punnet squares are an important part of genetics because of inheritance, but the stuff now is all gene expression and interaction. It's pretty terrifying, because that's where the real work is all going to be, but it's also incredibly exciting, because bio is going to be the science of this century.
:-) If you're at a University that's paying online fees, you can read journal articles that they link to from University IP's as well.
If you're interested in slightly higher level concepts, I just found this website at my college's webserver (it's a class I had to take, intro to Molecular Bio) and it looks like it's got some good info through the flash animations. If you want the hardcore stuff, go to the NCBI site where you can browse the genome, search for proteins and genes, and do all the stuff real biologists do
"I may not have morals, but I have standards."
Medicine Interaction related deaths are caused by either incompetent doctors, patients not disclosing medications fully, or foolish patients not reading warning labels. It's basically idiocy and carelessnes that causes this. When taking medication, remember that you are putting a chemical into your body, and we have a pretty good idea as to how they interact with other ones clinically, if not molecularly (experimenting with that's probably unethical anyhow). Medical interaction research isn't neglected, but is a standard and critical part of getting a drug approved for use. If you want to know more, go to www.fda.gov and look at their massive database on drugs. They've got info on interactions aplenty, particularly their medwatch database.
And as for why gene interaction is so hot, is that it's the real key to a lot problems. You thought that the human genome was it? No no no... that was only the beginning... it was the map for gene interactions. The genes are worthless if we can't figure out what they do and how they interact. I mean, we can't even tell you how an E. coli works even though we've got the genome. There will be a lot of profit out of finding protein interactions, sure, but it'll be to find cures. I work in a lab that's trying to figure out gene therapy in prostate cancer. We need to know the genetic mechanisms for therapy to be effective. Or don't you want cancer cured?
"I may not have morals, but I have standards."
Yeah, a nice way to improve it would be to do something like a genscan search, where you take the raw protein sequence (or gene sequence) and look for conserved portions that are known to interact with other conserved portions (kinda like the zinc finger motif and such). Then go through the literature like this project has done, or a new kind of database of genechip-type data, showing which genes are expressed together, and correlate the data together. Then go from there with things like Chromatin Immunoprecipitation (ChIP) to find out what's really interacting. The future's looking good for us biologists! :-)
"I may not have morals, but I have standards."
No offense, but this is really really different than an 8x8 punnet square (which isn't really that bad, I've done dozens of 'em by hand). This is hardcore datamining the scientific literature, involving lots and lots of parsing keywords and finding gene interactions. What I'd like to see is a tool to do this with raw gene and protein sequences (thinking... possible cool project for me!) Then a tool to combine those would be sweet! Mmmm... genes....
"I may not have morals, but I have standards."
Ruby looks really cool to me too. I've just downloaded it and installed it, and I'm planning to write a few test scripts in it. Since our server doesn't have a heavy load, I'd rather have our CGI's readable, and Ruby seems to be a good way to do it. I just need the time to go through the tutorial...
"I may not have morals, but I have standards."