I find this cause, and the NAMD one quite obnoxious. It's not really ethical to demand that someone cite your paper in their work, even though they quite obviously will in any case (if you didn't a referee is almost certainly going to pick you up on it).
My argument against 'junk' DNA and similar things; If it costs energy to do, then there is likely a reason it is being done. Otherwise, we would probably see it 'phased' out due to natural selection pressures.
Having unused DNA around could give you an evolutionary advantage. A higher mutation and duplication rate will let you adapt quickly to changes in the environment.
For example, an inexact duplicate of a gene is created. This then mutates in to something useful giving you a selective advantage. A lot of the time those duplicates will be useless, but sometimes they will be useful.
I have always found it irksome when biologists claim that a high percentage of our DNA is just junk (do-nothing) DNA. It's as though they were saying "we of course know what it does: It does not do anything".
Why not say "we don't know what it does, if anything at all"?
Most of them do, "Junk DNA" is a handy phrase and one that's been picked up by the media, the majority of Biologists are quite open minded on the subject. The fact that a lot of it is translated in to RNA even lends wait to the argument that it is of functional value. Aside from that things like telomeres (the ends of DNA that get eaten away as the replicates) and centomeres would be labelled as "junk" even though they have obvious functional value. Most scientists just use "junk" as a synonym for "non-protein coding" as a kind of shorthand.
What's more interesting to me is how they are going to obtain the DNA sequence of the gamers, that's a far from straight forward process, even the next-gen sequencers would have a tough time creating a reasonable sequence for $100,000. My guess is they are talking about mapping some common SNPs and that's it.
Still I'm tempted to enter just to get a copy of my genome.
That's all well and good, but how do you know the company's software is "good enough"? By the OP's own admission, there is little in the way of coding standards, testing, or any other sort of formalization. For all you know, there could be 10 critical flaws in the software right now, but you just haven't encountered them.
The entire reason we have formalized development practices and testing methodologies is to allow us to say with some degree of confidence, "The software is good enough." Without that, you can guess, but you don't know.
You make a judgment call, that's what you always do. Unit testing isn't going to tell you if you're using the correct algorithms it just tells you that the tests you wrote still pass (for example).
The CEO may be thinking ``refactoring this code will take 5 months, in 6 the current product will no longer be viable and we'll have a replacement in the market. I should dump this product and focus on the replacement. More over, making good code will mean that I'll need to retrain the entire software team, that's going to slow them down a lot and I need a new product out pronto. Hire good software engineers to replace them? Can't there's a skills shortage in their areas (e.g. they are image analysis specialists). Hire software engineers to refactor their code? Slows them down as well.''
I guess what is boils down to is skills, there's a shortage of people who are algorithm specialists (image analysis etc. etc.) and also good software engineers. So sometimes you have to be pragmatic, the code is ``as good as or better than the competition'' (for example produces an error rate on average X percent lower) and that's as good as it needs to be.
This is true, though with some of the next-gen sequencer vendors you can claim back the reagent costs for failed runs (well I guess if you're a big enough customer).
It's interesting to note that the Illumina device control software had a memory leak which would cause it crash every 9 hours or so. The solution? Why write some code to automatically relaunch the software of course!
It's gotten somewhat better over the past 5 years, but as the hardware lives for 20 years, we end users get to enjoy the crappy software long after the company has moved on. It certainly does color my decision about which hardware I will buy in the future, though.
Yea I wouldn't argue that ABI software sucks, but it's a useful stick to beat management with. I'm not sure it's got much better... They've not open sourced the primary data analysis or device control software for the SOLiD sequencers (which suck hard). From what I could see a lot of the device stuff uses messy perl scripts.
I really wish they, and Illumina the current next-gen leader, would open source their software (both device control and primary data analysis). If that were the case I'd be refactoring it, adding unit tests etc. right now.
It sounds like in your company there is no one doing this job. You've talked to the CEO. Get him to make you VP of software and tell him you'll solve the problem if he gives you responsibility.
Management may be doing its job perfectly well! This could quite possibly be R&D code that was hacked together by scientists with no formal training in programming (most likely Biologists). The R&D code then found it's way in to production (because they needed to get something out the door).
The software is good enough to get the device working, and it's the performance of the device that makes the company money, the software just has to work ``well enough'' the device is where the money is made.
Management maybe planning to hire a new development team to develop production software. Or they may realise that the current device isn't going to be in market long enough to warrant developing production style software. As I've mentioned in my other comment, I think the best solution here is to open source the software, it's the way to biotech industry is moving anyway and it will help you with you're software engineering problems.
Management are possibly right, the important thing is getting the product to market. If the R&D people write bad code, but code that works, and it gets the instrument to market then ship it. If it's instrument based, the software isn't the critical problem (if it works better than the other guys you win, doesn't matter if the primary data analysis software sucks so long as it more of less works).
However, you should try and convince you're management to open source the software. In this industry the probability is that if you don't open source it someone else will write an open source replacement (see Phred/Phrap, and the open source replacements of the primary data analysis software on next-gen sequencers which are starting to appear). That means your company losses control of the primary data analysis and possibly device control software, and that's bad for your company.
Open source has the added benefit that your development costs will fall (you can start using GPL code), it'll help you engage with the scientific community and you'll get people outside the company doing free work for you (seriously people want to get this stuff working, they'll help). You'll also get free peer review on your code which will drive standards up.
Scared of showing your crap code? Don't be, in this industry I've seen enough to know that most of it sucks (a lot of it's written by Biologists with no formal training). The clincher? "ABI are doing it, why can't we!" http://solidsoftwaretools.com/gf/
Any data that's really important isn't going to reproducible.
If you've just spent a few years compute, finding a large prime, or decrypting a message, or finding the cure for cancer, producing data that would be of significant scientific importance, or save lives then it's important that you don't lose it.
It may however be entirely reproducible (down to the bit level).
Last time I heard about the DWare stuff it generally wasn't considered a quantum computer, more like a very small analog computer. Is this still the case?
There are parents who know they have medical problems related to their genetics, and yet are still selfish enough to "try for one" instead of adopting one of the 50,000+ or so that die of starvation somewhere in the world.
Why would your DNA want to being up someone else's child?
Where do you think the data for/dev/urandom comes from? It's a pseudo-random number generator unless you've got a hardware random number generator
It's my understanding that urandom often uses data from interrupts, keyboard input, device controllers etc. to increase the entropy of the random numbers it produces.
hardware random number generator, but even that probably uses a pseudo-random algorithm.
Hardware random number generators are not considered pseudo-random. As I understand it they usually amplify noise, pick up random radio interference or use Quantum random sources. In any case they should all have drivers to check the "randomness" of source. The only way they could be considered pseudo-random if, against the trend of modern physics, you believe that "randomness" does not exist and the universe is inherently deterministic.
I would be more specific than just to say, "profound emotional problems." I think the real problem (for both guys) was obsessive thinking. These guys lived in a non-stop world of abstractions, symbols, logic and ideas.
I couldn't agree more, that's why I try to minimize my use of logic and symbolic abstractigluergle ibble murble gump000000000000.............
I work for a small business and I have been slowly outsourcing our email to GMAIL its free and it is easier and less work and expense on our end.
And your employees are basically paying for it by being forced to view ads. In the education sector this is even worse. I don't think HE should basically force students to view ads in order to complete there course requirements (unless they are paying google and msn for ad free versions). This is an essential service and HE is being paid to provide it not subsidize it through advertising.
Slashdot Mirror
I find this cause, and the NAMD one quite obnoxious. It's not really ethical to demand that someone cite your paper in their work, even though they quite obviously will in any case (if you didn't a referee is almost certainly going to pick you up on it).
My argument against 'junk' DNA and similar things; If it costs energy to do, then there is likely a reason it is being done. Otherwise, we would probably see it 'phased' out due to natural selection pressures.
Having unused DNA around could give you an evolutionary advantage. A higher mutation and duplication rate will let you adapt quickly to changes in the environment.
For example, an inexact duplicate of a gene is created. This then mutates in to something useful giving you a selective advantage. A lot of the time those duplicates will be useless, but sometimes they will be useful.
Vegan: Someone who slaughters and kills fruits, and vegetables.
I have always found it irksome when biologists claim that a high percentage of our DNA is just junk (do-nothing) DNA. It's as though they were saying "we of course know what it does: It does not do anything". Why not say "we don't know what it does, if anything at all"?
Most of them do, "Junk DNA" is a handy phrase and one that's been picked up by the media, the majority of Biologists are quite open minded on the subject. The fact that a lot of it is translated in to RNA even lends wait to the argument that it is of functional value. Aside from that things like telomeres (the ends of DNA that get eaten away as the replicates) and centomeres would be labelled as "junk" even though they have obvious functional value. Most scientists just use "junk" as a synonym for "non-protein coding" as a kind of shorthand.
Yea, I didn't RTFA. Is this stuff sRNA/ncRNA something like that? Does it look like it forms secondary structure? Someone smart reply please. :)
What's more interesting to me is how they are going to obtain the DNA sequence of the gamers, that's a far from straight forward process, even the next-gen sequencers would have a tough time creating a reasonable sequence for $100,000. My guess is they are talking about mapping some common SNPs and that's it. Still I'm tempted to enter just to get a copy of my genome.
Come on guys, I've come to every one of these and read nothing but negatives comments. Seriously can we get rid of idle now?
I agree, how can the iPhone access the web without an Ethernet port!
iPhone -> VNC Client -> Flash!
or even
iPhone -> ssh Client -> Gopher!
Come on guys you just need to Think Different (tm)
That's all well and good, but how do you know the company's software is "good enough"? By the OP's own admission, there is little in the way of coding standards, testing, or any other sort of formalization. For all you know, there could be 10 critical flaws in the software right now, but you just haven't encountered them.
The entire reason we have formalized development practices and testing methodologies is to allow us to say with some degree of confidence, "The software is good enough." Without that, you can guess, but you don't know.
You make a judgment call, that's what you always do. Unit testing isn't going to tell you if you're using the correct algorithms it just tells you that the tests you wrote still pass (for example).
The CEO may be thinking ``refactoring this code will take 5 months, in 6 the current product will no longer be viable and we'll have a replacement in the market. I should dump this product and focus on the replacement. More over, making good code will mean that I'll need to retrain the entire software team, that's going to slow them down a lot and I need a new product out pronto. Hire good software engineers to replace them? Can't there's a skills shortage in their areas (e.g. they are image analysis specialists). Hire software engineers to refactor their code? Slows them down as well.''
I guess what is boils down to is skills, there's a shortage of people who are algorithm specialists (image analysis etc. etc.) and also good software engineers. So sometimes you have to be pragmatic, the code is ``as good as or better than the competition'' (for example produces an error rate on average X percent lower) and that's as good as it needs to be.
This is true, though with some of the next-gen sequencer vendors you can claim back the reagent costs for failed runs (well I guess if you're a big enough customer).
It's interesting to note that the Illumina device control software had a memory leak which would cause it crash every 9 hours or so. The solution? Why write some code to automatically relaunch the software of course!
It's gotten somewhat better over the past 5 years, but as the hardware lives for 20 years, we end users get to enjoy the crappy software long after the company has moved on. It certainly does color my decision about which hardware I will buy in the future, though.
Yea I wouldn't argue that ABI software sucks, but it's a useful stick to beat management with. I'm not sure it's got much better... They've not open sourced the primary data analysis or device control software for the SOLiD sequencers (which suck hard). From what I could see a lot of the device stuff uses messy perl scripts.
I really wish they, and Illumina the current next-gen leader, would open source their software (both device control and primary data analysis). If that were the case I'd be refactoring it, adding unit tests etc. right now.
It sounds like in your company there is no one doing this job. You've talked to the CEO. Get him to make you VP of software and tell him you'll solve the problem if he gives you responsibility.
Management may be doing its job perfectly well! This could quite possibly be R&D code that was hacked together by scientists with no formal training in programming (most likely Biologists). The R&D code then found it's way in to production (because they needed to get something out the door).
The software is good enough to get the device working, and it's the performance of the device that makes the company money, the software just has to work ``well enough'' the device is where the money is made.
Management maybe planning to hire a new development team to develop production software. Or they may realise that the current device isn't going to be in market long enough to warrant developing production style software. As I've mentioned in my other comment, I think the best solution here is to open source the software, it's the way to biotech industry is moving anyway and it will help you with you're software engineering problems.
Management are possibly right, the important thing is getting the product to market. If the R&D people write bad code, but code that works, and it gets the instrument to market then ship it. If it's instrument based, the software isn't the critical problem (if it works better than the other guys you win, doesn't matter if the primary data analysis software sucks so long as it more of less works).
However, you should try and convince you're management to open source the software. In this industry the probability is that if you don't open source it someone else will write an open source replacement (see Phred/Phrap, and the open source replacements of the primary data analysis software on next-gen sequencers which are starting to appear). That means your company losses control of the primary data analysis and possibly device control software, and that's bad for your company.
Open source has the added benefit that your development costs will fall (you can start using GPL code), it'll help you engage with the scientific community and you'll get people outside the company doing free work for you (seriously people want to get this stuff working, they'll help). You'll also get free peer review on your code which will drive standards up.
Scared of showing your crap code? Don't be, in this industry I've seen enough to know that most of it sucks (a lot of it's written by Biologists with no formal training). The clincher? "ABI are doing it, why can't we!" http://solidsoftwaretools.com/gf/
Any data that's really important isn't going to reproducible.
If you've just spent a few years compute, finding a large prime, or decrypting a message, or finding the cure for cancer, producing data that would be of significant scientific importance, or save lives then it's important that you don't lose it. It may however be entirely reproducible (down to the bit level).
Last time I heard about the DWare stuff it generally wasn't considered a quantum computer, more like a very small analog computer. Is this still the case?
More likely the hardware than the software, but I think it will come.
k, I love these clicky keyboards but they piss off my work mates. Is there a good but slightly quieter keyboard I can get for the office?
Why would your DNA want to being up someone else's child?
captcha: condom
Hey! Me is that you!? I knew I'd invent time travel and get myself a better ID eventually.
...but...
oh God there has to be some reason I spent a week configuring mutt.