Some have suggested that certain Seattle, WA company are behind this. If that were so then we might conclude that they, struggling to make a case via FUD, argument (and some might say, interesting bargaining with OEMs), are now trying to insert an artificial barrier to entry (ie cost) into the marketplace. Some at this company may be hoping that by artificially adding to the TCO of Linux, then their OS becomes more attractive on the bottom line. Me - I could nt possibly commet.
Technically its the preferred creditors of the company at the time that it folded. When you went under, an insolvency practitioner should have been hired to carve up the wreckage. You should anonymously approach them.
They will try to work out how to best extract cash from the code and then (after expenses of course) distribute the cash amongst the creditors.
It gets kinda complicated right there. If there are lots of creditors then the value will go on legal fees (sending letters etc). It will be a waste of time.
Often the main preferred creditor is the main investor.
If there is one big creditor, they will assert their ownership of it. It will then be sold, inserted into another of their portfolio companies, or mothballed (ie forgotten). None of these outcomes involve GPL-ing the thing.
Corporate insolvency and venture captialism are murky worlds at best and unfortunately the legal process means that I think you will be lucky if you get to do anything constructive with the code.
There is hope. I recall NaN (Blender) went under and the "community" raised a couple of hundred thousand dollars to "take ownership of" (ie GPL) it.
You should decide how much work you are willing to put in. The money men will have you running round, making all the calls, advertising, going to meetings etc. It will be good business experience
for you but it will take a bit of effort and you may not like the results.
Kudos for trying though.
Before I answer any of the questions, please remember that in the interests of brevity I have omitted to insert the phrase "I think" before every sentence. Please feel free to insert the phrase yourself. It's my personal opinion and this is pretty leading edge stuff, so others in the field will probably disagree and in many cases with good reason. Anyhoo, here goes.
* In the long run, will biology rewrite computing or will modern day technology concepts and theory be integrated into biology? If both are true, which will have the greater effect? I understand long run is ambiguous in this question, but Iâ(TM)m interested in all thoughts using any applicable definition.
ANSWER: //Biology will not rewrite computing in the sense of hardware or even software. The reason is that biomolecules are pretty flaky. Once pesky bacterium gets in there and its curtains. Also, its has a habit of changing. Its just too UNCERTAIN.
However, all field sof engineering till benefit from in-depth study of biology. Biomechanics gives us new bridges, the immune system gives IBM an idea of self-repairing computers.
My view is that biology and computing will meet when computing ceases to be "digital". We are getting there. Big systems are now storing and processing so much data that the complexity is approaching that of simple molecules. Add quantum computing and who knows?
Biology is the ULTIMATE uncertain system. We need other UNCERTAIN systems to analyse it properly.
* Tied to the first question: How will the nature of computing, and how we perceive it, change due to biology integration? More to the point, how much of the theory we learn today may change?
//ANSWER
I dont see biology having an effect. See above. Too hard to look after. As for theory, well a lot has already changed. A CS will already be familiar with MC, GA and GP, SA, Neural nets, Inference networks, all that good stuff. For my lifetime, and with Moores Law still on the statue book, I think semiconductors running code will ba the hardware, but the algorithms will borrow heavily from nature.
* What will be the biggest issue determining the success of the adoption of biology-integrated computing? Will it be technology factors or will it be societal factors (e.g., rebellion by the Right Wing), or something else? What things must hold true to make the idea succeed?
//ANSWER
Assuming simple biomolecules get used, the sort of things we are talking about are bacteriorhodopsin for information storage, nucleic acids for intractable problem domains and (maybe) proteins for fast switching. These are not nearly biological systems as even a molecular biologist would understand them, never mind the public. Now putting a rat brain into a microwave - thats another story but that is not going to happen, well, ever. QNX on a microcontroller can look after a microwave.
I can see a future for complex sensor arrays being used by human beings to control hardware or to communicate with each other. But again, speaking with my biology hat on, it is far more likely that you would want to do this via conventional hardware detecting electrical signals than by integrating hardware into the body at the molecular level.
* And perhaps the hottest issue of all: Is there anything inherently wrong with pursuing this avenue? What may be some of the consequences?
//ANSWER
I dont see an issue in vitro. A company I was involved with was using protein arrays to map aspects of drug candidates' structures. We used a Linux cluster to crunch the data from the array to get an answer. The reason for this is that although QM and docking are neat, a REAL protein will bind and energetically minimise in femtoseconds where even a big cluster will take hours to do it using QM and compute time shortcuts, eg Gaussians.
The 64x10E6 currency unit question is what happens if we start tinkering in vivo. Rat brains con
There are several ways I can tackle this. I can bitch and moan, but thatll get me nowhere. I can sympathise (you can take that as read) but it wastes you time. Or i can do this...
I am a reasonably senior manager in IT. I have been around a bit and here are the facts.
A)
It is the resposibility of your manager to report to his manager, up the line to the CEO. The CEO works for the board. The board DO WHAT IS BEST FOR THE COMPANY SHAREHOLDERS. Not you. I'll come back to this point as its important.
B)
Any student of HR will understand that 12*7*6 is not tenable. Per day, assume 12 hours work, 1 hour break, 2*0.5=1 hour commuting, 8 hours sleep, 1 hour breakfast/wash/shave, 1 hour evening meal. Add it up. That is 23 hours. That leaves 7 hours a week for other things. Grocery store 1 hour, washing clothes 1 hour, etc. 12/7 working not only destroys your social life, it is MATHEMATICALLY intractable.
C)
Any student of psychology will know that in a given team of (say) 10, 2 will go the distance, 2 will do it under duress, 2 will do it but badly (see B, above), 2 will do a half-assed job and 2 will simply quit. Its a bell curve of human behaviour and RESPONSE UNDER PRESSURE. Thats the key. Some personalities (like mine) - Briggs-Meier ENTJ will simply quit. Google for Briggs-Meier, look at the behavioural motifs and then the responses of each type under stress. I predict you will lose 25% of your effectiveness over the duration of the project.
D)
I assume most people are familiar with the mythical man month so I wont go there other than to say hiring new contractors wont help.
OK. So what do we do. There has been good advice about not being the guy to put his head above the parapet. Especially in this market. So draft a letter, all sign it, and deliver ANONYMOUSLY to your management.
Make the points above. As a responsible manager, they SHOULD see impending doom and go straight back to the client and negotiate an extension such that critical cuntionality is delivered on-time and less critical thereafter. They can sweeten this with free support later. They HAVE to spread this load or the team will walk. There, you have turned this debate from a "they are trying to screw us - f*ck them" into a BUSINESS DECISION. Business is about weighing up risk. They need to clearly understand the risks. I can now refer to to point (A). The company's interests are clearly not served by doing this. What are the penalties if they fail? Can they risk failure if some of you guys take the ultimate sanction and walk. I refer you to point (C): other posters tell you to quit whiing and/or knuckle down. Yeah. Whatever. The truth is that certan personalities will QUIT whether it is logical to do so or not. Some personlaities UNDER PRESSURE will resort to self-destructive behaviours such as walking out with no job to go to and even sabotage. I have seen it happen.
Document EVERYTHING. If HR get involved (they will have to in this one I think), if people get fired, quit, sue (the whole gamut is possible - nay, probable here) you want to have some arrows to fire. Even if there is nothing to document - document the fact that there is nothing. Do it NOW.
If you win concessions, carrots, etc from management, get it up front and guaranteed IN WRITING from the guy who will ultimately write the cheque. Clue: that wont be your line manager. In these times, it's likely senior management/CFO. Your manager will piss and moan about you mistrusting him but the risks here are too great to not do it.
Regardless, get the company to formally request each of you in writing to do the work. Even if you as salaried employees are expected to do certain unpaid overtime, in a LEGAL situation the court will generally ask whether the request was REASONABLE. 12/5 or even 8/7 (sixtyish) hours might be reasonable but 84? for two months? in summer? Hmmm. A judge will have a long hard look at that.
There are lots of helpful IT tools around that are used in drug discovery. These range from simple sequence alignment algorithms right through to complex ab initio protein folding code - ie quantum mechanics.
While these programs are very helpful, they often contain shortcuts that reduce compute time. More compute crunch essentially means that these shortcuts can be removed and deeper/wider/more accurate analysis results. Which is good.
That said, more raw crunch and capacity brings in other issues such as capacity, I/O, network, concurrence, version control, security, recovery, UPS, climate and so on and so forth. The new iron, in other words, needs looking after. So some of the new hardware is there simply to look after the other hardware, if you get my drift.
Remember, there is more to drug discovery than meets the eye. Living systems are extremely complex. Drugs or hypotheses that look great in silico do not always pass muster in vitro never mind the real world. Moreover, FDA approval still relies on squirting compounds into cells, rats, humans etc. Until the FDA permits in silico proof of efficacy, toxicity, LD50 etc, we will need to maintain "traditional" avenues for experimentation.
It is good stuff, though and I for one welcome the investment in new compute capacity. I am keen however that no-one is seduced by the headlines; a lot of hard work has to be done in the lab to corroborate the evidence uncovered by the computers. In my experience the data is academically interesting but is only the beginning in terms of delivering an effective therapy to the patient.
Slashdot Mirror
Some have suggested that certain Seattle, WA company are behind this. If that were so then we might conclude that they, struggling to make a case via FUD, argument (and some might say, interesting bargaining with OEMs), are now trying to insert an artificial barrier to entry (ie cost) into the marketplace. Some at this company may be hoping that by artificially adding to the TCO of Linux, then their OS becomes more attractive on the bottom line. Me - I could nt possibly commet.
Technically its the preferred creditors of the company at the time that it folded. When you went under, an insolvency practitioner should have been hired to carve up the wreckage. You should anonymously approach them.
They will try to work out how to best extract cash from the code and then (after expenses of course) distribute the cash amongst the creditors.
It gets kinda complicated right there. If there are lots of creditors then the value will go on legal fees (sending letters etc). It will be a waste of time.
Often the main preferred creditor is the main investor.
If there is one big creditor, they will assert their ownership of it. It will then be sold, inserted into another of their portfolio companies, or mothballed (ie forgotten). None of these outcomes involve GPL-ing the thing.
Corporate insolvency and venture captialism are murky worlds at best and unfortunately the legal process means that I think you will be lucky if you get to do anything constructive with the code.
There is hope. I recall NaN (Blender) went under and the "community" raised a couple of hundred thousand dollars to "take ownership of" (ie GPL) it.
You should decide how much work you are willing to put in. The money men will have you running round, making all the calls, advertising, going to meetings etc. It will be good business experience for you but it will take a bit of effort and you may not like the results.
Kudos for trying though.
Before I answer any of the questions, please remember that in the interests of brevity I have omitted to insert the phrase "I think" before every sentence. Please feel free to insert the phrase yourself. It's my personal opinion and this is pretty leading edge stuff, so others in the field will probably disagree and in many cases with good reason. Anyhoo, here goes.
* In the long run, will biology rewrite computing or will modern day technology concepts and theory be integrated into biology? If both are true, which will have the greater effect? I understand long run is ambiguous in this question, but Iâ(TM)m interested in all thoughts using any applicable definition.
ANSWER:
//Biology will not rewrite computing in the sense of hardware or even software. The reason is that biomolecules are pretty flaky. Once pesky bacterium gets in there and its curtains. Also, its has a habit of changing. Its just too UNCERTAIN.
However, all field sof engineering till benefit from in-depth study of biology. Biomechanics gives us new bridges, the immune system gives IBM an idea of self-repairing computers.
My view is that biology and computing will meet when computing ceases to be "digital". We are getting there. Big systems are now storing and processing so much data that the complexity is approaching that of simple molecules. Add quantum computing and who knows?
Biology is the ULTIMATE uncertain system. We need other UNCERTAIN systems to analyse it properly.
* Tied to the first question: How will the nature of computing, and how we perceive it, change due to biology integration? More to the point, how much of the theory we learn today may change?
I dont see biology having an effect. See above. Too hard to look after. As for theory, well a lot has already changed. A CS will already be familiar with MC, GA and GP, SA, Neural nets, Inference networks, all that good stuff. For my lifetime, and with Moores Law still on the statue book, I think semiconductors running code will ba the hardware, but the algorithms will borrow heavily from nature.
* What will be the biggest issue determining the success of the adoption of biology-integrated computing? Will it be technology factors or will it be societal factors (e.g., rebellion by the Right Wing), or something else? What things must hold true to make the idea succeed?
Assuming simple biomolecules get used, the sort of things we are talking about are bacteriorhodopsin for information storage, nucleic acids for intractable problem domains and (maybe) proteins for fast switching. These are not nearly biological systems as even a molecular biologist would understand them, never mind the public. Now putting a rat brain into a microwave - thats another story but that is not going to happen, well, ever. QNX on a microcontroller can look after a microwave.
I can see a future for complex sensor arrays being used by human beings to control hardware or to communicate with each other. But again, speaking with my biology hat on, it is far more likely that you would want to do this via conventional hardware detecting electrical signals than by integrating hardware into the body at the molecular level.
* And perhaps the hottest issue of all: Is there anything inherently wrong with pursuing this avenue? What may be some of the consequences?
I dont see an issue in vitro. A company I was involved with was using protein arrays to map aspects of drug candidates' structures. We used a Linux cluster to crunch the data from the array to get an answer. The reason for this is that although QM and docking are neat, a REAL protein will bind and energetically minimise in femtoseconds where even a big cluster will take hours to do it using QM and compute time shortcuts, eg Gaussians.
The 64x10E6 currency unit question is what happens if we start tinkering in vivo. Rat brains con
I am a reasonably senior manager in IT. I have been around a bit and here are the facts.
A)
It is the resposibility of your manager to report to his manager, up the line to the CEO. The CEO works for the board. The board DO WHAT IS BEST FOR THE COMPANY SHAREHOLDERS. Not you. I'll come back to this point as its important.
B)
Any student of HR will understand that 12*7*6 is not tenable. Per day, assume 12 hours work, 1 hour break, 2*0.5=1 hour commuting, 8 hours sleep, 1 hour breakfast/wash/shave, 1 hour evening meal. Add it up. That is 23 hours. That leaves 7 hours a week for other things. Grocery store 1 hour, washing clothes 1 hour, etc. 12/7 working not only destroys your social life, it is MATHEMATICALLY intractable.
C)
Any student of psychology will know that in a given team of (say) 10, 2 will go the distance, 2 will do it under duress, 2 will do it but badly (see B, above), 2 will do a half-assed job and 2 will simply quit. Its a bell curve of human behaviour and RESPONSE UNDER PRESSURE. Thats the key. Some personalities (like mine) - Briggs-Meier ENTJ will simply quit. Google for Briggs-Meier, look at the behavioural motifs and then the responses of each type under stress. I predict you will lose 25% of your effectiveness over the duration of the project.
D)
I assume most people are familiar with the mythical man month so I wont go there other than to say hiring new contractors wont help.
OK. So what do we do. There has been good advice about not being the guy to put his head above the parapet. Especially in this market. So draft a letter, all sign it, and deliver ANONYMOUSLY to your management.
Make the points above. As a responsible manager, they SHOULD see impending doom and go straight back to the client and negotiate an extension such that critical cuntionality is delivered on-time and less critical thereafter. They can sweeten this with free support later. They HAVE to spread this load or the team will walk. There, you have turned this debate from a "they are trying to screw us - f*ck them" into a BUSINESS DECISION. Business is about weighing up risk. They need to clearly understand the risks. I can now refer to to point (A). The company's interests are clearly not served by doing this. What are the penalties if they fail? Can they risk failure if some of you guys take the ultimate sanction and walk. I refer you to point (C): other posters tell you to quit whiing and/or knuckle down. Yeah. Whatever. The truth is that certan personalities will QUIT whether it is logical to do so or not. Some personlaities UNDER PRESSURE will resort to self-destructive behaviours such as walking out with no job to go to and even sabotage. I have seen it happen.
Document EVERYTHING. If HR get involved (they will have to in this one I think), if people get fired, quit, sue (the whole gamut is possible - nay, probable here) you want to have some arrows to fire. Even if there is nothing to document - document the fact that there is nothing. Do it NOW.
If you win concessions, carrots, etc from management, get it up front and guaranteed IN WRITING from the guy who will ultimately write the cheque. Clue: that wont be your line manager. In these times, it's likely senior management/CFO. Your manager will piss and moan about you mistrusting him but the risks here are too great to not do it.
Regardless, get the company to formally request each of you in writing to do the work. Even if you as salaried employees are expected to do certain unpaid overtime, in a LEGAL situation the court will generally ask whether the request was REASONABLE. 12/5 or even 8/7 (sixtyish) hours might be reasonable but 84? for two months? in summer? Hmmm. A judge will have a long hard look at that.
And final
While these programs are very helpful, they often contain shortcuts that reduce compute time. More compute crunch essentially means that these shortcuts can be removed and deeper/wider/more accurate analysis results. Which is good.
That said, more raw crunch and capacity brings in other issues such as capacity, I/O, network, concurrence, version control, security, recovery, UPS, climate and so on and so forth. The new iron, in other words, needs looking after. So some of the new hardware is there simply to look after the other hardware, if you get my drift.
Remember, there is more to drug discovery than meets the eye. Living systems are extremely complex. Drugs or hypotheses that look great in silico do not always pass muster in vitro never mind the real world. Moreover, FDA approval still relies on squirting compounds into cells, rats, humans etc. Until the FDA permits in silico proof of efficacy, toxicity, LD50 etc, we will need to maintain "traditional" avenues for experimentation.
It is good stuff, though and I for one welcome the investment in new compute capacity. I am keen however that no-one is seduced by the headlines; a lot of hard work has to be done in the lab to corroborate the evidence uncovered by the computers. In my experience the data is academically interesting but is only the beginning in terms of delivering an effective therapy to the patient.
Not knocking it - merely a reality check!