Abstract: Classical studies show that for many proteins, the information required for specifying the tertiary structure is contained in the amino acid sequence. Here, we attempt to define the sequence rules for specifying a protein fold by computationally creating artificial protein sequences using only statistical information encoded in a multiple sequence alignment and no tertiary structure information. Experimental testing of libraries of artificial WW domain sequences shows that a simple statistical energy function capturing coevolution between amino acid residues is necessary and sufficient to specify sequences that fold into native structures. The artificial proteins show thermodynamic stabilities similar to natural WW domains, and structure determination of one artificial protein shows excellent agreement with the WW fold at atomic resolution. The relative simplicity of the information used for creating sequences suggests a marked reduction to the potential complexity of the protein-folding problem.
From this page: a WW domain is the smallest, monomeric, triple-stranded, anti-parallel beta-sheet protein domain that is stable in the absence of disulfide bonds, cofactors or ligands.
Prof. Church synthesizes long DNA sequences with remarkable fidelity by using parallel synthesis and amplification on a gene chip (ordered array of shorter DNA sequences). Paper.
Remember last year when researchers created polio virus from scratch? Paper. It took 3 years to make the 7500 bp genome -- this new technology would make this kind of project easier.
This article makes a lot of sense. We need a new business model, not just for music, but for any product that can be copied with high fidelity. Right now this is clearly the case with music and software; later it may extend to movies; and maybe far in the future, to nanotech constructors.
The current system is workable because people who pay for music and software subsidize people who don't pay for it. It's a stable system, as long as it's more convenient to buy a product than to pirate it. However, it will only get easier, not harder to freely distribute information, as programs like Napster show. As the cost of copying software drops, the price a developer can charge for software will have to drop as well, just so developers can compete against copies of their own product.
Which brings us to the question: how do we allow developers to charge a reasonable price for their software, while encouraging, not restricting, the free transfer of information?
Here's the proposal:
Allow music, software, etc. to be freely copied without restriction.
Have companies like Nielsen Media research develop product popularity metrics based on easily quantifiable demographics.
Have people pay a fixed fee every year for "intellectual property use" based on their demographic group.
Of course, some immediate objections come to mind:
I don't want to pay for someone else's software use.
If you buy software, you already are. This system will be more fair. Besides, there are plenty of situations where we subsidize a larger group based on statistical information, i.e. any sort of insurance, paying a flat fee for internet access, property taxes.
The system won't be accurate.
In the limit of perfect statistics, we could determine a person's software use exactly, and each person would pay for exactly what he used. We can't, and so we clump people together into larger groups, with good enough statistics so that the end result is roughly correct.
This is better than the current system, where the industry aspries to have each person pay for exactly what he uses by mandating that this be the case, rather than making a determination based on actual measurements.
Slashdot Mirror
Its effects are dramatic and well-established, whereas the case for memory exercises, environmental enrichment etc. is murkier --
http://www.nytimes.com/2007/11/08/opinion/08aamodt.html
It doesn't need to be injected -- inhaling oxytocin spray makes people more likely to hand over their money to a trustee to invest.
They could coat the display with self-healing plastic resin. Developed for cars, the plastic is fluid enough to erase scratches over time.
Full text of article, institutional/personal subscription required.
Abstract: Classical studies show that for many proteins, the information required for specifying the tertiary structure is contained in the amino acid sequence. Here, we attempt to define the sequence rules for specifying a protein fold by computationally creating artificial protein sequences using only statistical information encoded in a multiple sequence alignment and no tertiary structure information. Experimental testing of libraries of artificial WW domain sequences shows that a simple statistical energy function capturing coevolution between amino acid residues is necessary and sufficient to specify sequences that fold into native structures. The artificial proteins show thermodynamic stabilities similar to natural WW domains, and structure determination of one artificial protein shows excellent agreement with the WW fold at atomic resolution. The relative simplicity of the information used for creating sequences suggests a marked reduction to the potential complexity of the protein-folding problem.
From this page : a WW domain is the smallest, monomeric, triple-stranded, anti-parallel beta-sheet protein domain that is stable in the absence of disulfide bonds, cofactors or ligands.
Prof. Church synthesizes long DNA sequences with remarkable fidelity by using parallel synthesis and amplification on a gene chip (ordered array of shorter DNA sequences). Paper.
Remember last year when researchers created polio virus from scratch? Paper. It took 3 years to make the 7500 bp genome -- this new technology would make this kind of project easier.
Their own livejournal.
This article makes a lot of sense. We need a new business model, not just for music, but for any product that can be copied with high fidelity. Right now this is clearly the case with music and software; later it may extend to movies; and maybe far in the future, to nanotech constructors.
The current system is workable because people who pay for music and software subsidize people who don't pay for it. It's a stable system, as long as it's more convenient to buy a product than to pirate it. However, it will only get easier, not harder to freely distribute information, as programs like Napster show. As the cost of copying software drops, the price a developer can charge for software will have to drop as well, just so developers can compete against copies of their own product.
Which brings us to the question: how do we allow developers to charge a reasonable price for their software, while encouraging, not restricting, the free transfer of information?
Here's the proposal:
Of course, some immediate objections come to mind:
If you buy software, you already are. This system will be more fair. Besides, there are plenty of situations where we subsidize a larger group based on statistical information, i.e. any sort of insurance, paying a flat fee for internet access, property taxes.
In the limit of perfect statistics, we could determine a person's software use exactly, and each person would pay for exactly what he used. We can't, and so we clump people together into larger groups, with good enough statistics so that the end result is roughly correct.
This is better than the current system, where the industry aspries to have each person pay for exactly what he uses by mandating that this be the case, rather than making a determination based on actual measurements.