This research is not about the trait itself, but the topology of transfer. Darwinian evolution admits two major processes: random mutation and natural selection through survival of offspring. In other words, genes are transferred only vertically, from parent to offspring. The authors showed through simulation that this Darwinian mechanism alone cannot explain the universality of the code itself or its error-correcting properties. If one takes into account horizontal gene transfer, i.e. direct exchange of genetic material between members of the same generation, these properties themselves are the natural product of evolution. They further assert that in the early stages of evolution, this horizontal transfer was dominant over the vertical. As complexity grew and biological pathways became more sensitive, horizontal transfer became more likely a hindrance than a help, and vertical transfer became dominant. The article is worth a read and states this much more clearly than my terse summary.
Mathew 16:17-19:
Jesus said to him in reply, "Blessed are you, Simon son of Jonah. For flesh and blood has not revealed this to you, but my heavenly Father.
And so I say to you, you are Peter, and upon this rock I will build my church, and the gates of the netherworld shall not prevail against it.
I will give you the keys to the kingdom of heaven. Whatever you bind on earth shall be bound in heaven; and whatever you loose on earth shall be loosed in heaven."
Jesus did found his church upon Peter, as He said. And that same church, with the authority that Jesus gave it, and led by the Holy Spirit promised to guide it, believed that the office was intended to be propagated. After all, if Jesus believed that that church needed a head, a preeminent shepherd (see John 21:15-17), would it only need one for the couple of decades left to Peter? After Peter would be martyred, did Christ intend to leave His church again "...like sheep without a shepherd"?
I have not tried it for two reasons. First, to my knowledge there are no large public machines in the US being planned using AMD GPUs, so there is relatively little incentive to port the code to OpenCL. We run on large clusters and it appears for the moment that NVIDIA has the HPC cluster market tied up. Second, while OpenCL is quite similar to CUDA in many respects, it's also significantly less convenient from a coding perspective. NVIDIA added a few language extensions that makes launching kernels nearly as simple as a function call. As a pure C library, OpenCL requires much more setup code for each kernel invocation. If there was a strong incentive, such as the construction of a large NSF or DOE machine with AMD GPUs, I'd probably port it anyway, but without such a machine, it's not worth the time and effort.
It's important to note that on GPUs, peak performance data often doesn't translate into actual performance numbers. The 4870 had a higher peak floating point rate than the G200, but in graphics and some other benchmarks, the G200 usually came out ahead. I don't know if this will also be the case with Fermi vs. 5870's.
Finally, another large consideration is that AMD is pretty far behind on the software end. Besides mature compilers for both CUDA and OpenCL, NVIDIA provides profilers and debuggers that can debug GPU execution in hardware, and there is a growing ecosystem of CUDA libraries. For the sake of competition, I hope AMD adoption grows, but I've gotten the impression they are just not investing that much in general-purpose GPU computing.
Presently the G200 GPUs in this machine support double-precision, but at about 1/8 the peak rate of single-precision. In practice, since most codes tend to be bandwidth limited, and pointer arithmetic is the same for single and double precision, double-precision performance is usually closer to 1/2 that of single-precision performance, but not always. With the Fermi GPUs to be released early next year, double-precision peak FLOPS will be 1/2 of single-precision peak, just like on present X86 processors. Also note that many scientific research groups, such as my own, have found that contrary to dogma, single-precision is good enough for most of the computation, and that a judicious mix of single and double-precision arithmetic gives high-performance with sufficient accuracy. This is true for some, but not all, computational methods.
Along these lines, I recall an earlier Slashdot story about using water to create logic gates. If these were scaled up to make them more visible to the kids, and made interactive, it could make for an engaging exhibit. As a father of two little boys, I know that kids love to play with water.
I agree with this in principle, but, in practice, it doesn't seem to come up as often as one might think. I frequently use NCSA's Lincoln cluster with 384 Teslas. Early on, I discovered some "hard" memory errors (repeatable bad bits or rows). These were very early boards, which apparently hadn't been fully tested. This prompted the admins at NCSA to write the GPU equivalent of memtest86, which they ran for about a month if I recall. After removing the boards with bad memory (about 3-4, if I recall), they didn't encounter any "soft" errors (i.e. random bit flips). NVIDIA's Fermi will have ECC, which is reassuring, but I have found the present generation, without ECC, to be quite reliable. I should also note that the hard errors I found always resulted in NANs/INFs, etc., which are very obvious. I'd be more concerned with "silent" errors that subtly change the results.
I believe Cray made its partnership with AMD quite a while ago while they were still ahead of Intel in the performance/power ratio. In addition, these machines have a very fast interconnect (SeaStar) that is based on HyperTransport links.
I believe it was recently announced that Cray has formed a partnership with Intel, and I imagine they will port the technology to QuickPath for future machines, but QPI was not available at the time this machine was commissioned. One does not simply order a machine like this at the drop of a hat. Vendor decisions are typically made years ahead of time.
The children are not 'tainted' in any way and are in no way different than any other children. Consider children that were conceived through rape. The children are not responsible, in any way, for the means of their conception. Baptism is not denied to any person who sincerely desires it (and has not already been baptized).
The Church's teaching about contraception and in vitro fertilization came about through an extremely careful reasoning about the meaning of the human person and his/her sexual powers. This type of careful reasoning is by and large absent from the origins of the secular framework of sexual morality.
Much of the software which is run at the NCSA is home-grown software written by computational scientists, not computer scientists. For many of these massively parallel codes, written on top of MPI, fault tolerance really isn't all that easy. For a commercial production code on the order of Gaussian, this may be doable, but for bleeding-edge research codes, it may be a better use of the (human) time to push the algorithms rather than worry about fault-tolerance. From the user's perspective, jobs that are killed due to a hardware failure have their service units refunded, so there isn't a huge incentive to worry about it. When we get to petascale, there won't be any way around it, since the MTBF will probably be a few minutes.
A little over a week ago, I was at a conference and heard a talk by Francois Gygi, a researcher who was one of the big users of Blue Gene/L. He is the principal author of Qbox, a code written to perform quantum-level simulations of condensed matter (i.e. liquids and solids), on massively parallel machines. If I remember correctly, his team was able to use all 65k processors with about 80% parallel efficiency, an impressive achievement for which they won the 2006 Gordon-Bell award. The code is based on density functional theory in a plane-wave basis, so it makes heavy use of FFTs and matrix-matrix multiplies. The tricky part is organizing the topology of the communications, and the fact that there are no tools for debugging/optimization at that scale. So I believe there are some useful appliations that scale very well.
My friend, I ask in total sincerity, what is about Christianity that irritates you so much? Do you truly believe that all Christians are simply morons? You might consider that there a quite a few counterexamples to that assertion. That it is psychological weakness that brings us to accept this crutch? You would have to be ignorant of the demands of faith. That we are all hypocrites? There you may have more ground, for a Christian is just as human as any other, and we all harbor a greater or lesser degree of hypocrisy. That we are judgemental? There again, many times we are, but that is our failing, and not that of our faith, or of our God. I ask you only to consider that some of the greatest minds in history, and of our own time, have been those of Christians. If those as learned and intelligent as they, who questioned all things mightily, found reason to believe, might they not have seen something you missed? Or were they all simply fools?
After quite a bit of skepticism, I was convinced by all the positive reviews of Nespresso' machines and bought one for about $160. I bought the D150. It (and I believe all the machines) comes with an 18 bar pump. The downside is the cost of the capsules (50 cents each), but I find the convenience and the great espresso it produces is worth the price. In my opinion, it produces a better espresso than some of the $1000+ super-automatics. Also, each capsule is prepacked to the right compression and is completely sealed, so the coffee stays pretty fresh. If you drink many cups a day, however, the cost could get prohibitive.
What you allude to is called "the problem of evil" in theology, and it really isn't as simple as you claim. I believe that your implicit claim is that if there were a God who as omnipotent, omniscient, and omnibenevolent, He would not PERMIT evil to occur. However, if He did not so permit, then true moral good could also not exist, since for something to be a moral good, it must be chosen freely. Charity and love are not charity and love if they are not freely given. Self sacrifice is no such thing if it is forced. Thus, God permits evil, because in His omnipotence He can make a greater good come of it. Permitting evil and causing evil are two different things, even in the case of an omnipotent being. This is a terribly complex subject, and one in which I am no expert, but I know enough to point this much out. If God and His ways were completely simple to understand, it would be hard to imagine that He was God.
Most of the attack on free well I have seen coming from the neuroscience front assume that you must have Cartesian dualism to have free will. In a nutshell, this is Descartes' belief that the soul resides in the body essentially as a "ghost in the machine". The Christian concept of the human person is rather a unity of body and soul, and the concept of strict duality, against which the neuroscientists argue, is clearly inadequate. This situation is not black and white. I believe it is obvious from a moment of introspection that "free will" is neither absolute, nor nonexistent. Certainly, the condition of the body influences the degree to which any decision is "free". Illness, inebriation, addiction, and even simply habit reduce the degree of freedom we have in our actions. To the belief that neuroscience will somehow prove that free will that free will does not exist, I would say that this is silly. Does the body influence our decisions? Absolutely -- anyone who has ever had a drink too many knows this. Does this mean free will does not exist? To assert this is deny all of the evidence of your own existence. Take a look at http://www.nd.edu/~afreddos/papers/soul.htm for greater depth.
"Religion is pretty much self-admittedly not based on logic and rationality - it is based on faith.
The two are largely irreconcilable on a logical basis unless one of them is adapted."
As a physicist and a Catholic, I'm rather perplexed by this assertion. The belief that faith is irrational is a rather ideosyncratic concept that has been in vogue in the Western world for a few decades. This is not to say that no one holds irrational beliefs -- some people certainly do. This does not imply, however, that faith is irreconcilable with reason. I would recommend that anyone who believes they are should read a bit of systematic theology, e.g. the Summa Theologica of St. Thomas Aquinas. Be forewarned, however that if you are unfamiliar with Aristotelian philosophy, some of the terminology may be confusing.
Some may be interested to know that those who go to seminary to become a Catholic priest are taught philosophy and logic before they even begin to study theology. Faith does transcend reason, but it is, at the same time, eminently reasonable. If you believe that faith is blind, you haven't taken enough time to understand the rational underpinnings of faith. You might also take a glance at the encyclical letter Fides et Ratio (On Faith and Reason) penned by the late John Paul II.
I believe that many are missing a critical point in this discussion. The universe, by definition, encompasses all events which are causally connected, and therefore observable, at least in theory. As such, studying the universe falls within the realm of science. Discussion about what preceded the universe is, by definition, a discussion about things that cannot, even in principle, be observationally confirmed or refuted. As such, it is not science, but speculation. If you want to make such speculations, go ahead, but it shouldn't be passed off as science. I believe the Pope's comments were not intended to curtail legitimate science, but philosophy disguised as science.
Slashdot Mirror
The Church does do many good works. It's just not fashionable to report on them. A quick summary was given by a Jewish businessman a couple of years ago: http://fratres.wordpress.com/2008/06/24/redemption-comes-through-the-jews-jewish-businessman-sam-miller-whaps-anti-catholic-bias-in-news-media-full-text/
This research is not about the trait itself, but the topology of transfer. Darwinian evolution admits two major processes: random mutation and natural selection through survival of offspring. In other words, genes are transferred only vertically, from parent to offspring. The authors showed through simulation that this Darwinian mechanism alone cannot explain the universality of the code itself or its error-correcting properties. If one takes into account horizontal gene transfer, i.e. direct exchange of genetic material between members of the same generation, these properties themselves are the natural product of evolution. They further assert that in the early stages of evolution, this horizontal transfer was dominant over the vertical. As complexity grew and biological pathways became more sensitive, horizontal transfer became more likely a hindrance than a help, and vertical transfer became dominant. The article is worth a read and states this much more clearly than my terse summary.
Mathew 16:17-19:
Jesus said to him in reply, "Blessed are you, Simon son of Jonah. For flesh and blood has not revealed this to you, but my heavenly Father. And so I say to you, you are Peter, and upon this rock I will build my church, and the gates of the netherworld shall not prevail against it. I will give you the keys to the kingdom of heaven. Whatever you bind on earth shall be bound in heaven; and whatever you loose on earth shall be loosed in heaven."
Jesus did found his church upon Peter, as He said. And that same church, with the authority that Jesus gave it, and led by the Holy Spirit promised to guide it, believed that the office was intended to be propagated. After all, if Jesus believed that that church needed a head, a preeminent shepherd (see John 21:15-17), would it only need one for the couple of decades left to Peter? After Peter would be martyred, did Christ intend to leave His church again "...like sheep without a shepherd"?
I have not tried it for two reasons. First, to my knowledge there are no large public machines in the US being planned using AMD GPUs, so there is relatively little incentive to port the code to OpenCL. We run on large clusters and it appears for the moment that NVIDIA has the HPC cluster market tied up. Second, while OpenCL is quite similar to CUDA in many respects, it's also significantly less convenient from a coding perspective. NVIDIA added a few language extensions that makes launching kernels nearly as simple as a function call. As a pure C library, OpenCL requires much more setup code for each kernel invocation. If there was a strong incentive, such as the construction of a large NSF or DOE machine with AMD GPUs, I'd probably port it anyway, but without such a machine, it's not worth the time and effort. It's important to note that on GPUs, peak performance data often doesn't translate into actual performance numbers. The 4870 had a higher peak floating point rate than the G200, but in graphics and some other benchmarks, the G200 usually came out ahead. I don't know if this will also be the case with Fermi vs. 5870's. Finally, another large consideration is that AMD is pretty far behind on the software end. Besides mature compilers for both CUDA and OpenCL, NVIDIA provides profilers and debuggers that can debug GPU execution in hardware, and there is a growing ecosystem of CUDA libraries. For the sake of competition, I hope AMD adoption grows, but I've gotten the impression they are just not investing that much in general-purpose GPU computing.
Presently the G200 GPUs in this machine support double-precision, but at about 1/8 the peak rate of single-precision. In practice, since most codes tend to be bandwidth limited, and pointer arithmetic is the same for single and double precision, double-precision performance is usually closer to 1/2 that of single-precision performance, but not always. With the Fermi GPUs to be released early next year, double-precision peak FLOPS will be 1/2 of single-precision peak, just like on present X86 processors. Also note that many scientific research groups, such as my own, have found that contrary to dogma, single-precision is good enough for most of the computation, and that a judicious mix of single and double-precision arithmetic gives high-performance with sufficient accuracy. This is true for some, but not all, computational methods.
Along these lines, I recall an earlier Slashdot story about using water to create logic gates. If these were scaled up to make them more visible to the kids, and made interactive, it could make for an engaging exhibit. As a father of two little boys, I know that kids love to play with water.
I agree with this in principle, but, in practice, it doesn't seem to come up as often as one might think. I frequently use NCSA's Lincoln cluster with 384 Teslas. Early on, I discovered some "hard" memory errors (repeatable bad bits or rows). These were very early boards, which apparently hadn't been fully tested. This prompted the admins at NCSA to write the GPU equivalent of memtest86, which they ran for about a month if I recall. After removing the boards with bad memory (about 3-4, if I recall), they didn't encounter any "soft" errors (i.e. random bit flips). NVIDIA's Fermi will have ECC, which is reassuring, but I have found the present generation, without ECC, to be quite reliable. I should also note that the hard errors I found always resulted in NANs/INFs, etc., which are very obvious. I'd be more concerned with "silent" errors that subtly change the results.
I believe Cray made its partnership with AMD quite a while ago while they were still ahead of Intel in the performance/power ratio. In addition, these machines have a very fast interconnect (SeaStar) that is based on HyperTransport links. I believe it was recently announced that Cray has formed a partnership with Intel, and I imagine they will port the technology to QuickPath for future machines, but QPI was not available at the time this machine was commissioned. One does not simply order a machine like this at the drop of a hat. Vendor decisions are typically made years ahead of time.
The children are not 'tainted' in any way and are in no way different than any other children. Consider children that were conceived through rape. The children are not responsible, in any way, for the means of their conception. Baptism is not denied to any person who sincerely desires it (and has not already been baptized).
The Church's teaching about contraception and in vitro fertilization came about through an extremely careful reasoning about the meaning of the human person and his/her sexual powers. This type of careful reasoning is by and large absent from the origins of the secular framework of sexual morality.
Much of the software which is run at the NCSA is home-grown software written by computational scientists, not computer scientists. For many of these massively parallel codes, written on top of MPI, fault tolerance really isn't all that easy. For a commercial production code on the order of Gaussian, this may be doable, but for bleeding-edge research codes, it may be a better use of the (human) time to push the algorithms rather than worry about fault-tolerance. From the user's perspective, jobs that are killed due to a hardware failure have their service units refunded, so there isn't a huge incentive to worry about it. When we get to petascale, there won't be any way around it, since the MTBF will probably be a few minutes.
A little over a week ago, I was at a conference and heard a talk by Francois Gygi, a researcher who was one of the big users of Blue Gene/L. He is the principal author of Qbox, a code written to perform quantum-level simulations of condensed matter (i.e. liquids and solids), on massively parallel machines. If I remember correctly, his team was able to use all 65k processors with about 80% parallel efficiency, an impressive achievement for which they won the 2006 Gordon-Bell award. The code is based on density functional theory in a plane-wave basis, so it makes heavy use of FFTs and matrix-matrix multiplies. The tricky part is organizing the topology of the communications, and the fact that there are no tools for debugging/optimization at that scale. So I believe there are some useful appliations that scale very well.
My friend, I ask in total sincerity, what is about Christianity that irritates you so much? Do you truly believe that all Christians are simply morons? You might consider that there a quite a few counterexamples to that assertion. That it is psychological weakness that brings us to accept this crutch? You would have to be ignorant of the demands of faith. That we are all hypocrites? There you may have more ground, for a Christian is just as human as any other, and we all harbor a greater or lesser degree of hypocrisy. That we are judgemental? There again, many times we are, but that is our failing, and not that of our faith, or of our God. I ask you only to consider that some of the greatest minds in history, and of our own time, have been those of Christians. If those as learned and intelligent as they, who questioned all things mightily, found reason to believe, might they not have seen something you missed? Or were they all simply fools?
After quite a bit of skepticism, I was convinced by all the positive reviews of Nespresso' machines and bought one for about $160. I bought the D150. It (and I believe all the machines) comes with an 18 bar pump. The downside is the cost of the capsules (50 cents each), but I find the convenience and the great espresso it produces is worth the price. In my opinion, it produces a better espresso than some of the $1000+ super-automatics. Also, each capsule is prepacked to the right compression and is completely sealed, so the coffee stays pretty fresh. If you drink many cups a day, however, the cost could get prohibitive.
What you allude to is called "the problem of evil" in theology, and it really isn't as simple as you claim. I believe that your implicit claim is that if there were a God who as omnipotent, omniscient, and omnibenevolent, He would not PERMIT evil to occur. However, if He did not so permit, then true moral good could also not exist, since for something to be a moral good, it must be chosen freely. Charity and love are not charity and love if they are not freely given. Self sacrifice is no such thing if it is forced. Thus, God permits evil, because in His omnipotence He can make a greater good come of it. Permitting evil and causing evil are two different things, even in the case of an omnipotent being. This is a terribly complex subject, and one in which I am no expert, but I know enough to point this much out. If God and His ways were completely simple to understand, it would be hard to imagine that He was God.
Most of the attack on free well I have seen coming from the neuroscience front assume that you must have Cartesian dualism to have free will. In a nutshell, this is Descartes' belief that the soul resides in the body essentially as a "ghost in the machine". The Christian concept of the human person is rather a unity of body and soul, and the concept of strict duality, against which the neuroscientists argue, is clearly inadequate. This situation is not black and white. I believe it is obvious from a moment of introspection that "free will" is neither absolute, nor nonexistent. Certainly, the condition of the body influences the degree to which any decision is "free". Illness, inebriation, addiction, and even simply habit reduce the degree of freedom we have in our actions. To the belief that neuroscience will somehow prove that free will that free will does not exist, I would say that this is silly. Does the body influence our decisions? Absolutely -- anyone who has ever had a drink too many knows this. Does this mean free will does not exist? To assert this is deny all of the evidence of your own existence. Take a look at http://www.nd.edu/~afreddos/papers/soul.htm for greater depth.
"Religion is pretty much self-admittedly not based on logic and rationality - it is based on faith. The two are largely irreconcilable on a logical basis unless one of them is adapted."
As a physicist and a Catholic, I'm rather perplexed by this assertion. The belief that faith is irrational is a rather ideosyncratic concept that has been in vogue in the Western world for a few decades. This is not to say that no one holds irrational beliefs -- some people certainly do. This does not imply, however, that faith is irreconcilable with reason. I would recommend that anyone who believes they are should read a bit of systematic theology, e.g. the Summa Theologica of St. Thomas Aquinas. Be forewarned, however that if you are unfamiliar with Aristotelian philosophy, some of the terminology may be confusing.
Some may be interested to know that those who go to seminary to become a Catholic priest are taught philosophy and logic before they even begin to study theology. Faith does transcend reason, but it is, at the same time, eminently reasonable. If you believe that faith is blind, you haven't taken enough time to understand the rational underpinnings of faith. You might also take a glance at the encyclical letter Fides et Ratio (On Faith and Reason) penned by the late John Paul II.
I believe that many are missing a critical point in this discussion. The universe, by definition, encompasses all events which are causally connected, and therefore observable, at least in theory. As such, studying the universe falls within the realm of science. Discussion about what preceded the universe is, by definition, a discussion about things that cannot, even in principle, be observationally confirmed or refuted. As such, it is not science, but speculation. If you want to make such speculations, go ahead, but it shouldn't be passed off as science. I believe the Pope's comments were not intended to curtail legitimate science, but philosophy disguised as science.