For those current in the field, this discovery is not surprising. Several people have created synthetic ribozymes already, most doing some trivial and superfluous task. It was only a matter of time until someone created a self-replicating ribozyme. Yet, they do serve as basic evidence that the RNA-world hypothesis may be correct.
However, a soup of replicating molecules is still a far cry from life, and, indeed, there are many more complicated features of life as we know it, even at the most basic level, for which there is no creation hypothesis. We know that membranes can self-assemble into micelles, and one key component of all life is a membrane layer to separate the living environment from the surroundings. However, if, by chance, a micelle happened to self-assemble around a ribozyme, how does the ribozyme continue to function, now that it has no ready source of diffusing ribonucleotides (the building block of RNA)?
Second, how did the first micelles replicate? Did they simply continue to grow as more membrane molecules spontaneously add to them until they broke apart into two? Perhaps life arose in some sort of thermally-cycling environment and the micelles broke apart at high temperture, releasing the contents, and then reformed again, with new randomized contents when the temperature cooled.
Third, how did we transition from RNA contents with lipid membranes into the vastly richer information of the amino acid world? Is there a reductionist "alphabet" for amino acids that may have served as the starting point, from which the extra amino acids were added slowly. Is our alphabet 'optimal' (virtually all life uses the same 20-acid alphabet, which minor variations of 1 or 2 in extreme organisms)? Or perhaps the alphabet only evolved once, and thus had no competition and could be completely far from optimal.
As you can see, there are a number of interesting questions to be explored. We have, however, gone from not knowing how the basic components of cells (proteins, DNA, lipids) functioned, to knowing that DNA encodes the 'heritable' information, to its structure, to the Miller-Urey experiment, and now on to knowing immense details about the complicated protein functional networks within cells, and between cells as well creating synthetic molecules that can evolve via natural selection, all in the span of just more than a century. It's going to be extremely fun to see what we know by the end of the 21st century. Right now we feel like we know all of the basics and just have to work on the hard stuff. I will bet dollars to donuts that we have a lot to learn, and, by 2100, several discoveries will have been made that future people will wonder how we ever thought we knew anything without.
For what it's worth, I signed up for the trial. Despite the level-1 tech support's crappiness, and the relative overpricing of their services, Comcast's network department does a pretty good on the backend. Our area has gone from 3mbps to 16mbps (with a 50mbps tier available) in 8 years, and has already completed the analog reclamation process in our area. Good on them for getting a head start on IPv6.
I presume they are going to want to do end-to-end IPv6 eventually, instead of assigning a single IPv6 address to my modem, and then continuing to use IPv4 NAT behind it. However, if they are going to do that, several things are going to have to change:
1. Router default settings will have to change. Out of the box, most home routers use NAT by default, and, since most people don't change the settings (based on the number of 2WIRE### SSID's broadcast to my house), they'll have to redo them for IPv6. 2. Auto discovery services will have to get better. I can say, categorically, that OS X is better than Windows and Linux at automatically finding nearby machines and devices that do not have a static IP/DNS A record assigned to them. The other 2 OSes will have to catch up, because, while a quartet of triplets is annoying but manageable to type, an IPv6 address will be a bear to copy down. 3. A debate between static and dynamic IP addresses will have to take place. Ideally, a device would get a static IPv6 address assigned to it and keep it forever, no matter where it roamed and went. It'd be akin to a routable MAC address. However, if we do that, we'll run out of IPv6 addresses more quickly (though still not fast), since things like phones get recycled fairly frequently. But there are several obvious downsides to continuing to use totally dynamic IPs.
Finally, as an aside, it's interesting to me, at least, how Apple Airport Base Stations do IPv6 routing automatically via a tunnel provider (as another commenter noted). Comcast doesn't support any IPv6, but when I'm connected to my router at home I get full IPv6 support transparently. Apple doesn't even mention this as a feature on the box, and it's not highly configurable either. So why did they spend all the effort to get it that way? Are they trying to stay so far ahead of the IPv6 curve no one will ever complain they're behind?
I use the 30 second skip button on my Tivo to flash through the commercials. This typically means that the only commercial I see is either the first one of the break, or the last one of the break. If the first one catches my attention in the first 3 seconds, I end up watching it, and if the last 5 seconds of the last one is intriguing (say, has a punch line but not the setup), I will rewind to watch it. Occasionally, I will end up watching a commercial in the middle if the quick flash draws my brain in too (typically with some sort of interesting colors, etc).
Otherwise, I just skip through them. Seems like there could be money made studying the unique commercial viewing habits of DVR users. I'm not sure if my own experiences are unique or common.
Also, is 'had commercial playing' the finest granularity Nielsen can provide? What percent of those people actually remembered what the ad was about? And how does that percentage compare to live TV watchers?
This logic always irks me. Do you really believe the speculative pundits they interview for these articles are more likely to come up with a new idea than the talented and probably extremely intelligent programmers who wrote up the Conficker worm in the first place?
Yes, perhaps some less-than-average person has now read this article and has seen the new idea for the first time, but that's no one to worry about. Usually if you are smart enough to implement some genius idea, you think of it first.
Normally I have to preface my posts with "I am not a XXXX, but". However, in this case, I actually am a molecular biologist deeply involved in the synthetic biology community. Here are a few thoughts:
First, the amount of ignorance regarding genetic engineering and it's facets (such as GMO food) is astounding. Anecdotally, I've heard that a significant fraction of British folks polled said they would prefer DNA-free food. (Think about it until you realize the ridiculousness). People typically imagine we are trying to create hybrid organisms or bizarre clone armies or something, when it reality, it's just mixing DNA that encodes for a series of proteins you would find useful in combination. To make glow in the dark yogurt that responds to melamine would be fairly simple if you had the right set of genes: a melamine sensor that, when bound to melamine, binds to a specific DNA sequence (a promoter) that drives expression of a fluorescent protein such as green fluorescent protein ("GFP", a widely used fluorescent marker derived from a jellyfish). It's not difficult, and it's not unsafe. The vast majority of DNA and proteins are degraded rapidly in your stomache, so they are safe to eat (toxins, parasites, and infectious agents excluded).
Second, people underestimate how difficult it is to accomplish something genetically. Yes, the circuit logic above is fairly simple. Unlike electrical circuits, though, where you can control electron flow with wires there is no such spatial regulation of biological parts. It's very stochastic. One has to tune the concentrations such that the melamine sensor will strongly bind to DNA at the concentrations of melamine likely to be in food, without prematurely activating and freaking people out, while also avoiding being sued because it didn't activate when it should have and someone died. Once you get the sensor right, you have to then tune the promoter so that you get expression of GFP the same way-- no leaky expression causing permanently green yogurt, but enough expression when activated such that you can see it. I can build a simple circuit to drive GFP in the presence of melamine, but getting it commercially relevant is extremely difficult.
Finally, and most importantly, the regulations of these types of technologies are, well, 2 steps from insane. There are no regulations on the transport of DNA encoding some severe toxin, to list one example. Take botulism toxin: the DNA encoding it is well known, and short enough that one could order it directly from a DNA synthesis company. From there you can use PCR to make as many copies of it as you need. Then, put it in your bacterium of choice, produce a whole bunch, and purify it out. That entire process could be done with someone with basic college level biology and about $5k. Anybody can find the botulism toxin DNA on, say, NBCI (run by the NIH) and get to work. And there are NO regulations on any of the steps required to produce it. A person with practical experience could do it much faster. I could produce enough to kill my entire university, starting from scratch, in about 2 weeks, give or take, maybe faster
A second example is the definition of 'natural' when it comes to food. Any chemical produced in a flask, chemically, is considered artificial, even if it's molecularly identical to the natural flavor molecule. On the other hand, any synthetic flavor produced by bacteria in a vat is considered natural, as long as the sugar used to feed the bacteria is also natural. The food industry is spending billions trying to engineer bacteria to produce flavors in large quantities, because the average person will think 'all natural' means healthier or better for me.
A third example involves regulation of the types of bacteria used to produce flavors: if I randomly mutagenize bacteria with UV light until I find one I like, that's considered safe, even though I probably have no idea what mutations I've actually made. On the other hand, if I go in and, with ultra-precision, make a single, target
Parent is probably the most detailed response to my original post, so I'll address it, even though the chances (several hours after the article hit the front page) of someone reading or modding it are virtually nil.
Comparing a virus to a mule is a false comparison. With objections to those who seek a single, simply, unified definition, the standards for a living mammal simply do not compare to those of a single celled organism, let alone a virus. The simple fact that a mule cannot reproduce does not negate the fact that it has virtually all of the reproductive machinery and virtually all of the capacity to reproduce, plus a few defects (and, in fact, some mules can reproduce). No virus is prevented from independent reproduction due to a simple defect or mutation.
Saying that a virus 'lives' within a cell is a subtle argument that has merit. I find it lacking, though. To explain why requires an extension of my original argument: A virus, while able to harness the energy sources around it, does not have the enzymatic capacity to transmute energy sources into the ones it needs to survive and replicate. In addition, a virus is unable to respond to changing conditions around it, such as increased heat, a modified energy source, etc. Within the 'lifespan' (using the term loosely), a virus invades and replicates, period. Our cells can respond to various signaling components, change metabolism based on condition, and reproduce when asked. A virus simply cannot.
Mitochondria are not alive, because they cannot survive outside the confines of the cell, let alone replicate. Is your heart alive? By the very same token, yeast are indeed alive. Mules are alive, though reproductively deficient. Following the same idea, and borrowing your definition, a robot that could create another copy of itself would be considered alive in the 'environment' of the factory where it was built.
No, they are not alive even if they can get sick. Viruses, even infected ones, cannot self-replicate as they require the use of a host and host machinery. If you can find me a self-templating virus, then we'd have an interesting discussion...
Actually, the above only occurs as I had 'su'ed to another user, then ran the above command. If, instead of using su I simply try to touch a file in the second account, it works just fine. So I retract the above.
Okay, so I tested it and the whoami returns 'root'.
However, I also logged out of my account and into an account that has no permissions to access my regular home directory (normally I log in with short name "me"), then ran: osascript -e 'tell app "ARDAgent" to do shell script "touch/Users/me/Downloads/test.txt"'
It doesn't do anything for a long time, and then returns execution error: ARDAgent got an error: AppleEvent timed out. (-1712)
Same thing happens if I bundle the command into a sh file and try to execute that instead. I am not a hacker, but it would seem, at least at first glance, that ARDAgent is not entirely privileged.
I work in a protein engineering/structure lab that has strong connections to the Baker lab, both in people and in scientific collaboration. The biggest project to come out the Baker lab is a protein structural modeling, simulation and prediction suite known as ROSETTA. While I'll gloss over some of the nitty-gritty about the methodology, suffice it to say that ROSETTA, through a combination of knowledge based and physics based modeling, has knocked the pants off of just about every other program out there used to simulate, design, and fold proteins. (Quantum-based physics models can be much better than ROSETTA, at the expense of a few extra superclusters and months of simulation time).
I no longer work as a ROSETTA developer or the "protein folding problem", but many of my lab mates do. They struggle with ROSETTA sometimes, as it comes close to predicting the real structure of a protein, and then falls away and wanders into another structure far from reality. If only it could 'see' the best structure when it came close!
The problem can be analogized with surveying a landscape. Imagine every square feet of dirt you can see is one possible protein structure, and you want to find the lowest elevation square foot. For a human, the visual search process is fairly quick and rapid. You can see a few hills out in the distance, but a much lower valley on the other side, where the land is lowest. It takes only a few seconds. On the other hand,a computer with no prior knowledge of the landscape can take a very long time to find that global minimum. The computer essentially has to drop a ball on the landscape and watch where it rolls, then pick it up, put it somewhere else and watch again (Physics and computer modelers forgive me!). It may never pick the right starting point to get over that far away hill.
Perhaps the brain can be as good at finding great protein structures as we are at finding lowest elevation points. Perhaps intuition about how a protein 'should' look can get us places a computer program never can without a ton of time and power. That's what this game is all about. The baker lab has done a fantastic job of turning a very hard scientific problem into a competitive game that is simultaneously fun, provides possible scientific information, and represents something of a human experiment on how our brains work.
This could be the next leap forward if it turns out some people have an innate knack for folding. It should be interesting to watch.
I only have anecdotal evidence to back this up, but:
I used to live in Minneapolis. There, yellow lights are relatively long, and there is almost always a delay between signal changes. You know what happened? People figured out there was a delay and were willing to run an even redder light. Eventually, they lengthened the delay, and people just ran the light even further. Last I checked, people were almost always egregiously running red lights as many as several seconds into the red, enough that 1 or 2 cars usually go through after my signal has turned green.
On the other hand, here in San Francisco, very few lights have delays before the next signal is green. Yet, I usually only have to wait for 1 or 2 cars once my signal has changed.
In both places I have to watch carefully before entering, because it's still not impossible for some idiot to blow through the light long after I'd be in the middle of the intersection if I didn't stop and look
If you are concerned about your privacy, then only keep the base OS on the installed hard drive, and carry your personal documents and information on a flash drive, preferrably concealed as a pen, thermos bottom, etc (they've become quite common and cheap these days). Another option is using something like an iPod, which most people would assume can only play music, and can't be used as a disk.
Of course, this is just security by obscurity, because I'm sure customs could easily force you to turn over your flash drive too, but it's something.
You don't like to go in because you feel like you don't belong? Unless your apple store is very different than the one local to me, that's all in your head. Same with the lingerie department. Once you get over that feeling, you'll find that 1) the people in the apple store are just regular people, and 2) Once you get comfortable with lingerie, you can buy something your significant other will wear (insert oblig. this is/. joke) that you find really attractive too.
That all said, I still get uncomfortable in a place like Louis Vutton. I feel like they instinctively know I don't have as much money as I feel like I am supposed to have, and will treat me accordingly. But that's all in my head.
Apparently, the facebook tracking system is getting ridiculous. It's even following me to slashdot, and predicting that I dislike facebook tracking and sending me to an AP article about it.
(If this was evidence editors don't RTFA before posting...) Or am I the only one to get an odd story when I click on the link?
That is, again, speculation on the part of the authors. In the paper, the authors only say they believe the cells are fusing because eukaryotic cells also fuse in the same medium, with again no evidence to support the claim. So, we don't even know for sure whether the bacteria are fusing, let alone whether the concentration they used is somehow optimal for fusion to take place.
While this work is a good step forward toward the ability to insert completely synthetic genomes into living cells, there are some questions left unanswered by the paper that demand answers before the technique can be widely adopted. First, the authors only speculate freely on how the mycoides genome made it into the capricolum cells. It's believed that perhaps two capricolum cells fuse around a mycoides genome, but no evidence to support this claim is given in the paper. Second, the authors do only a single PCR of a single gene to look for the presence of capricolum DNA in the supposed 'new' mycoides cells. This is not nearly enough testing, in my opinion, especially compared to the extensive testing they did on the cells in order to prove the mycoides DNA was present, in it's original genomic form, without insertions.
Until we know how the DNA got there and where the original DNA went, the technique will remain a laboratory curiosity and not something, for example, that can be used in any sort of medical fashion. Still, the paper is fascinating and raises some interesting philosophical questions about what constitutes the information belonging to a species.
The counter to your claim they are wasting money beyond what the computer is worth is:
If they cave and give this guy a computer, then it sets a precedent. Do you, as a shareholder, want them to start giving away computers to everyone who bitches enough? Also, many courts will grant attorneys fees to the winner, so if Gateway wins, it might not cost very much at all.
Why would you submit a journal paper in a closed, binary format? I'm surprised those two journals would even accept Microsoft formats. It makes a lot more sense to use something like TeX, to split the markup from the content, much the same way CSS and HTML work together. Not only is it easier to edit and send around the lab for editing, it's also much easier on the copy editors when they want to typeset it for printing. As far as I know, the journal only takes your images and text, and lays them out on the page. All of the extra crap Word stuffs into it's files is superfluous anyway.
I can't speak for the rest of the world, or even the programming community. That disclaimer spoken, however, I can say that parallel programming is indeed hard. The trivial examples, like simply running many processes in parallel that are doing the same thing (as in, for example, Monte Carlo sampling) are easy, but the more difficult examples of parallelized mathematical algorithms I've seen, such as those in linear algebra are difficult to conceptualize, let alone program. Trying to manage multiple threads and process communication in an efficient way when actually implementing it adds an additional level of complexity.
I think the biggest reason why it is difficult is that people tend to process information in a linear fashion. I break large projects into a series of chronologically ordered steps and complete one at a time. Sometimes if I am working on multiple projects, I will multitask and do them in parallel, but that is really an example of trivial parallelization.
Ironically, the best parallel programmers may be those good managers, who have to break exceptionally large projects into parallel units for their employees to simultaneously complete. Unfortunately, trying to explain any sort of technical algorithm to my managers usually exacts a look of panic and confusion.
why does linux lag windows in features?
on
VMware Fusion goes Beta
·
· Score: 2, Interesting
I use Parallels, but only for Linux (MATLAB, which is not OS X/Intel native yet). I've noticed that the features available for virtualizing Windows are far beyond those available for Linux, and that it's only getting worse. According to the article summary, the same is true for VMWare.
For example, I cannot: -Install Parallels tools for linux, so everytime I suspend my VM, the clock freezes and ends up several days behind schedule when I resume -Use the nifty new feature that eliminates the Windows desktop and instead just shows the application window on the OS X desktop -Copy and paste directly between machines (I have to rsync between hosts, though because the VM IP is changing, is only convenient in one direction) -Easily change resolutions of the Linux VM.
The list goes on.
Now, is this because Windows is just what everyone is running in a VM, so all of the resources are going toward it, or is there some inherent difficulty in replicating these features in Linux. As an aside, couldn't someone in the OSS community (I am not talented enough, sorry) program Linux-based additions to faciliate some of those features, above (like the clock sync)?
I agree with the assessment that Microsoft's labeling of RC's is a bit silly.
But "If they are fixing bugs.... perhaps what they released was a beta" takes it a little too far. If they didn't fix any bugs, it would be simply a Release, not a Candidate.
Slashdot Mirror
For those current in the field, this discovery is not surprising. Several people have created synthetic ribozymes already, most doing some trivial and superfluous task. It was only a matter of time until someone created a self-replicating ribozyme. Yet, they do serve as basic evidence that the RNA-world hypothesis may be correct.
However, a soup of replicating molecules is still a far cry from life, and, indeed, there are many more complicated features of life as we know it, even at the most basic level, for which there is no creation hypothesis. We know that membranes can self-assemble into micelles, and one key component of all life is a membrane layer to separate the living environment from the surroundings. However, if, by chance, a micelle happened to self-assemble around a ribozyme, how does the ribozyme continue to function, now that it has no ready source of diffusing ribonucleotides (the building block of RNA)?
Second, how did the first micelles replicate? Did they simply continue to grow as more membrane molecules spontaneously add to them until they broke apart into two? Perhaps life arose in some sort of thermally-cycling environment and the micelles broke apart at high temperture, releasing the contents, and then reformed again, with new randomized contents when the temperature cooled.
Third, how did we transition from RNA contents with lipid membranes into the vastly richer information of the amino acid world? Is there a reductionist "alphabet" for amino acids that may have served as the starting point, from which the extra amino acids were added slowly. Is our alphabet 'optimal' (virtually all life uses the same 20-acid alphabet, which minor variations of 1 or 2 in extreme organisms)? Or perhaps the alphabet only evolved once, and thus had no competition and could be completely far from optimal.
As you can see, there are a number of interesting questions to be explored. We have, however, gone from not knowing how the basic components of cells (proteins, DNA, lipids) functioned, to knowing that DNA encodes the 'heritable' information, to its structure, to the Miller-Urey experiment, and now on to knowing immense details about the complicated protein functional networks within cells, and between cells as well creating synthetic molecules that can evolve via natural selection, all in the span of just more than a century. It's going to be extremely fun to see what we know by the end of the 21st century. Right now we feel like we know all of the basics and just have to work on the hard stuff. I will bet dollars to donuts that we have a lot to learn, and, by 2100, several discoveries will have been made that future people will wonder how we ever thought we knew anything without.
For what it's worth, I signed up for the trial. Despite the level-1 tech support's crappiness, and the relative overpricing of their services, Comcast's network department does a pretty good on the backend. Our area has gone from 3mbps to 16mbps (with a 50mbps tier available) in 8 years, and has already completed the analog reclamation process in our area. Good on them for getting a head start on IPv6.
I presume they are going to want to do end-to-end IPv6 eventually, instead of assigning a single IPv6 address to my modem, and then continuing to use IPv4 NAT behind it. However, if they are going to do that, several things are going to have to change:
1. Router default settings will have to change. Out of the box, most home routers use NAT by default, and, since most people don't change the settings (based on the number of 2WIRE### SSID's broadcast to my house), they'll have to redo them for IPv6.
2. Auto discovery services will have to get better. I can say, categorically, that OS X is better than Windows and Linux at automatically finding nearby machines and devices that do not have a static IP/DNS A record assigned to them. The other 2 OSes will have to catch up, because, while a quartet of triplets is annoying but manageable to type, an IPv6 address will be a bear to copy down.
3. A debate between static and dynamic IP addresses will have to take place. Ideally, a device would get a static IPv6 address assigned to it and keep it forever, no matter where it roamed and went. It'd be akin to a routable MAC address. However, if we do that, we'll run out of IPv6 addresses more quickly (though still not fast), since things like phones get recycled fairly frequently. But there are several obvious downsides to continuing to use totally dynamic IPs.
Finally, as an aside, it's interesting to me, at least, how Apple Airport Base Stations do IPv6 routing automatically via a tunnel provider (as another commenter noted). Comcast doesn't support any IPv6, but when I'm connected to my router at home I get full IPv6 support transparently. Apple doesn't even mention this as a feature on the box, and it's not highly configurable either. So why did they spend all the effort to get it that way? Are they trying to stay so far ahead of the IPv6 curve no one will ever complain they're behind?
I use the 30 second skip button on my Tivo to flash through the commercials. This typically means that the only commercial I see is either the first one of the break, or the last one of the break. If the first one catches my attention in the first 3 seconds, I end up watching it, and if the last 5 seconds of the last one is intriguing (say, has a punch line but not the setup), I will rewind to watch it. Occasionally, I will end up watching a commercial in the middle if the quick flash draws my brain in too (typically with some sort of interesting colors, etc).
Otherwise, I just skip through them. Seems like there could be money made studying the unique commercial viewing habits of DVR users. I'm not sure if my own experiences are unique or common.
Also, is 'had commercial playing' the finest granularity Nielsen can provide? What percent of those people actually remembered what the ad was about? And how does that percentage compare to live TV watchers?
This logic always irks me. Do you really believe the speculative pundits they interview for these articles are more likely to come up with a new idea than the talented and probably extremely intelligent programmers who wrote up the Conficker worm in the first place?
Yes, perhaps some less-than-average person has now read this article and has seen the new idea for the first time, but that's no one to worry about. Usually if you are smart enough to implement some genius idea, you think of it first.
Sorry, the missing word at the end of my post was supposed to be a link to Synberc. I munged the HTML, even though I previewed my post.
Normally I have to preface my posts with "I am not a XXXX, but". However, in this case, I actually am a molecular biologist deeply involved in the synthetic biology community. Here are a few thoughts:
First, the amount of ignorance regarding genetic engineering and it's facets (such as GMO food) is astounding. Anecdotally, I've heard that a significant fraction of British folks polled said they would prefer DNA-free food. (Think about it until you realize the ridiculousness). People typically imagine we are trying to create hybrid organisms or bizarre clone armies or something, when it reality, it's just mixing DNA that encodes for a series of proteins you would find useful in combination. To make glow in the dark yogurt that responds to melamine would be fairly simple if you had the right set of genes: a melamine sensor that, when bound to melamine, binds to a specific DNA sequence (a promoter) that drives expression of a fluorescent protein such as green fluorescent protein ("GFP", a widely used fluorescent marker derived from a jellyfish). It's not difficult, and it's not unsafe. The vast majority of DNA and proteins are degraded rapidly in your stomache, so they are safe to eat (toxins, parasites, and infectious agents excluded).
Second, people underestimate how difficult it is to accomplish something genetically. Yes, the circuit logic above is fairly simple. Unlike electrical circuits, though, where you can control electron flow with wires there is no such spatial regulation of biological parts. It's very stochastic. One has to tune the concentrations such that the melamine sensor will strongly bind to DNA at the concentrations of melamine likely to be in food, without prematurely activating and freaking people out, while also avoiding being sued because it didn't activate when it should have and someone died. Once you get the sensor right, you have to then tune the promoter so that you get expression of GFP the same way-- no leaky expression causing permanently green yogurt, but enough expression when activated such that you can see it. I can build a simple circuit to drive GFP in the presence of melamine, but getting it commercially relevant is extremely difficult.
Finally, and most importantly, the regulations of these types of technologies are, well, 2 steps from insane. There are no regulations on the transport of DNA encoding some severe toxin, to list one example. Take botulism toxin: the DNA encoding it is well known, and short enough that one could order it directly from a DNA synthesis company. From there you can use PCR to make as many copies of it as you need. Then, put it in your bacterium of choice, produce a whole bunch, and purify it out. That entire process could be done with someone with basic college level biology and about $5k. Anybody can find the botulism toxin DNA on, say, NBCI (run by the NIH) and get to work. And there are NO regulations on any of the steps required to produce it. A person with practical experience could do it much faster. I could produce enough to kill my entire university, starting from scratch, in about 2 weeks, give or take, maybe faster
A second example is the definition of 'natural' when it comes to food. Any chemical produced in a flask, chemically, is considered artificial, even if it's molecularly identical to the natural flavor molecule. On the other hand, any synthetic flavor produced by bacteria in a vat is considered natural, as long as the sugar used to feed the bacteria is also natural. The food industry is spending billions trying to engineer bacteria to produce flavors in large quantities, because the average person will think 'all natural' means healthier or better for me.
A third example involves regulation of the types of bacteria used to produce flavors: if I randomly mutagenize bacteria with UV light until I find one I like, that's considered safe, even though I probably have no idea what mutations I've actually made. On the other hand, if I go in and, with ultra-precision, make a single, target
Parent is probably the most detailed response to my original post, so I'll address it, even though the chances (several hours after the article hit the front page) of someone reading or modding it are virtually nil.
Comparing a virus to a mule is a false comparison. With objections to those who seek a single, simply, unified definition, the standards for a living mammal simply do not compare to those of a single celled organism, let alone a virus. The simple fact that a mule cannot reproduce does not negate the fact that it has virtually all of the reproductive machinery and virtually all of the capacity to reproduce, plus a few defects (and, in fact, some mules can reproduce). No virus is prevented from independent reproduction due to a simple defect or mutation.
Saying that a virus 'lives' within a cell is a subtle argument that has merit. I find it lacking, though. To explain why requires an extension of my original argument: A virus, while able to harness the energy sources around it, does not have the enzymatic capacity to transmute energy sources into the ones it needs to survive and replicate. In addition, a virus is unable to respond to changing conditions around it, such as increased heat, a modified energy source, etc. Within the 'lifespan' (using the term loosely), a virus invades and replicates, period. Our cells can respond to various signaling components, change metabolism based on condition, and reproduce when asked. A virus simply cannot.
Mitochondria are not alive, because they cannot survive outside the confines of the cell, let alone replicate. Is your heart alive? By the very same token, yeast are indeed alive. Mules are alive, though reproductively deficient. Following the same idea, and borrowing your definition, a robot that could create another copy of itself would be considered alive in the 'environment' of the factory where it was built.
No, they are not alive even if they can get sick. Viruses, even infected ones, cannot self-replicate as they require the use of a host and host machinery. If you can find me a self-templating virus, then we'd have an interesting discussion...
viruses infecting viruses is still cool though.
Just because the stock market is higher today than it was yesterday doesn't mean we're not in a bear market.
Actually, the above only occurs as I had 'su'ed to another user, then ran the above command. If, instead of using su I simply try to touch a file in the second account, it works just fine. So I retract the above.
Okay, so I tested it and the whoami returns 'root'.
/Users/me/Downloads/test.txt"'
However, I also logged out of my account and into an account that has no permissions to access my regular home directory (normally I log in with short name "me"), then ran:
osascript -e 'tell app "ARDAgent" to do shell script "touch
It doesn't do anything for a long time, and then returns
execution error: ARDAgent got an error: AppleEvent timed out. (-1712)
Same thing happens if I bundle the command into a sh file and try to execute that instead. I am not a hacker, but it would seem, at least at first glance, that ARDAgent is not entirely privileged.
I work in a protein engineering/structure lab that has strong connections to the Baker lab, both in people and in scientific collaboration. The biggest project to come out the Baker lab is a protein structural modeling, simulation and prediction suite known as ROSETTA. While I'll gloss over some of the nitty-gritty about the methodology, suffice it to say that ROSETTA, through a combination of knowledge based and physics based modeling, has knocked the pants off of just about every other program out there used to simulate, design, and fold proteins. (Quantum-based physics models can be much better than ROSETTA, at the expense of a few extra superclusters and months of simulation time).
I no longer work as a ROSETTA developer or the "protein folding problem", but many of my lab mates do. They struggle with ROSETTA sometimes, as it comes close to predicting the real structure of a protein, and then falls away and wanders into another structure far from reality. If only it could 'see' the best structure when it came close!
The problem can be analogized with surveying a landscape. Imagine every square feet of dirt you can see is one possible protein structure, and you want to find the lowest elevation square foot. For a human, the visual search process is fairly quick and rapid. You can see a few hills out in the distance, but a much lower valley on the other side, where the land is lowest. It takes only a few seconds. On the other hand,a computer with no prior knowledge of the landscape can take a very long time to find that global minimum. The computer essentially has to drop a ball on the landscape and watch where it rolls, then pick it up, put it somewhere else and watch again (Physics and computer modelers forgive me!). It may never pick the right starting point to get over that far away hill.
Perhaps the brain can be as good at finding great protein structures as we are at finding lowest elevation points. Perhaps intuition about how a protein 'should' look can get us places a computer program never can without a ton of time and power. That's what this game is all about. The baker lab has done a fantastic job of turning a very hard scientific problem into a competitive game that is simultaneously fun, provides possible scientific information, and represents something of a human experiment on how our brains work.
This could be the next leap forward if it turns out some people have an innate knack for folding. It should be interesting to watch.
I only have anecdotal evidence to back this up, but:
I used to live in Minneapolis. There, yellow lights are relatively long, and there is almost always a delay between signal changes. You know what happened? People figured out there was a delay and were willing to run an even redder light. Eventually, they lengthened the delay, and people just ran the light even further. Last I checked, people were almost always egregiously running red lights as many as several seconds into the red, enough that 1 or 2 cars usually go through after my signal has turned green.
On the other hand, here in San Francisco, very few lights have delays before the next signal is green. Yet, I usually only have to wait for 1 or 2 cars once my signal has changed.
In both places I have to watch carefully before entering, because it's still not impossible for some idiot to blow through the light long after I'd be in the middle of the intersection if I didn't stop and look
They can justify the cost because we continue to reward them with lots of our dollars.
If you are concerned about your privacy, then only keep the base OS on the installed hard drive, and carry your personal documents and information on a flash drive, preferrably concealed as a pen, thermos bottom, etc (they've become quite common and cheap these days). Another option is using something like an iPod, which most people would assume can only play music, and can't be used as a disk.
Of course, this is just security by obscurity, because I'm sure customs could easily force you to turn over your flash drive too, but it's something.
You don't like to go in because you feel like you don't belong? Unless your apple store is very different than the one local to me, that's all in your head. Same with the lingerie department. Once you get over that feeling, you'll find that 1) the people in the apple store are just regular people, and 2) Once you get comfortable with lingerie, you can buy something your significant other will wear (insert oblig. this is /. joke) that you find really attractive too.
That all said, I still get uncomfortable in a place like Louis Vutton. I feel like they instinctively know I don't have as much money as I feel like I am supposed to have, and will treat me accordingly. But that's all in my head.
Apparently, the facebook tracking system is getting ridiculous. It's even following me to slashdot, and predicting that I dislike facebook tracking and sending me to an AP article about it.
(If this was evidence editors don't RTFA before posting...) Or am I the only one to get an odd story when I click on the link?
That is, again, speculation on the part of the authors. In the paper, the authors only say they believe the cells are fusing because eukaryotic cells also fuse in the same medium, with again no evidence to support the claim. So, we don't even know for sure whether the bacteria are fusing, let alone whether the concentration they used is somehow optimal for fusion to take place.
While this work is a good step forward toward the ability to insert completely synthetic genomes into living cells, there are some questions left unanswered by the paper that demand answers before the technique can be widely adopted. First, the authors only speculate freely on how the mycoides genome made it into the capricolum cells. It's believed that perhaps two capricolum cells fuse around a mycoides genome, but no evidence to support this claim is given in the paper. Second, the authors do only a single PCR of a single gene to look for the presence of capricolum DNA in the supposed 'new' mycoides cells. This is not nearly enough testing, in my opinion, especially compared to the extensive testing they did on the cells in order to prove the mycoides DNA was present, in it's original genomic form, without insertions.
Until we know how the DNA got there and where the original DNA went, the technique will remain a laboratory curiosity and not something, for example, that can be used in any sort of medical fashion. Still, the paper is fascinating and raises some interesting philosophical questions about what constitutes the information belonging to a species.
The counter to your claim they are wasting money beyond what the computer is worth is:
If they cave and give this guy a computer, then it sets a precedent. Do you, as a shareholder, want them to start giving away computers to everyone who bitches enough? Also, many courts will grant attorneys fees to the winner, so if Gateway wins, it might not cost very much at all.
Why would you submit a journal paper in a closed, binary format? I'm surprised those two journals would even accept Microsoft formats. It makes a lot more sense to use something like TeX, to split the markup from the content, much the same way CSS and HTML work together. Not only is it easier to edit and send around the lab for editing, it's also much easier on the copy editors when they want to typeset it for printing. As far as I know, the journal only takes your images and text, and lays them out on the page. All of the extra crap Word stuffs into it's files is superfluous anyway.
I can't speak for the rest of the world, or even the programming community. That disclaimer spoken, however, I can say that parallel programming is indeed hard. The trivial examples, like simply running many processes in parallel that are doing the same thing (as in, for example, Monte Carlo sampling) are easy, but the more difficult examples of parallelized mathematical algorithms I've seen, such as those in linear algebra are difficult to conceptualize, let alone program. Trying to manage multiple threads and process communication in an efficient way when actually implementing it adds an additional level of complexity.
I think the biggest reason why it is difficult is that people tend to process information in a linear fashion. I break large projects into a series of chronologically ordered steps and complete one at a time. Sometimes if I am working on multiple projects, I will multitask and do them in parallel, but that is really an example of trivial parallelization.
Ironically, the best parallel programmers may be those good managers, who have to break exceptionally large projects into parallel units for their employees to simultaneously complete. Unfortunately, trying to explain any sort of technical algorithm to my managers usually exacts a look of panic and confusion.
I use Parallels, but only for Linux (MATLAB, which is not OS X/Intel native yet). I've noticed that the features available for virtualizing Windows are far beyond those available for Linux, and that it's only getting worse. According to the article summary, the same is true for VMWare.
For example, I cannot:
-Install Parallels tools for linux, so everytime I suspend my VM, the clock freezes and ends up several days behind schedule when I resume
-Use the nifty new feature that eliminates the Windows desktop and instead just shows the application window on the OS X desktop
-Copy and paste directly between machines (I have to rsync between hosts, though because the VM IP is changing, is only convenient in one direction)
-Easily change resolutions of the Linux VM.
The list goes on.
Now, is this because Windows is just what everyone is running in a VM, so all of the resources are going toward it, or is there some inherent difficulty in replicating these features in Linux. As an aside, couldn't someone in the OSS community (I am not talented enough, sorry) program Linux-based additions to faciliate some of those features, above (like the clock sync)?
I agree with the assessment that Microsoft's labeling of RC's is a bit silly.
But "If they are fixing bugs.... perhaps what they released was a beta" takes it a little too far. If they didn't fix any bugs, it would be simply a Release, not a Candidate.
If you are aware of the message, it's not subliminal--it's just plain liminal.
There is a lot of subliminal messages in advertising, especially on TV. Given our consumerist culture, i'd say it's working fairly well.