At least my pack rat nature has been channelled in digital things that can be stored on hard drives. Sure I spend 250 dollars last month upgrading because I'd filled every drive I owned, but I'm lucky.
My dad accumulates books. Online used book stores like abebooks are the worst thing to ever happen to my mother. Now five or six books arrive in the mail most weeks from all over the country. Last time I was home pretty much every open wall in the house had vanished behind bookshelves.
Hording in the digital age may still be expensive, but at least it takes up a lot less total volume in meatspace
A lot of it has to do with where you live. When I moved I kept the same insurance company, same car, and my rates nearly tripled moving from the midwest to big west coast city.
There's never a time, however, when I persist in presenting something false as true.
Then it seems we actually have nothing to disagree about. As long as it isn't being used to avoid acknowledging one's own errors I don't have a problem with trying to teach children how to NOT be the sort of people we all dread dealing with in meetings...
I definitely agree with the first part of your response.
As to your second point, I can definitely see where you're coming from. In a lot of ways teaching in middle/high school is making a presentation to a hostile audience. There are plenty of students who are just waiting to catch any mistake (I should know I was one of them in classes where a teacher and I did not get along).
But to some degree the rational behind the correction doesn't matter. We've all had to give meetings to people who didn't want to hear what we had to say, and there are plenty of tricks to the situation. One I've seen used to great effect is intentionally leaving obvious holes in your argument as lures for questions you have the answers for. But just because a student has a chip on his or her shoulder is no reason for the teacher to live down to the student's expectations with an "I'm in charge here so it doesn't matter what's true only what I say" reaction.
Great, so not only can we get rid of the bad teachers, we can pay the good ones twice as much! (assuming we started out with classes of 33 1/2 students)
In all seriousness, back when I was in high school I'd have gladly traded sitting in a class of 67 to be taught by a competent and fair minded individual. I imagine many on slashdot felt similarly in their time. Bad teachers aren't just less good than good teachers, they have an actively negative impact on the students in their classes. Better to put them in bigger classes, or even shorten the school day if the only alternative is to protect terrible teachers because they "can't be spared".
Similar experience. 24 yo here, and even though the high school teachers I encounter these days are more likely to be my own age and friends of someone in my social circle, my gut reaction is still extremely hostile.
I imagine schools anywhere end up creating an "us vs. them" mentality among the teachers towards the students, but society will still be dealing with the consequences long after those burned-out/incompetent/power-tripping tenured teachers are dead and buried.
In my personal opinion the minute a teacher decides: "Correcting false information is less important than maintaining my own aura of authority," they stop being an educator and start down the road to becoming a tyrant in a teapot.
Personally I would argue the reason high school students are so merciless is because by the time they encounter even one nice teacher they've been exposed to far too many of the "dickheads" and don't know how to interact with someone who is genuinely trying to teach them.
The best way to develop the technology and bring the cost down to something affordable is to have it in production. And right now Telsa is producing 15 MORE zero emission cars a week than all of the Detroit automakers combined.
To deal with the cold, hard logic of computers all day, you need to be comfortable with such an unemotional, machine-like environment. As an IT worker, I can tell you firsthand that many women aren't comfortable in situations like that. Far too many ex-girlfriends of mine have told me I'm "too much like a robot." To which I reply, "a sex robot?" And they say no.:-(
You can get around the need for primers by fracturing the DNA using restriction enzymes or mechanical sheering to break the unknown DNA into shorter fragments and then ligating adaptors onto the ends of your new 100-1000 bp fragments. Then you use primers complementary to your adaptors and viola you're in business.
My question is why we'd expect life on Mars to use DNA at all.
The average person, no. The obsessed amature with training in a closely related enough field to be able to follow protocols precisely (any branch of biology and a lot of chemistry), with enough money to afford these supplies (probably dozens of times over given how finicky PCR can be even under controlled laboratory conditions) would probably genotype themselves for 5-10 alleles.
But I think a lot of people are missing the point of this article. It's not that everyone could do it, or even anyone really SHOULD do it. It's that these techniques have become simple enough and cheap enough that people who are sufficiently interested can do this at home. It's the same reason people install Linux on their toasters, or mod a 360 into a laptop, not because the end result is that useful, but because it's so cool that they CAN.
Requiring the test results not be released to anyone but the PATIENT would strike me as a benefit to privacy. No releasing to anyone but the doctor is a whole different issue, having nothing to do with privacy and everything to do with an (justified or not) lack of faith in the general public's ability to have access to their own data without turning into raging hypochondriacs.
Even if I transformed a new gene incorporating these bases into cells in your body, the higher mutation rate is only going to affect the specific positions where the new bases are present. It wouldn't do anything to change the mutant rates of the proto-oncogenes and cancer-suppresser genes that are still encoded with normal As Cs Ts and Gs.
And this doesn't even get into the complication that sequences with the new bases could only be replicated in vivo as long as there's a supply of the new bases being synthesized in the cell.
Key point: synthetic dna bases aren't going to give you cancer.
...either way you have to build your own new tRNA's with your new weird amino acids or whatever ready to be linked into your protein, but this guy's approach might mean that's *all* you have to do (plus use his patented system) rather than also having to proofread the whole genome repeatedly.
Here's a list of what you'd have to add to the organism (it's a little complicated, but you've definitely grasped the essentials):
1. A gene using codons incorporating one or both of these new bases to encode your novel protein of interest containing something beyond the standard 20 amino acids.
2. tRNA genes that have the reverse compliment of any new codons you've introduced (otherwise the sequence functions like a stop codon).
3. Gene encoding an amyl transferase protein that binds your novel animo acids to the tail end of your novel tRNAs.
4. Genes encoding the biochemical pathway to synthesize the novel animo acids you were using.
5. Genes encoding the the biochemical pathway to synthesize the two new nucleotide bases developed in this paper.
There's obviously a lot of work left to do before this gets incorporated into synthetic biology, but it'll be very cool when it does.
As others have said, the essential difference between journals and other forms of publishing discoveries is peer review and with it the implicit endorsement that other credible experts find these experiments valid.
Any replacement for the current journal format is going to need to replicate the essential elements of the journal format in that:
1. Theories and data should only be presented when they have been reviewed and found valid by others uninvolved in the research project.
2. Those who do the reviewing are correctly selected as experts well trained enough in the area of research to be able to make valid judgements regarding the veracity of the information.
3. The format must become widely enough accepted that those who use it won't be disadvantaged in hiring and tenure decisions. (Which often hinge the opinions of professors older than 60.)
There's no hard and fast reason these conditions couldn't be met in other forums than scientific journals, but so far they haven't been, and institutional inertia is going to make meeting #3 relatively difficult.
Maybe the fact that it was non-christian was part of the process of initially dating the site at around a thousand years ago, based on the when the religion reached Scandinavia? I'm just guessing.
I also immediately thought of the Neandertal work that's being done. The phrase "authentic DNA" being used twice makes me wonder if perhaps these researchers are trying to cast doubt on the previous work by other groups? (I don't know about the historical work, but the Neandertal stuff at least seems pretty solid.)
He's talking about a method of tracing ancestry through the female line. Current person whether male or female, their mother, their mother's mother etc.
This doesn't correspond to genes with any visible phenotypes (two people in haplogroup T2 aren't necessarily going to share any traits), but it can tell you something about which populations mixed in the past and how recently. Also since 20% of the samples contain mutations not found in current populations, we can conclude that a number of the maternal lines for the vikings died out. (I don't know much population genetics, so I don't know if 20% loss over 1000 years is high or low, or what you'd expect).
A program at my previous college would graduate 5-6 bioinformaticians with PhDs a year. The ones who got snapped up were the ones who also had a substantial background in the biology they were working with.
Take whatever genetic/bio courses you can fit in along with your bioinformatics work. When choosing a doctoral project, try to find one that involves collaboration between your advisor and professor in the genetics or cell biology department.
As some posted above, bioinformaticians can find jobs pretty much anywhere biologists are employed, but the biologists will be important in making any hiring decisions and they want someone who understands the biology in addition to being a wiz at the computational stuff.
The short answer to your question is yes. It wouldn't even have to be multiple sources because any biological tissue is made up of uncountable numbers of cells, each with their own copy of the genome. So really if you extract DNA from a big enough sample and can sequence enough small enough pieces of DNA, the problem becomes simple a computational one of lining them all up into chromosomes based on overlap.
With current technology we're on the edge of being able to sequence something like a Nanderthal. For dinosaurs, there might be almost no DNA left, since the fossils aren't biological tissue, so I don't know if that will ever be possible.
http://www.sciencemag.org/cgi/content/abstract/314/5802/1113
Face it, this is just like green peace singling out Apple as the computer company they were going to harass about manufacturing methods. They pick the brand best known to their political base and go after it for practices shared by the whole industry because they get a lot more press coverage attacking a "hip" company like Nintendo or Apple, than a boring one like HP or Microsoft.
Ok, now I understand what you're talking about. You're right, there's genetic data for a wide range of species, but that's because it's a lot easier to clone and sequence individual genes, (or randomly sample the parts of the genome that are being expressed as RNA using rtPCR techniques) than it is to sequence the whole genome and put all the pieces of each chromosome together in the correct order. That's why there's such a long gap between the isolation of the first gene in 1969 and the sequencing of the first genome in the mid-1990s.
Until recently the only two published plant genomes where arabidopsis and rice. There are now arguably (depending on when you want to call a genome complete) close to 10 sequenced genomes, the new ones I can name off the top of my head are: maize, pea, grape, papaya, and poplar. Sorghum has been sequenced, but I don't think they're done assembling it yet.
Slashdot Mirror
At least my pack rat nature has been channelled in digital things that can be stored on hard drives. Sure I spend 250 dollars last month upgrading because I'd filled every drive I owned, but I'm lucky.
My dad accumulates books. Online used book stores like abebooks are the worst thing to ever happen to my mother. Now five or six books arrive in the mail most weeks from all over the country. Last time I was home pretty much every open wall in the house had vanished behind bookshelves.
Hording in the digital age may still be expensive, but at least it takes up a lot less total volume in meatspace
A lot of it has to do with where you live. When I moved I kept the same insurance company, same car, and my rates nearly tripled moving from the midwest to big west coast city.
There's never a time, however, when I persist in presenting something false as true.
Then it seems we actually have nothing to disagree about. As long as it isn't being used to avoid acknowledging one's own errors I don't have a problem with trying to teach children how to NOT be the sort of people we all dread dealing with in meetings...
I definitely agree with the first part of your response.
As to your second point, I can definitely see where you're coming from. In a lot of ways teaching in middle/high school is making a presentation to a hostile audience. There are plenty of students who are just waiting to catch any mistake (I should know I was one of them in classes where a teacher and I did not get along).
But to some degree the rational behind the correction doesn't matter. We've all had to give meetings to people who didn't want to hear what we had to say, and there are plenty of tricks to the situation. One I've seen used to great effect is intentionally leaving obvious holes in your argument as lures for questions you have the answers for. But just because a student has a chip on his or her shoulder is no reason for the teacher to live down to the student's expectations with an "I'm in charge here so it doesn't matter what's true only what I say" reaction.
Great, so not only can we get rid of the bad teachers, we can pay the good ones twice as much! (assuming we started out with classes of 33 1/2 students)
In all seriousness, back when I was in high school I'd have gladly traded sitting in a class of 67 to be taught by a competent and fair minded individual. I imagine many on slashdot felt similarly in their time. Bad teachers aren't just less good than good teachers, they have an actively negative impact on the students in their classes. Better to put them in bigger classes, or even shorten the school day if the only alternative is to protect terrible teachers because they "can't be spared".
Similar experience. 24 yo here, and even though the high school teachers I encounter these days are more likely to be my own age and friends of someone in my social circle, my gut reaction is still extremely hostile.
I imagine schools anywhere end up creating an "us vs. them" mentality among the teachers towards the students, but society will still be dealing with the consequences long after those burned-out/incompetent/power-tripping tenured teachers are dead and buried.
In my personal opinion the minute a teacher decides: "Correcting false information is less important than maintaining my own aura of authority," they stop being an educator and start down the road to becoming a tyrant in a teapot. Personally I would argue the reason high school students are so merciless is because by the time they encounter even one nice teacher they've been exposed to far too many of the "dickheads" and don't know how to interact with someone who is genuinely trying to teach them.
That's not totally fair, there's a night life for school children in Fargo... it just involves meth and cow tipping!
I agree completely.
The best way to develop the technology and bring the cost down to something affordable is to have it in production. And right now Telsa is producing 15 MORE zero emission cars a week than all of the Detroit automakers combined.
To deal with the cold, hard logic of computers all day, you need to be comfortable with such an unemotional, machine-like environment. As an IT worker, I can tell you firsthand that many women aren't comfortable in situations like that. Far too many ex-girlfriends of mine have told me I'm "too much like a robot." To which I reply, "a sex robot?" And they say no. :-(
Man, you just made my day...
You can get around the need for primers by fracturing the DNA using restriction enzymes or mechanical sheering to break the unknown DNA into shorter fragments and then ligating adaptors onto the ends of your new 100-1000 bp fragments. Then you use primers complementary to your adaptors and viola you're in business.
My question is why we'd expect life on Mars to use DNA at all.
The average person, no. The obsessed amature with training in a closely related enough field to be able to follow protocols precisely (any branch of biology and a lot of chemistry), with enough money to afford these supplies (probably dozens of times over given how finicky PCR can be even under controlled laboratory conditions) would probably genotype themselves for 5-10 alleles. But I think a lot of people are missing the point of this article. It's not that everyone could do it, or even anyone really SHOULD do it. It's that these techniques have become simple enough and cheap enough that people who are sufficiently interested can do this at home. It's the same reason people install Linux on their toasters, or mod a 360 into a laptop, not because the end result is that useful, but because it's so cool that they CAN.
Requiring the test results not be released to anyone but the PATIENT would strike me as a benefit to privacy. No releasing to anyone but the doctor is a whole different issue, having nothing to do with privacy and everything to do with an (justified or not) lack of faith in the general public's ability to have access to their own data without turning into raging hypochondriacs.
I've been inspired! Spent like three hours on newegg putting my own system together. Thank you man.
Even if I transformed a new gene incorporating these bases into cells in your body, the higher mutation rate is only going to affect the specific positions where the new bases are present. It wouldn't do anything to change the mutant rates of the proto-oncogenes and cancer-suppresser genes that are still encoded with normal As Cs Ts and Gs.
And this doesn't even get into the complication that sequences with the new bases could only be replicated in vivo as long as there's a supply of the new bases being synthesized in the cell.
Key point: synthetic dna bases aren't going to give you cancer.
...either way you have to build your own new tRNA's with your new weird amino acids or whatever ready to be linked into your protein, but this guy's approach might mean that's *all* you have to do (plus use his patented system) rather than also having to proofread the whole genome repeatedly.
Here's a list of what you'd have to add to the organism (it's a little complicated, but you've definitely grasped the essentials):
1. A gene using codons incorporating one or both of these new bases to encode your novel protein of interest containing something beyond the standard 20 amino acids.
2. tRNA genes that have the reverse compliment of any new codons you've introduced (otherwise the sequence functions like a stop codon).
3. Gene encoding an amyl transferase protein that binds your novel animo acids to the tail end of your novel tRNAs.
4. Genes encoding the biochemical pathway to synthesize the novel animo acids you were using.
5. Genes encoding the the biochemical pathway to synthesize the two new nucleotide bases developed in this paper.
There's obviously a lot of work left to do before this gets incorporated into synthetic biology, but it'll be very cool when it does.
As others have said, the essential difference between journals and other forms of publishing discoveries is peer review and with it the implicit endorsement that other credible experts find these experiments valid. Any replacement for the current journal format is going to need to replicate the essential elements of the journal format in that: 1. Theories and data should only be presented when they have been reviewed and found valid by others uninvolved in the research project. 2. Those who do the reviewing are correctly selected as experts well trained enough in the area of research to be able to make valid judgements regarding the veracity of the information. 3. The format must become widely enough accepted that those who use it won't be disadvantaged in hiring and tenure decisions. (Which often hinge the opinions of professors older than 60.) There's no hard and fast reason these conditions couldn't be met in other forums than scientific journals, but so far they haven't been, and institutional inertia is going to make meeting #3 relatively difficult.
Maybe the fact that it was non-christian was part of the process of initially dating the site at around a thousand years ago, based on the when the religion reached Scandinavia? I'm just guessing.
I also immediately thought of the Neandertal work that's being done. The phrase "authentic DNA" being used twice makes me wonder if perhaps these researchers are trying to cast doubt on the previous work by other groups? (I don't know about the historical work, but the Neandertal stuff at least seems pretty solid.)
He's talking about a method of tracing ancestry through the female line. Current person whether male or female, their mother, their mother's mother etc. This doesn't correspond to genes with any visible phenotypes (two people in haplogroup T2 aren't necessarily going to share any traits), but it can tell you something about which populations mixed in the past and how recently. Also since 20% of the samples contain mutations not found in current populations, we can conclude that a number of the maternal lines for the vikings died out. (I don't know much population genetics, so I don't know if 20% loss over 1000 years is high or low, or what you'd expect).
A program at my previous college would graduate 5-6 bioinformaticians with PhDs a year. The ones who got snapped up were the ones who also had a substantial background in the biology they were working with. Take whatever genetic/bio courses you can fit in along with your bioinformatics work. When choosing a doctoral project, try to find one that involves collaboration between your advisor and professor in the genetics or cell biology department. As some posted above, bioinformaticians can find jobs pretty much anywhere biologists are employed, but the biologists will be important in making any hiring decisions and they want someone who understands the biology in addition to being a wiz at the computational stuff.
The short answer to your question is yes. It wouldn't even have to be multiple sources because any biological tissue is made up of uncountable numbers of cells, each with their own copy of the genome. So really if you extract DNA from a big enough sample and can sequence enough small enough pieces of DNA, the problem becomes simple a computational one of lining them all up into chromosomes based on overlap. With current technology we're on the edge of being able to sequence something like a Nanderthal. For dinosaurs, there might be almost no DNA left, since the fossils aren't biological tissue, so I don't know if that will ever be possible. http://www.sciencemag.org/cgi/content/abstract/314/5802/1113
Face it, this is just like green peace singling out Apple as the computer company they were going to harass about manufacturing methods. They pick the brand best known to their political base and go after it for practices shared by the whole industry because they get a lot more press coverage attacking a "hip" company like Nintendo or Apple, than a boring one like HP or Microsoft.
Jeez. I was actually hopeful there for a sec. Thanks for pointing out this release is less (far less) than it appears.
Ok, now I understand what you're talking about. You're right, there's genetic data for a wide range of species, but that's because it's a lot easier to clone and sequence individual genes, (or randomly sample the parts of the genome that are being expressed as RNA using rtPCR techniques) than it is to sequence the whole genome and put all the pieces of each chromosome together in the correct order. That's why there's such a long gap between the isolation of the first gene in 1969 and the sequencing of the first genome in the mid-1990s. Until recently the only two published plant genomes where arabidopsis and rice. There are now arguably (depending on when you want to call a genome complete) close to 10 sequenced genomes, the new ones I can name off the top of my head are: maize, pea, grape, papaya, and poplar. Sorghum has been sequenced, but I don't think they're done assembling it yet.