1.Assuming we all evolved from a universal common ancestor we are all equidistant to the original tree of life
2.The organism did not evolve x years ago...it has and will continue to evolve throughout it's existence
Testing for genetic differences that lead to well characterized diseases are better done methods other than sequencing. Methods such as real time PCR and microarray analysis costs large amounts of money to set up and validate but are much cheaper once they are up and running. This is why places like 32andme are $400 and not $1000s.
The power of next gen sequencing like ion torrent is that you can go fishing for things you don't know about. Deep sequencing is a good example. Many cancers result from spontaneous mutations or chromosomal rearrangements. Catching them early requires identifying sequence differences in a very rare cells. Because Ion torrent and many of the other next gen sequencers are capable of massively parallel sequencing they can sequence regions of DNA prone to rearrangement or oncogenes over and over, finding that one in a 1000 cells, or one in 100,000 cells that is the beginning of cancer.
They can also be used to sequence novel genomes, such as newly emerging strains of pathogenic E. coli, and find what changes have led to the change.
Each well is just large enough to allow one microsphere in it. This microshpere has copies of the DNA to be sequenced attached to it. Each of the 4 bases are then added to the chip one at that time and the pH is measured. When a nucleotide is incorporated it changes the pH and the signal is recorded. The $50K pricetag is a little decieving, you also need the machinery to produce the DNA coated microspheres and a hefty server to process the millions of ~100 base reads form the machine and assemble them into a useful file. I'm not sure of the specs on our server but I believe it has 12 cores and around 20 gigs of ram, and takes 2-8 hours of processing for each run. There is also the consumables to think about. The DNA oligonucleotides that server as primers and the chemicals. All tolled it is more like $150K for the parts adn 500-1500 per run.
Martin coined the term working with actual mouse embryos at multiple stages of development rather that the single stage used in in vitro treatment. The hypocrisyis not in using a less precise term but in banning a use of these cells on the grounds that we are killing embryos when in fact this research has no impact on the number of embryos that will be killed.
I have not yet heard one person opposed to stem cell research suggest actually stopping in vitro fertilization,which would be the only way to stop these embryos from being killed.
The absurdity of this "debate" is astounding. Blastocysts, which is the correct, but less headline grabbing, name for the clump of cells the "Embryotic Stems cells" are harvested from are all the result of in-vitro fertilization. The excess eggs that are a invariably a result of this procedure are then left in a freezer until become inviable and are discarded. "Embrytoic" stem cell research puts these cells to a use that benefits mankind rather that throwing them in a trashbin. Anyone who truly has a problem with destroying blastocytes needs to rail against the procedure that causes them, in vitro fertilization.
But of course this makes for a far less compelling election speech or political rant.
Making something open sourced or putting most things in the public domain does not remove the ability to hide things. Anyone who wants to use this technology in private will be able to do so regardless of the communities openness. TFA seems to miss this fact.
The problem was not the sample size, pilot studies like this are common. The problem was the dubious methodology that Wakefield used in generating the paper, namely not disclosing his a patent application, payment by an attorney specifically to support the claim that the MMR is linked to autism, and his selection of children whose parents were involved in such law suits by the same attorny when he said he randomly selected them. This was brought up first by Brian Deer http://www.timesonline.co.uk/tol/life_and_style/health/article5683671.ece and led to a two-and-a-half year ethics investigation by the General Medical Council, which found the he acted “dishonestly and irresponsibly" http://news.bbc.co.uk/2/hi/health/8483865.stm
This is old news, Woses paper "on the evolution of cells" explained this concept 8 years ago http://www.pnas.org/content/99/13/8742.long. Even within the protocell or primordial soup where horizontal gene transfer is hypothesized to play a dominant role natural selection still takes place. The molecules that replicate best increase in number and those that don't die out. Also, several evolutionary biologists such as Woese himself and many of his collegues have made their careers out of studying this phenomenon, so the suggestion " its consequences have hardly been explored" is a bit disingenuous.
I'm not sure about the Netherlands but the US uses the vaccine adverse event reporting system to track all vaccine associated illness and its public ally available....the side effects seem to be about the same as most seasonal flu shots.
the reason for concern is legitimate, albeit possibly overtcautipus. Two traits make this flu serious. One is the observation that a higher percentage of deaths are occuring in young people and two is that, being a strain with genes that have recently jumped from swine and possibly birds makes it less stable.
Seasonal flu kills, on average 33,000-50,000 people per year in the US [http://www.globalsecurity.org/security/ops/hsc-scen-3_flu-pandemic-deaths.htm.]
Mortality rates for flu vaccines are almost nonexistent.
False dichotomy aside (most adult bicyclists also own cars and pay the same taxes you do) gas tax and registration tax make up only a portion of the revenue used for roadway construction and repair. In addition, bicyclists contribute a minuscule amount of wear and tear on our roadways compared to cars and trucks. I bike and drive in Portland and see jackasses in both categories. I've not seen or heard of a motorist hurt by a cyclist, however I have to look no further than tonights evening news to hear about another a hit and run death of a cyclist by someone in a car (see KATU, it's not on line yer).
Bikes are considered to be vehicles in Oregon and should be treated as such. Police overlook cyclists running stoplights and weaving through traffic as much as they overlook motorists illegally passing cyclists or using bike lanes to turn in. Neither side is without fault so suck it up, follow the laws, and remember the multi-thousand pound vehicle does a hell of a lot more damage than a bike.
I have never heard of a journal or publication what would not allow you to cite your own or others work. A journals impact factor, the main metric used to rank journals is based on the citations its articles garner, so to do so would be detrimental to the publisher as well as the author, so the whole premise here makes no sense to me. Sure open access is great, but with $2000 publishing fees in places like PLoS it places a heavy burden on many researchers in these times of scarce funding.
The number of people that must be sequenced to interpolate data on a disease depends on what the prevalence of that disease is in the population. A disease like xeroderma pigmentosum is quite rare and would require hundreds of thousands of genomes, while something more common like the BRCA1 gene mutation that leads to a susceptibility to some breast cancers would take 10 to 100 times fewer.
In reality however, each individual has unique mutations that may or may not effect their susceptibility to disease or ability to live a long life, and each new genome we sequence adds to our ability to correlate genes to disease. Indeed, individual actions of persons today could have far-reaching consequences for generations of people to come, particularly for their own progeny.
To have coverage so that 50% of criminals could be identified would require two components, a genome database and a relative database that distinguishes individuals related by blood rather than by marriage. The completeness of each database would determine the exact numbers needed.
That being said I don't think I would submit my personal genome to the database with the current uncertainty of personal protection and the state of the health care industry.
There are several flaws in the articles reasoning:
1. Retracted papers are retracted for many reasons...a small fraction of which is because the fundamental principal of the paper is wrong. Most often it has to do with smaller things.
2. Prediction is not a zero sum game. Just because someones theory about the risk is incorrect does not mean the worst case scenario will happen.
3. The risk assessment of the LHC is not based on one persons theory, but a collection of scientists theories. As with most scientists, they disagree on a multitude of minor points and some major ones. Despite this the consensus from the vast majority of physicists is that there is little or no danger in smashing particles at the energys used in the LHC. For this to be incorrect the hypotheses of not one but all of the scientists would have to be in error, bringing us back to a very small probability of death by black hole.
It seems like the Norberg's comments fall in a rather blurry area between libel and opinion. Rather than taking this to court, generating more bad publicity and awarding only the lawyers, why does the chiropractor simply publish a rebuttal to the review, explaining his side of the story?
Yes, I know, one bad review is worth ten good ones etc. etc., but I personally prefer to make a decision based on reading many points of view. Just like you and the other slashdotters that have made it this far down the forum.
Slashdot Mirror
1.Assuming we all evolved from a universal common ancestor we are all equidistant to the original tree of life
2.The organism did not evolve x years ago...it has and will continue to evolve throughout it's existence
Testing for genetic differences that lead to well characterized diseases are better done methods other than sequencing. Methods such as real time PCR and microarray analysis costs large amounts of money to set up and validate but are much cheaper once they are up and running. This is why places like 32andme are $400 and not $1000s. The power of next gen sequencing like ion torrent is that you can go fishing for things you don't know about. Deep sequencing is a good example. Many cancers result from spontaneous mutations or chromosomal rearrangements. Catching them early requires identifying sequence differences in a very rare cells. Because Ion torrent and many of the other next gen sequencers are capable of massively parallel sequencing they can sequence regions of DNA prone to rearrangement or oncogenes over and over, finding that one in a 1000 cells, or one in 100,000 cells that is the beginning of cancer. They can also be used to sequence novel genomes, such as newly emerging strains of pathogenic E. coli, and find what changes have led to the change.
Each well is just large enough to allow one microsphere in it. This microshpere has copies of the DNA to be sequenced attached to it. Each of the 4 bases are then added to the chip one at that time and the pH is measured. When a nucleotide is incorporated it changes the pH and the signal is recorded. The $50K pricetag is a little decieving, you also need the machinery to produce the DNA coated microspheres and a hefty server to process the millions of ~100 base reads form the machine and assemble them into a useful file. I'm not sure of the specs on our server but I believe it has 12 cores and around 20 gigs of ram, and takes 2-8 hours of processing for each run. There is also the consumables to think about. The DNA oligonucleotides that server as primers and the chemicals. All tolled it is more like $150K for the parts adn 500-1500 per run.
Martin coined the term working with actual mouse embryos at multiple stages of development rather that the single stage used in in vitro treatment. The hypocrisyis not in using a less precise term but in banning a use of these cells on the grounds that we are killing embryos when in fact this research has no impact on the number of embryos that will be killed. I have not yet heard one person opposed to stem cell research suggest actually stopping in vitro fertilization,which would be the only way to stop these embryos from being killed.
The absurdity of this "debate" is astounding. Blastocysts, which is the correct, but less headline grabbing, name for the clump of cells the "Embryotic Stems cells" are harvested from are all the result of in-vitro fertilization. The excess eggs that are a invariably a result of this procedure are then left in a freezer until become inviable and are discarded. "Embrytoic" stem cell research puts these cells to a use that benefits mankind rather that throwing them in a trashbin. Anyone who truly has a problem with destroying blastocytes needs to rail against the procedure that causes them, in vitro fertilization. But of course this makes for a far less compelling election speech or political rant.
Making something open sourced or putting most things in the public domain does not remove the ability to hide things. Anyone who wants to use this technology in private will be able to do so regardless of the communities openness. TFA seems to miss this fact.
Here is the Lancets published reasons for the retraction http://download.thelancet.com/flatcontentassets/pdfs/S0140673610601754.pdf
The problem was not the sample size, pilot studies like this are common. The problem was the dubious methodology that Wakefield used in generating the paper, namely not disclosing his a patent application, payment by an attorney specifically to support the claim that the MMR is linked to autism, and his selection of children whose parents were involved in such law suits by the same attorny when he said he randomly selected them. This was brought up first by Brian Deer http://www.timesonline.co.uk/tol/life_and_style/health/article5683671.ece and led to a two-and-a-half year ethics investigation by the General Medical Council, which found the he acted “dishonestly and irresponsibly" http://news.bbc.co.uk/2/hi/health/8483865.stm
You can order a kit to do just that http://www.epibio.com/item.asp?ID=291 the kit is based on a naturally occuring DNA sequence called a transposon http://en.wikipedia.org/wiki/Transposon that can cut out and splice in DNA allowing it to move around the genome
This is old news, Woses paper "on the evolution of cells" explained this concept 8 years ago http://www.pnas.org/content/99/13/8742.long. Even within the protocell or primordial soup where horizontal gene transfer is hypothesized to play a dominant role natural selection still takes place. The molecules that replicate best increase in number and those that don't die out. Also, several evolutionary biologists such as Woese himself and many of his collegues have made their careers out of studying this phenomenon, so the suggestion " its consequences have hardly been explored" is a bit disingenuous.
I'm not sure about the Netherlands but the US uses the vaccine adverse event reporting system to track all vaccine associated illness and its public ally available....the side effects seem to be about the same as most seasonal flu shots.
the reason for concern is legitimate, albeit possibly overtcautipus. Two traits make this flu serious. One is the observation that a higher percentage of deaths are occuring in young people and two is that, being a strain with genes that have recently jumped from swine and possibly birds makes it less stable.
Seasonal flu kills, on average 33,000-50,000 people per year in the US [http://www.globalsecurity.org/security/ops/hsc-scen-3_flu-pandemic-deaths.htm.] Mortality rates for flu vaccines are almost nonexistent.
False dichotomy aside (most adult bicyclists also own cars and pay the same taxes you do) gas tax and registration tax make up only a portion of the revenue used for roadway construction and repair. In addition, bicyclists contribute a minuscule amount of wear and tear on our roadways compared to cars and trucks. I bike and drive in Portland and see jackasses in both categories. I've not seen or heard of a motorist hurt by a cyclist, however I have to look no further than tonights evening news to hear about another a hit and run death of a cyclist by someone in a car (see KATU, it's not on line yer).
Bikes are considered to be vehicles in Oregon and should be treated as such. Police overlook cyclists running stoplights and weaving through traffic as much as they overlook motorists illegally passing cyclists or using bike lanes to turn in. Neither side is without fault so suck it up, follow the laws, and remember the multi-thousand pound vehicle does a hell of a lot more damage than a bike.
I have never heard of a journal or publication what would not allow you to cite your own or others work. A journals impact factor, the main metric used to rank journals is based on the citations its articles garner, so to do so would be detrimental to the publisher as well as the author, so the whole premise here makes no sense to me. Sure open access is great, but with $2000 publishing fees in places like PLoS it places a heavy burden on many researchers in these times of scarce funding.
This is loophole that needs to be filled. a detailed discussion why is here
The number of people that must be sequenced to interpolate data on a disease depends on what the prevalence of that disease is in the population. A disease like xeroderma pigmentosum is quite rare and would require hundreds of thousands of genomes, while something more common like the BRCA1 gene mutation that leads to a susceptibility to some breast cancers would take 10 to 100 times fewer.
In reality however, each individual has unique mutations that may or may not effect their susceptibility to disease or ability to live a long life, and each new genome we sequence adds to our ability to correlate genes to disease. Indeed, individual actions of persons today could have far-reaching consequences for generations of people to come, particularly for their own progeny.
To have coverage so that 50% of criminals could be identified would require two components, a genome database and a relative database that distinguishes individuals related by blood rather than by marriage. The completeness of each database would determine the exact numbers needed. That being said I don't think I would submit my personal genome to the database with the current uncertainty of personal protection and the state of the health care industry.
actually, plants do contain fat soluble vitamins, particularly leafy green ones, hence the reason vegans don't (all) suffer from theses deficiencies
There are several flaws in the articles reasoning:
1. Retracted papers are retracted for many reasons...a small fraction of which is because the fundamental principal of the paper is wrong. Most often it has to do with smaller things.
2. Prediction is not a zero sum game. Just because someones theory about the risk is incorrect does not mean the worst case scenario will happen.
3. The risk assessment of the LHC is not based on one persons theory, but a collection of scientists theories. As with most scientists, they disagree on a multitude of minor points and some major ones. Despite this the consensus from the vast majority of physicists is that there is little or no danger in smashing particles at the energys used in the LHC. For this to be incorrect the hypotheses of not one but all of the scientists would have to be in error, bringing us back to a very small probability of death by black hole.
It seems like the Norberg's comments fall in a rather blurry area between libel and opinion. Rather than taking this to court, generating more bad publicity and awarding only the lawyers, why does the chiropractor simply publish a rebuttal to the review, explaining his side of the story? Yes, I know, one bad review is worth ten good ones etc. etc., but I personally prefer to make a decision based on reading many points of view. Just like you and the other slashdotters that have made it this far down the forum.
I don't think anyone really enjoys or wants more [insert your favorite ad hominem argument here]