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Comment: Re:Sounds great? (Score 1) 65

by fusellovirus (#36860434) Attached to: Personal DNA Sequencing Machine One Step Closer
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.

Comment: Re:Essentially a Proprietary Hydrogen Ion Sensor (Score 2) 65

by fusellovirus (#36860272) Attached to: Personal DNA Sequencing Machine One Step Closer
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.

Comment: Re:Was this one of Obama's first things to do? (Score 1) 388

by fusellovirus (#33356694) Attached to: Court Rules Against Stem Cell Policy
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.

Comment: Re:Was this one of Obama's first things to do? (Score 5, Informative) 388

by fusellovirus (#33349728) Attached to: Court Rules Against Stem Cell Policy
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.

Comment: Re:But (Score 4, Informative) 590

by fusellovirus (#31003538) Attached to: The Lancet Recants Study Linking Autism To Vaccine
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

Comment: Re:I realize scientists need a breakthrough (Score 2, Informative) 313

by fusellovirus (#30914210) Attached to: Darwinian Evolution Considered As a Phase
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.

Comment: Re:Where does the money go? (Score 3, Informative) 138

by fusellovirus (#30185506) Attached to: WHO Says Swine Flu May Have Peaked In the US
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.

Comment: Re:toposhaba (Score 1) 792

by fusellovirus (#29435531) Attached to: Congress Mulls Research Into a Vehicle Mileage Tax
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.

Comment: Can't cite data??? nonsense (Score 1) 349

by fusellovirus (#28842613) Attached to: Should Copyright of Academic Works Be Abolished?
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.

You can measure a programmer's perspective by noting his attitude on the continuing viability of FORTRAN. -- Alan Perlis

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