Re-assembly approach like human genome sequencing
on
Picking Up the Pieces
·
· Score: 1
The first thought that occurred to me as I read the description of this process of shredded paper re-assembly is that it greatly resembles the so-called 'shotgun' approach to DNA sequencing popularized by Venter et al. for use on the human genome project. There, one takes a bunch of copies of the human genomic DNA (the unshredded document(s)), then blows it apart using enzymes to yield an array of overlapping fragments (the shredding). One then sequences all the individual fragments (roughly analogous to scanning all those bits of shredded paper), and has a program match up all the overlapping fragments until the original is re-assembled.
You may ask why we 'shred' the genome in the first place? This has to do with current technical limitations of the size of a fragment that can be reliably sequenced at one time. It's as if our current 'scanners' only have flatbed areas of 1 square cm, making it necessary to do lots of individual scans of the large genome 'page' before re-assembly.
As best I can tell after reading the National Post article, the reporter was to some extent sensationalising what is a very simple fact: injury often leads to pain, but injury does not exactly equal pain.
What might have saved the article from blistering critiques (but garnered far less readership) would have been to clearly differentiate injury and pain, terms which the medical profession clearly distinguish from each other.
Injury = physical, objectively measurable damage
Pain = distressful or unpleasant sensation or experience
I must say that as a graduate student for the past 6 years in the life sciences, the situation as far as online access to fulltext journals has improved dramatically at our institution, the University of British Columbia. Through word of mouth, I hear that other universities across North America have similarly improved access to articles in diverse fields online.
Recently, however, our university's trial subscription to the online edition of the prestigious journal Nature and its associated monthlies expired. Our university decided to join with Harvard, Cornell, Princeton, and the University of California in boycotting what was deemed an untenably pricey subscription fee by the Nature publishing group ($30,000 CDN) for a service with significant restrictions in the timeliness of content. Our librarian's letter outlines our school's position on this issue. Nature's own site licensing policies are available here.
Slashdot Mirror
You may ask why we 'shred' the genome in the first place? This has to do with current technical limitations of the size of a fragment that can be reliably sequenced at one time. It's as if our current 'scanners' only have flatbed areas of 1 square cm, making it necessary to do lots of individual scans of the large genome 'page' before re-assembly.
See, for example: http://nema.cap.ed.ac.uk/teaching/genomics/Genomic s3.html
As best I can tell after reading the National Post article, the reporter was to some extent sensationalising what is a very simple fact: injury often leads to pain, but injury does not exactly equal pain. What might have saved the article from blistering critiques (but garnered far less readership) would have been to clearly differentiate injury and pain, terms which the medical profession clearly distinguish from each other. Injury = physical, objectively measurable damage Pain = distressful or unpleasant sensation or experience
Recently, however, our university's trial subscription to the online edition of the prestigious journal Nature and its associated monthlies expired. Our university decided to join with Harvard, Cornell, Princeton, and the University of California in boycotting what was deemed an untenably pricey subscription fee by the Nature publishing group ($30,000 CDN) for a service with significant restrictions in the timeliness of content. Our librarian's letter outlines our school's position on this issue. Nature's own site licensing policies are available here.