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Published online 16 April 2008 | 452, 788 (2008) | doi:10.1038/452788b
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James Watson's genome sequenced at high speed
New-generation technology takes just four months and costs a fraction of old method.
The first full genome to be sequenced using next-generation rapid-sequencing technology is published today (see page 872.
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Venter genome exhibited 2.8 million known SNPs and about 0.74 million novel SNPs. In close agreement, Watson DNA sequence harbours 2.72 million known and 0.61 million novel SNPs. In contrast, an initial analysis (unpublished) of genome of an anonymous African male using Illumina's Genome Analyzer has reportedly shown over 3.7 million SNPs of which more than one million are novel. A higher number of novel SNPs in the later study may not be however surprising.
Although leaders of that technically powerful but intellectually blind genetic technology apparently understand that they "see everything but understand nothing" (see the end of this news article), their dangerous experimentation continues in the same way, i.e. far from any real understanding of genuine genome dynamics. The underlying logic is probably that of "let's first have it and then try to understand it", but things do not seem to go that way in real life. While formal sequencing, as well as related “linear� genome modification, advances in great steps, understanding of the "mystery of life" in general and unreduced genome dynamics in particular is always missing (cf. http://www.nature.com/embor/journal/v8/n8/full/7401041.html ). All the superficial games of official "systems biology" are but word plays: in the best case, they only understand that they should understand... Any serious progress in this and other life-science problems is impossible without the consistent, causally complete solution of the underlying many-body interaction problem, but it remains "unsolvable", within the official science doctrine, starting already from three interacting bodies. A recently found solution for the general case and its application to genetic problems ( http://arxiv.org/abs/physics/0502133 ) shows the huge difference of the unreduced system dynamics from its "linear" projection in the official paradigm (including its obviously inconsistent "science of complexity"). Using the established fundamental laws of the unreduced dynamic complexity (of real systems!), these results demonstrate, in particular, that the "exponentially huge" power of real genomic interaction is such that, on average, every base interacts with any other one, i.e. genome is a "completely entangled" network of links rather than a visible "linear chain" (or "computer programme") as they still seem to imagine by absolute domination of that linear sequencing approach (cf. e.g. "I view biology as an analog world that DNA sequencing has taking into the digital world" by J. Craig Venter, http://www.edge.org/documents/life/life_index.html ). So that's what they are actually doing and will increasingly do, a straightforward linear modification of extremely nonlinear, entangled system, which is ... your life, baby! The inevitable result is a delayed-action "genetic bomb" (see the above arXiv paper), another weapon of mass destruction silently put into action right now, without any declaration of war... I think you have at least the right to know it, baby...
Shi V. Liu's advice: Avoid Boring Papers in Nature --------- I guess this DNA sequencing paper would be rejected right away by Nature if it is not on DNA of James Watson. However, in today's science, it is not the KNOWLEDGE but the SUBJECT that matters most in weighing the "significance" of a manuscript for publication. A life-like feature coming from a Martian sample will occupy the front page of any top journal. However, a real knowledge on the true life of an Earth organism will be rejected as having no general interest.------- So even though this Watson genome sequence paper really does not offer any knowledge for the much hyped "personalized medicine", the data-description-only paper was still published as a "milestone". However, other than being a nice piece for library display, what practical value this landmark paper will give to us today? So my advice to truth-seeking scientists is: avoiding this boring paper in Nature, particularly when it was even politically corrected to avoid touching any sensitive topics such as how 16% "black DNA" was enriched in Watson's genome. If anyone wishes to know what other KNOWLEDGE in life science can teach us better lessons on life and medicine, please visit Truthfinding Cyberpress at http://im1.biz. As a matter of fact, some papers on James Watson and his DNA published there(http://im1.biz/Watson.htm) may be more interesting to read than this data-only boring paper in Nature. ------- Shi V. Liu (SVL@logibio.com)
A Disappointing Personal Genome ------ Now I have found a little time to refresh my memory on another personal genome – the Craig Venter's diploid genome sequence published in PLoS Biology last year (V5: e254, 2007). Comparing with the rich information contained in that publication, which includes not just much detailed descriptions on DNA sequence but also some data on the personal, medical and phenotypic traits, the Nature publication on James Watson's personal genome is much poor in information, not to say lack of any valuable KNOWLEDGE. ------- Then, how could these two personal genomes ended up in two different publishing spaces? Was it because that Craig Venter was more open-minded (willing to share many more of his personal information than just the personal DNA sequence) than James Watson (refused releasing some key DNA sequences related to some important diseases)? Or was it simply due to a fact that somehow Nature (thanks god) did not rejected Watson et al.'s hypothesis on a DNA structure that turned out to be very correct? ------ What criteria were really used by Nature in selecting what to publish and what not to publish? ------- If general interest is a key factor in determining the suitability of publishing or the desire to publish, then why didn't Nature insist on the provision of some answers to the most curious and still enigmatic question of the putative "black" DNA in Watson's genome? ------ In the PLoS Biology paper describing Craig Venter's personal genome, a DNA pedigree was shown to cover three generations of Venter's family. That analysis proved that his DNA is at least 99.5% similar to the DNA samples of northern and western European ancestry. Can Watson also do the same to show that the so-called "black DNA" in his genome is not any true inheritance from a much speculated black ancestor but a true misunderstanding on how human evolution occurred? ----- As the greatest biological scientist and a very public figure, Watson may have some more obligations to share more of his personal information to the human society than any other ordinary citizens. If he thought that his personal genome paper deserves a high-profile publication in Nature, then he should also be willing to answer some curiosities on his personal genome (for the benefit of human society). Otherwise just keep a personal genome as private information. ---- Shi V. Liu (SVL@logibio.com)
A Research Plan for Identifying Genes for Intelligence ------ I believe that personal genomes have a very long way to go before they can be used for any personalized medicine. However, studying personal genomes may lead some quick solutions to the debate on a genetic basis for human intelligence. ------ Since the most successful (and thus got to be intelligent) individuals are more likely to be selected for the proof-of-principle test of any new technology for fast sequencing (personal) genomes, it will be easy to complete an intelligence genome project than any other disease-oriented genome project. This is because we just need to add a control group of the most dump people. In addition, as a bonus point, we might also select some smart animals for individual animal genome sequencing. ------ With these three groups of individual genome sequences in hands, we may be able to check if there are any genes which give human the unique human intelligence. We may even be able to tell if there are any genes which make certain human beings more intelligent. ----- I will call this project the Human Intelligence Genome Project (HIGP). I wish all the intelligent supporters for the previous HGP will endorse this project. Any other smart companies are also welcome to join this intelligence-decoding effort. ---- Shi V. Liu (SVL@logibio.com)
Finally I think it will be possible to sequence a genome pretty cheap (<$3000) and all the patients in the hospitals can have this test. However the amount of information we will gain sequencing all the genomes will be huge. There will be a lot of clinical studies to correlate certain mutations with diseases and treatments in a world of evidence based medicine. The personalized medicine is far away.
I was surprised that they just use HGP reference sequence as a template for assembly. This implies that no matter how many coverage the sequencer can afford, it still cannot independently assemble the complex sequences. After all, this technology is better than the Illumina's technology in which only 35-bp fragment can be sequenced. This technology will lead the field of molecular medicine to another level, especially focusing on mutation/SNP discovery.