It will not stop by 3 companies (23andme backed by Google and Genentech, Navigenics backed by KPCB, MDV and Sequoia, and DeCodeMe that started on money from Roche). Competitor IT companies (Microsoft, Apple etc), competitor VC companies (DFJ, Abingworth; many from the at least 50 VC-s that listened to Venter on Sand Hill Road last week will join the fray). Big Pharma in addition to Genentech and Roche will also join in (Pfizer, Merck, Novartis, etc). However, the business models (securing privacy) and the technology to work out the information system is a task for "technology focal points" such as Silicon Valley, Texas, San Diego, Boston (with outsourcing, of course, globally). The underlying biotech is presently the microarrays by Illumina (presently leading) and Affymetrix (already trailing). Since neither was developed for "Online PostGenetic Medicine", chances are that this "internet boom, round two" will also revolutionize microarray technology, and eventually merge it with the already announced "$100 whole genome sequencing" (Complete Genomics). See more analysis at http://example.com/
Slashdot reader should be happy. The momentary 3 companies (remember Netscape?) will result in "Personalized Genomics" and even larger, "PostGenetic Medicine, largely on-line" with every person's highest ranking motivation - health. This "GenomeNet boom" will be orders of magnitude larger than the "Internet boom" ever was - since it carries the internet itself to a higher level as a subset: Issues are tracked for years on http://www.junkdna.com/
Just as with "Internet", privacy issues will be horrendous; the threat is much more severe than with "Internet". The present business models are obviously unripe; cf. DeCodeMe and 23andMe both wrestling with "anonymous" DNA sample submission. Loopholes abound.
For the usual slashdot reader, however, there are incredibly lucrative opportunities:
The technology is much more demanding compared to challenges of "Internet boom". (Among others, interdisciplinary domain-expertise is fetches high prices).
The science, underlying both "Personalized Genomics" and "PostGenetic Medicine" is turning from molecular biology to informatics. The "ENCODE-release" (June 14, 2007) was essentially a capitulation of molecular biology to informatics.
Both Big Pharma, Big IT and Big Venture Capital are already incomparably more involved than at the time of Netscape. (Merck bought and essentially informatics-company [SiRNA] for $1.1 Billion, one (23andMe) of the presently 3 "Personalized Genomics for Consumers" companies is backed by BOTH a Big Pharma (Genentech)and a Big IT (Google). Another of the 3 (Navigenics) is backed by THREE of the most prestigeous VCs (KPCB, MDV and Sequoia).
I suggest, nobody should lose out from this one!
pellionisz_at_junkdna.com
What was Scifi in Jules Verne's time is today's science & technology. The "Genome inside a Genome" (and as seen in Junk DNA Portal ) also, "an entire Gene in the intron of another Gene", the Genome seems to show an architecture (algorithm) of nested hierarchies, that can e.g. be described by (multi)fractals.
What is truly mind-boggling, that with the ENCODE-Report (led by NIH, a USA Government Agency) essentially all dogma of Genomics (as we knew it) are invalidated; "Junk DNA" is dead as a doornail, "Gene" concept needs "an updated definition", "Central Dogma" (of Crick) is demonstrably invalid.
Now, this finding "offers new mechanisms of evolution"...
pellionisz_at_junkdna.com
There are two factual errors in the argument that leaving "junk" in the Genome is cheap and safe. First, recombination requires energy - and mind you, the DNA *IN EACH AND EVERY CELL* when it replicates consumes a lot of energy with recombination. Second, while you can "comment out" useless "junk" in the sw code, we know that tons of "junk DNA diseases" (see http://www.junkdna.com/junkdna_diseases.html) are caused by glitches "in the Junk". Therefore, Nature not only has an incentive of getting rid of unneded code for reasons of energy, but also to save itself from "junk DNA diseases" - if the "junk" is truly trash.
However, it is now clear not only to pioneers (http://www.postgenetics.org see tab "Founders") - but is also "blessed by NIH" that there is "no more Junk". The challenge is no longer "why is it there", but "how does it work"?
pellionisz_at_junkdna.com
The "Information Theory" of Shannon kicked off von Neumann' "Computer Science". "Genomic Information", however, is even less clearly defined than (loose) "Biological Information". With Fig.30. from "Supplementary material", featured on http://www.junkdna.com/ it is downing to all that "all A,C,T,G letters are equal - but some are more equal than others" (to paraphrase in PostGenetic Genome Farm George Orwell). Someone pointed out that DNA sequences compress very poorly - another reminder that "genomic information" (*all* information there is to define organelles, organs and organisms) is already compressed; to the extreme. Since living systems are "built" from the "bricks and mortar" of proteins, the genome must specify the "raw materials" (protein-coding sequences, formerly called "genes" do that for a living). However, as already pointed out in 2002 by FractoGene, the "architecture" of *what kind of a building* a genome erects is compressed into the "blueprint of life" - and the sets of auxiliary information of how to put together the "bricks and mortar", since the "compression" is fractal, looked like a self-similar repetitive jumble; termed by non-algorithmic thinkers like the late Dr. Ohno "Junk". Readers of this column (techies) be happy - there is a colossal "boom" in the offing for "information technology of Genomics" (beyond Genes). It will be incomparably bigger than the "Internet boom" - since it *includes* the Internet itself - but goes much further by establishing an entirely new (transdisciplinary) discipline. Pls. look at the presently 53 Founders of International PostGenetics Society (http://www.postgenetics.org) and you will be amazed of the kinds of "leading edge" mathematicians, computer scientists, neural network experts - and of course bioinformaticians - in addition to "wet" genomists. Please join IPGS if you care, and be part of it as much or as little as you can. pellionisz_at_junkdna.com
This is one of the landmark-quotes on the "Junk DNA Portal" http://www.junkdna.com/ . The collection of articles since Dr. Ohno coined the term "Junk DNA" in 1972 features, of course, the "NIH Blessing" that "Junk DNA" is anything, but... Will there be life after the "death of Junk DNA"? Of course. Those who are searching for a name of "Genomics beyond Genes" will find that International PostGenetics Society (http://www.postgenetics.org) established in 2005 defined "PostGenetics" as going beyond genes, and in its European Inaugural became the first international organization to formally abandon this catchy misnomer. "PostGenetics" is the postmodern era of "Genetics" (1905-2005). Techies (the readership of slashdot) will not rest until the algorithm of genomic coding ("beyond genes") will be available, since algorithms are "software enabling", while loose talk on "wet biology only" is generally "software unfriendly". http://www.fractogene.com/ provides an algorithmic approach - and also provides insights to the myriads of "junkdna diseases" where the genes are pristine but glitches in the "junk" might doom you at any time; http://www.junkdna.com/junkdna_diseases.html . "PostGenetics" has been an "uphill battle" from 2002 (FractoGene) till yesterday. Now it is expected that (1) the press will look beyond the "life and death of junk dna" and will "discover" PostGenetics (the wonderful opportunity is the 35th Anniversary on 30th of June of Dr. Ohno's coining the term "junk DNA"), (2) a similar "cut-throat race" will emerge between slow but huge and rich government programs for a "DECADE OF DECODE" (after ENCODE) on one hand, and focused and streamlined private domain industry, going directly for tangible results in Bioenergy, Synthetic Genomics (etc). While they are already well underway, it is clear that "regulation" is a key factor, and both in Bioenergy and Synthetic Genomics (let alone bio-based Nano- and Information Technology) a software-enabling understanding of Genome Regulation will be vital. pellionisz_at_junkdna.com
The genome is fractal - governing fractal growth of organelles, organs and organisms. Even from a single fractal template (e.g. the algorithm of z=z^2+C) an enormously "complex" pattern, full of self-similar repetitions will develop. The "gene"-parts of the genome determine "fractal templates" of proteins, while the "PostGene"-sequences supply the auxiliary information necessary for iterative hierarchical development (architecture of complex protein structures). This concept/utility (FractoGene) triggered 300+ entries in slashdot in 2002 when an algorithmic approach first challenged the "gene/junk" dogma. The saga (including slashdot reference) is recorded at http://www.junkdna.com/ (as well as on http://www.fractogene.com/ )
Of course it is not junk... "junkDNA" is not a scientific term any more - but an important nickname for "the biggest mistake in the history of molecular biology".
pellionisz_at_junkdna.com
The patent application (read it) is clearly not claiming "synthetic life". Journalists (alas, including Slashdot) often have no clue "how to hang a major story". ("MicrobeSoft" *is* a major story, and from a number of viewpoints...). For a scientific analysis, see SlashDot and other coverage in http://www.junkdna.com/ . Commentator (A. Pellionisz) welcomes public replies here, or privately at pellionisz_at_junkdna.com
It may sound scary, but there are at least 64 commercial "synthetic genomics" companies (see http://www.junkdna.com/ ) that can turn INFORMATION (of A,C,T and G-s) into actual DNA.
Thus, the two DVD information is really, our "blueprint".
Even scarier, the DVD is a rather primitive carrier of the DNA information. A sperm and an ovum are MUCH tinier...
Yes, this is a juncture of time when everybody has reasons to be "completely torn". Just as at every paradigm-shift in the history of science & technology. When the automobile appeared... When the A and H bombs appeared... When the home computer appeared... When the Internet appeared... (etc).
If human kind is racing towards good or evil, is a question of philosophy. Fact remains, that the race has just accelerated (presently, for most people, beyond comprehension).
There will be winners and losers (see above examples). Optimists may focus on the the possibility (virtual certainty) that e.g. if your Personal Genome harbors one of those "Junk DNA disease" glitches ( see http://www.junkdna.com/junkdna_diseases.html ), you will hugely benefit from your "Personal Genome". Even for healthy people their "Personal Genome" will help selecting those foods, medicines, activities (even partners) that are the best (and worst) for them.
Pessimists may well worry about unprecedented "privacy" issues. While experts are already working on minimizing such effects ( see http://www.safedna.com/ ), the challenge is so great that even the biggest companies may "swim or sink" on this issue. (Just as IBM was the loser in the PC paradigm shift and Microsoft was the big winner; this issue already popped up with Google/23andme - with Microsoft and other IT giants not far behind).
If Christiansen is right ("The innovator's dilemma"), like in every disruptive technology the biggest companies with largest inertia are at a disadvantage - while small and agile business can hugely benefit from the opportunity.
Scientifically, PostGenetics (see http://www.postgenetics.org/ is likely to be a major beneficiary, since most of the Personal Diversity of Genomes is in "Genomics beyond Genes" (in what used to be called "Junk" DNA).
While the term "decyphered" is incorrect (Jim Watson' and Craig Venter' genomes have "only" been REVEALED) - true "decyphering" will be much easier when a statistically significant Personal Genomes will be available. Thus far, it was ZERO (the one published was a "mix").
The two Personal Genomes will be practically identical as far as the "genes" are concerned.
However, there will be much diversity in the "non-coding" (formerly "junk") DNA (see ample background at http://www.junkdna.com/
"Genomics beyond Genes" will catapult "Personalized PostGenetics".
Slashdot Mirror
Sorry, the link is http://www.junkdna.com/
It will not stop by 3 companies (23andme backed by Google and Genentech, Navigenics backed by KPCB, MDV and Sequoia, and DeCodeMe that started on money from Roche). Competitor IT companies (Microsoft, Apple etc), competitor VC companies (DFJ, Abingworth; many from the at least 50 VC-s that listened to Venter on Sand Hill Road last week will join the fray). Big Pharma in addition to Genentech and Roche will also join in (Pfizer, Merck, Novartis, etc). However, the business models (securing privacy) and the technology to work out the information system is a task for "technology focal points" such as Silicon Valley, Texas, San Diego, Boston (with outsourcing, of course, globally). The underlying biotech is presently the microarrays by Illumina (presently leading) and Affymetrix (already trailing). Since neither was developed for "Online PostGenetic Medicine", chances are that this "internet boom, round two" will also revolutionize microarray technology, and eventually merge it with the already announced "$100 whole genome sequencing" (Complete Genomics). See more analysis at http://example.com/
Slashdot reader should be happy. The momentary 3 companies (remember Netscape?) will result in "Personalized Genomics" and even larger, "PostGenetic Medicine, largely on-line" with every person's highest ranking motivation - health. This "GenomeNet boom" will be orders of magnitude larger than the "Internet boom" ever was - since it carries the internet itself to a higher level as a subset: Issues are tracked for years on http://www.junkdna.com/ Just as with "Internet", privacy issues will be horrendous; the threat is much more severe than with "Internet". The present business models are obviously unripe; cf. DeCodeMe and 23andMe both wrestling with "anonymous" DNA sample submission. Loopholes abound. For the usual slashdot reader, however, there are incredibly lucrative opportunities: The technology is much more demanding compared to challenges of "Internet boom". (Among others, interdisciplinary domain-expertise is fetches high prices). The science, underlying both "Personalized Genomics" and "PostGenetic Medicine" is turning from molecular biology to informatics. The "ENCODE-release" (June 14, 2007) was essentially a capitulation of molecular biology to informatics. Both Big Pharma, Big IT and Big Venture Capital are already incomparably more involved than at the time of Netscape. (Merck bought and essentially informatics-company [SiRNA] for $1.1 Billion, one (23andMe) of the presently 3 "Personalized Genomics for Consumers" companies is backed by BOTH a Big Pharma (Genentech)and a Big IT (Google). Another of the 3 (Navigenics) is backed by THREE of the most prestigeous VCs (KPCB, MDV and Sequoia). I suggest, nobody should lose out from this one! pellionisz_at_junkdna.com
What was Scifi in Jules Verne's time is today's science & technology. The "Genome inside a Genome" (and as seen in Junk DNA Portal ) also, "an entire Gene in the intron of another Gene", the Genome seems to show an architecture (algorithm) of nested hierarchies, that can e.g. be described by (multi)fractals. What is truly mind-boggling, that with the ENCODE-Report (led by NIH, a USA Government Agency) essentially all dogma of Genomics (as we knew it) are invalidated; "Junk DNA" is dead as a doornail, "Gene" concept needs "an updated definition", "Central Dogma" (of Crick) is demonstrably invalid. Now, this finding "offers new mechanisms of evolution"... pellionisz_at_junkdna.com
There are two factual errors in the argument that leaving "junk" in the Genome is cheap and safe. First, recombination requires energy - and mind you, the DNA *IN EACH AND EVERY CELL* when it replicates consumes a lot of energy with recombination. Second, while you can "comment out" useless "junk" in the sw code, we know that tons of "junk DNA diseases" (see http://www.junkdna.com/junkdna_diseases.html) are caused by glitches "in the Junk". Therefore, Nature not only has an incentive of getting rid of unneded code for reasons of energy, but also to save itself from "junk DNA diseases" - if the "junk" is truly trash. However, it is now clear not only to pioneers (http://www.postgenetics.org see tab "Founders") - but is also "blessed by NIH" that there is "no more Junk". The challenge is no longer "why is it there", but "how does it work"? pellionisz_at_junkdna.com
Those wishing to look beyond "websites" for FractoGene can look up the refereed science paper (in full) at http://www.junkdna.com/fractogene/05_simons_pellio nisz.pdf
The "Information Theory" of Shannon kicked off von Neumann' "Computer Science". "Genomic Information", however, is even less clearly defined than (loose) "Biological Information". With Fig.30. from "Supplementary material", featured on http://www.junkdna.com/ it is downing to all that "all A,C,T,G letters are equal - but some are more equal than others" (to paraphrase in PostGenetic Genome Farm George Orwell). Someone pointed out that DNA sequences compress very poorly - another reminder that "genomic information" (*all* information there is to define organelles, organs and organisms) is already compressed; to the extreme. Since living systems are "built" from the "bricks and mortar" of proteins, the genome must specify the "raw materials" (protein-coding sequences, formerly called "genes" do that for a living). However, as already pointed out in 2002 by FractoGene, the "architecture" of *what kind of a building* a genome erects is compressed into the "blueprint of life" - and the sets of auxiliary information of how to put together the "bricks and mortar", since the "compression" is fractal, looked like a self-similar repetitive jumble; termed by non-algorithmic thinkers like the late Dr. Ohno "Junk". Readers of this column (techies) be happy - there is a colossal "boom" in the offing for "information technology of Genomics" (beyond Genes). It will be incomparably bigger than the "Internet boom" - since it *includes* the Internet itself - but goes much further by establishing an entirely new (transdisciplinary) discipline. Pls. look at the presently 53 Founders of International PostGenetics Society (http://www.postgenetics.org) and you will be amazed of the kinds of "leading edge" mathematicians, computer scientists, neural network experts - and of course bioinformaticians - in addition to "wet" genomists. Please join IPGS if you care, and be part of it as much or as little as you can. pellionisz_at_junkdna.com
This is one of the landmark-quotes on the "Junk DNA Portal" http://www.junkdna.com/ . The collection of articles since Dr. Ohno coined the term "Junk DNA" in 1972 features, of course, the "NIH Blessing" that "Junk DNA" is anything, but... Will there be life after the "death of Junk DNA"? Of course. Those who are searching for a name of "Genomics beyond Genes" will find that International PostGenetics Society (http://www.postgenetics.org) established in 2005 defined "PostGenetics" as going beyond genes, and in its European Inaugural became the first international organization to formally abandon this catchy misnomer. "PostGenetics" is the postmodern era of "Genetics" (1905-2005). Techies (the readership of slashdot) will not rest until the algorithm of genomic coding ("beyond genes") will be available, since algorithms are "software enabling", while loose talk on "wet biology only" is generally "software unfriendly". http://www.fractogene.com/ provides an algorithmic approach - and also provides insights to the myriads of "junkdna diseases" where the genes are pristine but glitches in the "junk" might doom you at any time; http://www.junkdna.com/junkdna_diseases.html . "PostGenetics" has been an "uphill battle" from 2002 (FractoGene) till yesterday. Now it is expected that (1) the press will look beyond the "life and death of junk dna" and will "discover" PostGenetics (the wonderful opportunity is the 35th Anniversary on 30th of June of Dr. Ohno's coining the term "junk DNA"), (2) a similar "cut-throat race" will emerge between slow but huge and rich government programs for a "DECADE OF DECODE" (after ENCODE) on one hand, and focused and streamlined private domain industry, going directly for tangible results in Bioenergy, Synthetic Genomics (etc). While they are already well underway, it is clear that "regulation" is a key factor, and both in Bioenergy and Synthetic Genomics (let alone bio-based Nano- and Information Technology) a software-enabling understanding of Genome Regulation will be vital. pellionisz_at_junkdna.com
http://science.slashdot.org/article.pl?sid=02/11/2 2/1347202&mode=thread&tid=134
The genome is fractal - governing fractal growth of organelles, organs and organisms. Even from a single fractal template (e.g. the algorithm of z=z^2+C) an enormously "complex" pattern, full of self-similar repetitions will develop. The "gene"-parts of the genome determine "fractal templates" of proteins, while the "PostGene"-sequences supply the auxiliary information necessary for iterative hierarchical development (architecture of complex protein structures). This concept/utility (FractoGene) triggered 300+ entries in slashdot in 2002 when an algorithmic approach first challenged the "gene/junk" dogma. The saga (including slashdot reference) is recorded at http://www.junkdna.com/ (as well as on http://www.fractogene.com/ ) Of course it is not junk... "junkDNA" is not a scientific term any more - but an important nickname for "the biggest mistake in the history of molecular biology". pellionisz_at_junkdna.com
The patent application (read it) is clearly not claiming "synthetic life". Journalists (alas, including Slashdot) often have no clue "how to hang a major story". ("MicrobeSoft" *is* a major story, and from a number of viewpoints...). For a scientific analysis, see SlashDot and other coverage in http://www.junkdna.com/ . Commentator (A. Pellionisz) welcomes public replies here, or privately at pellionisz_at_junkdna.com
It may sound scary, but there are at least 64 commercial "synthetic genomics" companies (see http://www.junkdna.com/ ) that can turn INFORMATION (of A,C,T and G-s) into actual DNA. Thus, the two DVD information is really, our "blueprint". Even scarier, the DVD is a rather primitive carrier of the DNA information. A sperm and an ovum are MUCH tinier...
Yes, this is a juncture of time when everybody has reasons to be "completely torn". Just as at every paradigm-shift in the history of science & technology. When the automobile appeared... When the A and H bombs appeared... When the home computer appeared... When the Internet appeared... (etc). If human kind is racing towards good or evil, is a question of philosophy. Fact remains, that the race has just accelerated (presently, for most people, beyond comprehension). There will be winners and losers (see above examples). Optimists may focus on the the possibility (virtual certainty) that e.g. if your Personal Genome harbors one of those "Junk DNA disease" glitches ( see http://www.junkdna.com/junkdna_diseases.html ), you will hugely benefit from your "Personal Genome". Even for healthy people their "Personal Genome" will help selecting those foods, medicines, activities (even partners) that are the best (and worst) for them. Pessimists may well worry about unprecedented "privacy" issues. While experts are already working on minimizing such effects ( see http://www.safedna.com/ ), the challenge is so great that even the biggest companies may "swim or sink" on this issue. (Just as IBM was the loser in the PC paradigm shift and Microsoft was the big winner; this issue already popped up with Google/23andme - with Microsoft and other IT giants not far behind). If Christiansen is right ("The innovator's dilemma"), like in every disruptive technology the biggest companies with largest inertia are at a disadvantage - while small and agile business can hugely benefit from the opportunity. Scientifically, PostGenetics (see http://www.postgenetics.org/ is likely to be a major beneficiary, since most of the Personal Diversity of Genomes is in "Genomics beyond Genes" (in what used to be called "Junk" DNA).
While the term "decyphered" is incorrect (Jim Watson' and Craig Venter' genomes have "only" been REVEALED) - true "decyphering" will be much easier when a statistically significant Personal Genomes will be available. Thus far, it was ZERO (the one published was a "mix"). The two Personal Genomes will be practically identical as far as the "genes" are concerned. However, there will be much diversity in the "non-coding" (formerly "junk") DNA (see ample background at http://www.junkdna.com/ "Genomics beyond Genes" will catapult "Personalized PostGenetics".