There's a revolution underway. It's digital, but not in the computing sector. I'm referring to the world of genomics, which deals with the data that resides inside all living things: DNA. As most people know, DNA uses four chemical compounds - adenine, cytosine, guanine and thymine - to encode various structures, most notably proteins, which are represented by stretches of DNA called genes.
As a recent DailyDirt noted, opinions on the safety of genetically modified organisms (GMOs) are sharply divided. But that heated argument tends to obscure another problem that Techdirt has often written about in other fields: the use of patent monopolies to exert control, in this case over the food chain. By inserting DNA sequences into plants and animals and obtaining patents, the biotech industry is granted surprisingly wide-ranging powers over how its products are used, as the Bowman case made clear. That's potentially problematic when those products are the foods that keep us alive.
Two of the key arguments during the Myriad Genetics trial were that gene patent monopolies stifle innovation by preventing others from building on and extending key knowledge, and that they can cause unnecessary suffering and even death by driving up prices for medical treatment beyond the reach of many people. Even though the Supreme Court struck down Myriad's key patents, reducing those issues for DNA, a new technology with major ramifications for health runs the risk of suffering from precisely the same problems.
Seeds might seem far from the world of high tech and free software, but they have much in common. Seeds contain DNA, which is a (quaternary) digital code much like a binary program. Just as there is free software that anyone may use and share, there are free seeds - those that are part of the ancient seeds commons, created over thousands of years, available for use by anyone. And just as free software is threatened by software patents, so seeds are equally endangered by seed patents.
The computing revolution is not the only one driven by constant scaling of technologies: the field of genomics -- the study of DNA sequences -- has also enjoyed rapid falls in basic costs over the last decade and a half. This means that whereas the first human genome cost around $3 billion to sequence, we are fast approaching the point where it will cost first a few thousand, and then a few hundred dollars to sequence anyone's complete DNA. An interesting post on the Health Affairs Blog points out that neither the law nor society is ready for this.
One new approach to teasing apart the complex relationships between genes and common diseases such as cancer, heart disease, asthma and diabetes is by creating huge biobanks of medical data and samples. The idea is that by tracking the health and habits of very large populations across many years, and then examining their DNA, it will be possible to spot factors in common. Here's a major biobank that is shortly opening up its holdings for research:
Here's a sad story, but not for the reason you might expect:Developing therapies from human embryonic stem cells is under threat in Europe, say scientists.
In a letter to Nature, they express "profound concern" about moves at the European Court of Justice to ban patent protection for embryonic stem cell lines.
...
In their letter to Nature, the scientists argue that industry would have no incentive to invest in this area unless their innovations could be protected with patents.
This is the old FUD that unless patents are given for every possible advance, industry will never "invest". Well, even assuming that were true, scientists shouldn't be worrying about that: they are *scientists*, not managers. They are supposed to be motivated by love of knowledge, by the joy of research. Patents weren't allowed on the results of the Human Genome Project, and yet somehow that came to splendid fruition: why should stem cell research be any different?
And the idea that industry doesn't invest without patents is nonsense: that's precisely what happened in the world of software until a misguided court decision allowed programs to be patented in the US. But the introduction of patents in that field has led to a net *loss* for the industry of billions of dollars, as the book "Patent Failure" - written by two supporters of patents - explains in great detail.
The central motivation for innovation is not to get a patent, but to use that innovation to surpass rivals and win business as a result - it's a means to an end. Even if those rivals then use that same invention, they are still at a disadvantage because they are simply following in the original innovator's footsteps. And if they manage to develop the work further, then they advance the field and provide more ideas for yet more innovation - that's how things are supposed to work.
But what's really sad about this whole episode is the fact that scientists have become so corrupted by the trend towards turning knowledge into property that they can't conceive of carrying out exciting science without the nominal incentives of patents. This indicates that something bad has happened to very DNA of science - and patented stem cell research certainly isn't going to fix it.
Follow me @glynmoody on Twitter or identi.ca.
Here's a textbook case of how gene patents not only do *not* promote innovation, as is so frequently claimed, but slow it down - and will probably cause millions to suffer as a result.
An AIA lawsuit filed in February 2010 against the Jackson Laboratory in Bar Harbor, Maine — a source of laboratory mice funded by the US National Institutes of Health (NIH) — now threatens hundreds of government-sponsored Alzheimer's researchers with litigation.
But wait, what patent might that be?
The suit concerns an AIA patent on a human DNA sequence used in mouse models of Alzheimer's disease. The sequence encodes the 'Swedish mutation' (discovered in a Swedish family), which causes early-onset Alzheimer's. Michael Mullan, a biomedical researcher who is now head of the Roskamp Institute in Sarasota, Florida, patented the sequence in 1995, then sold it to the AIA.
So this concerns a *human* DNA sequence, found in a Swedish family. That is, it is something natural, that was discovered, not invented in any sense. And yet a patent was granted on this non-invention, and this ill-considered move is now casting a chill over an entire field of research that could potentially alleviate the suffering of millions.
Now, tell me again how gene patents promote innovation and progress...?
Follow me @glynmoody on Twitter or identi.ca.
The oceans belong to everyone - well, more or less. That is, they form a classic commons. But of course, that fact doesn't stop people claiming that they own stuff even here:Molecules derived from marine resources and used for medical applications were worth over $1 billion in 2005, and heat-stable enzymes obtained at undersea vents were worth $150 million. Not surprisingly, the business community has responded by patenting genes derived from marine organisms; the authors were able to identify over 8,500 sequences derived from a total of 520 species in a US gene patent database.
This is a double insult to humanity. Genes are part of the DNA commons, and "belong" to everyone or to no one, but certainly not to any one entity. Those genes were extracted from marine animals, which form part of another commons, the oceans' ecosystems, that also belong to everyone or to no one.
But instead of simply recognising those commons, and letting everyone benefit from them directly, the best the patent maximalists can come up with is a cartel, a.k.a. patent pool:they also suggest that, in the case of marine materials, a patent pool organized within this framework might improve access to genetic information and distribute the risk and profits broadly among far more nations, rather than limiting it to the few countries that can afford high-throughput DNA sequencing.
The logic here seems to be that of course we need patents otherwise nobody will go to the trouble of sequencing all these interesting organisms. What this overlooks is that the cost of sequencing genomes has come down from a billion dollars (for the first human genome) to a few thousand. Next year it will probably be under $1000, and the year after that a few hundred. In a decade, sequencing will cost almost nothing.
What this means is that, once more, intellectual monopolies are being given away needlessly - no quid pro quo is in fact necessary because practically anyone will be able to do this for very low cost. And once again it's you and me who lose out, as knowledge is sent to the intellectual equivalent of Davey Jones's Locker....
Craig Venter is a bit tiresome at times, but indubitably clever. And to prove his cleverness (again) when he was creating artificial life, he thought he'd throw into the DNA a quotation or two:In order to distinguish their synthetic DNA from that naturally present in the bacterium, Venter’s team coded several famous quotes into their DNA, including one from James Joyce’s A Portrait of the Artist of a Young Man: “To live, to err, to fall, to triumph, to recreate life out of life.”
Rather witty, no? Sadly, the humourless Joyce Estate didn't see it that way:After announcing their work, Venter explained, his team received a cease and desist letter from Joyce’s estate, saying that he’d used the Irish writer’s work without permission. ”We thought it fell under fair use,” said Venter.
Yeah, we really need Draconian copyright laws to protect (dead) artists from this kind of evil infringement.
Follow me @glynmoody on Twitter or identi.ca.
It is somewhat ironic that the man behind WikiLeaks, Julian Assange, is not a fan of being in the spotlight; and therefore perhaps poetic justice that he is increasingly the focus of in-depth profiles. The best one so far has just appeared in The New Yorker, and includes this memorable description:WikiLeaks receives about thirty submissions a day, and typically posts the ones it deems credible in their raw, unedited state, with commentary alongside. Assange told me, “I want to set up a new standard: ‘scientific journalism.’ If you publish a paper on DNA, you are required, by all the good biological journals, to submit the data that has informed your research—the idea being that people will replicate it, check it, verify it. So this is something that needs to be done for journalism as well. There is an immediate power imbalance, in that readers are unable to verify what they are being told, and that leads to abuse.” Because Assange publishes his source material, he believes that WikiLeaks is free to offer its analysis, no matter how speculative.
I'm sure Sir John Sulston had no idea how far his idea of openness would be taken when he drew up the Bermuda Principles....
Part of the problem with extending the DNA database is that doing so increases the likelihood of this happening:After a seven-day trial, Jama had been convicted of raping a 40-year-old woman in the toilets at a suburban nightclub.
The only evidence linking him to the crime was a DNA sample taken from the woman's rape kit.
...
Jama had steadfastly denied the charge of rape and said he had never been to that nightclub, not on that cold Melbourne night, not ever. He repeatedly stated he was with his critically ill father on the other side of Melbourne, reading him passages from the Koran.
But the judge and the jury did not buy his alibi, despite supporting evidence from his father, brother and friend. Instead, they believed the forensic scientist who testified there was a one in 800 billion chance that the DNA belonged to someone other than the accused man.
This week Jama gave the lie to that absurdly remote statistic. After prosecutors admitted human error in the DNA testing on which the case against Jama was built, his conviction was overturned.
Prosecutors said they could not rule out contamination of the DNA sample after it emerged the same forensic medical officer who used the rape kit had taken an earlier sample from Jama in an unrelated matter. They admitted a "serious miscarriage of justice".
DNA is an important forensic tool - when used properly. But it is not foolproof, not least because contamination can lead to false positives.
The more DNA profiles that are stored on a database, the more likely there will be a match found due to such false positives. And such is the belief in the infallibility of DNA testing - thanks to the impressive-sound "one in 800 billion chance that the DNA belonged to someone other than the accused man" - that it is likely to lead to more *innocent* people being convicted. The best solution is to keep the DNA database small, tight and useful.
Follow me @glynmoody on Twitter or identi.ca.
Talking of DNA, another brilliant use of it - and brilliantly obvious like all great ideas - is DNA Barcoding:DNA barcoding is a new technique that uses a short DNA sequence from a standardized and agreed-upon position in the genome as a molecular diagnostic for species-level identification. DNA barcode sequences are very short relative to the entire genome and they can be obtained reasonably quickly and cheaply. The "Folmer region" at the 5' end of the cytochrome c oxidase subunit 1 mitochondrial region (COI) is emerging as the standard barcode region for almost all groups of higher animals. This region is 648 nucleotide base pairs long in most groups and is flanked by regions of conserved sequences, making it relatively easy to isolate and analyze. A growing number of studies have shown that COI sequence variability is very low (generally less than 1-2%) and that the COI sequences of even closely related species differ by several percent, making it possible to identify species with high confidence.
However, readers of this will probably have guessed the fly in the ointment here: DNA barcoding is such a powerful idea that the parasites have moved in, and started trying to *patent* bits of the idea:
Systematic and phylogenetics, indeed much of evolutionary science, has long and great tradition of making resources and knowledge freely available to other resources. Instead of cash, all an author asks for is a citation or a credit. Therefore, it sounded incredulous to me that one researcher was trying to patent a DNA barcode snippet for a plant gene that was being worked on over several years by a large group of researchers.
It's a classic situation: not only are scientific techniques being patented, they are techniques that are well established and have been used for years - something that is explicitly excluded even in the most deranged patent regimes. And people say the system is working just fine... (Via Jonathan Eisen.)
Follow me @glynmoody on Twitter and identi.ca.
Nanotechnology is one of those subjects that seem to veer between hope and hype. DNA-based solutions look among the most promising, because of the fact that the material has evolved to solve many of the same problems as nanotechnology; more subtly, it is inherently digital, which makes its manipulation much easier - and promises structures of almost infinite complexity under computer control.
To do that, or course, you need software, so it's great to see that there is already free software that lets you create DNA-based nanostructures:caDNAno is open-source software based on the Adobe AIR platform for design of three-dimensional DNA origami nanostructures. It was written with the goal of providing a fast and intuitive means to create and modify DNA origami designs. You can learn how to use it, download a copy of the program and some example designs, or even modify the source code.
The software makes heavy use of several fantastic open-source libraries and resources, especially Papervision3D for 3D rendering, Michael Baczynski's AS3 data structures and tutorials, the Tango Desktop Project for icons, and the Blueprint CSS framework for this website. Additional people and resources are acknowledged on the links page.
As you can see from this, there's already quite a rich ecosystem of free code in this area, which augurs well for the future. The last thing we need is for nanotechnology to turn into the smallest black box ever made.
Follow me @glynmoody on Twitter and identi.ca.
To change the world, it is not enough to have revolutionary ideas: you also have the inner force to be able to realise them in the face of near-universal opposition/indifference/derision. Great examples of this include Richard Stallman, who ploughed his lonely GNU furrow for years before anyone took much notice, and Michael Hart, who did the same for Project Gutenberg.
Another of these rare beings with both vision and tenacity is Pat Brown, a personal hero of mine. Not content with inventing one of the most important experimental tools in genomics - DNA microarrays - Brown decided he wanted to do something ambitious: open access publishing. This urge turned into the Public Library of Science (PLoS) - and even that is just the start:
PLoS is just part of a longer range plan. The idea is to completely change the way the whole system works for scientific communication.
At the start, I knew nothing about the scientific publishing business. I just decided this would be a fun and important thing to do. Mike Eisen, who was a post-doc in my lab, and I have been brain-storming a strategic plan, and PLoS was a large part of it. When I started working on this, almost everyone said, “You are completely out of your mind. You are obviously a complete idiot about how publishing works, and besides, this is a dilettante thing that you're doing.” Which I didn't feel at all.
I know I'm serious about it and I know it's doable and I know it's going to be easy. I could see the thermodynamics were in my favor, because the system is not in its lowest energy state. It's going to be much more economically efficient and serve the customers a lot better being open access. You just need a catalyst to GET it there. And part of the strategy to get it over the energy barrier is to apply heat—literally, I piss people off all the time.
In case you hadn't noticed, that little plan "to completely change the way the whole system works for scientific communication" is coming along quite nicely. So, perhaps buoyed up by this, Brown has decided to try something even more challenging:Brown: ... I'm going to do my sabbatical on this: I am going to devote myself, for a year, to trying to the maximum extent possible to eliminate animal farming on the planet Earth.
Gitschier: [Pause. Sensation of jaw dropping.]
Brown: And you are thinking I'm out of my mind.
Gitschier: [Continued silence.]
Brown: I feel like I can go a long way toward doing it, and I love the project because it is purely strategy. And it involves learning about economics, agriculture, world trade, behavioral psychology, and even an interesting component of it is creative food science.
Animal farming is by far the most environmentally destructive identified practice on the planet. Do you believe that? More greenhouse production than all transportation combined. It is also the major single source of water pollution on the planet. It is incredibly destructive. The major reason reefs are dying off and dead zones exist in the ocean—from nutrient run-off. Overwhelmingly it is the largest driving force of deforestation. And the leading cause of biodiversity loss.
And if you think I'm bullshitting, the Food and Agricultural Organization of the UN, whose job is to promote agricultural development, published a study, not knowing what they were getting into, looking at the environmental impact of animal farming, and it is a beautiful study! And the bottom line is that it is the most destructive and fastest growing environmental problem.
Gitschier: So what is your plan?
Brown: The gist of my strategy is to rigorously calculate the costs of repairing and mitigating all the environmental damage and make the case that if we don't pay as we go for this, we are just dumping this huge burden on our children. Paying these costs will drive up the price of a Big Mac and consumption will go down a lot. The other thing is to come up with yummy, nutritious, affordable mass-marketable alternatives, so that people who are totally addicted to animal foods will find alternatives that are inherently attractive to eat, so much so that McDonald's will market them, too. I want to recruit the world's most creative chefs—here's a REAL creative challenge!
I've talked with a lot of smart people who are very keen on it actually. They say, “You have no chance of success, but I really hope you're successful.” That's just the kind of project I love.
Pat, the world desperately needs nutters like you. Let's just hope that the thermodynamics are in your favour once more.
Follow me @glynmoody on Twitter or identi.ca.
This is what the virus really looks like:
1 atgaaggcaa tactagtagt tctgctatat acatttgcaa ccgcaaatgc agacacatta
61 tgtataggtt atcatgcgaa caattcaaca gacactgtag acacagtact agaaaagaat
121 gtaacagtaa cacactctgt taaccttcta gaagacaagc ataacgggaa actatgcaaa
181 ctaagagggg tagccccatt gcatttgggt aaatgtaaca ttgctggctg gatcctggga
241 aatccagagt gtgaatcact ctccacagca agctcatggt cctacattgt ggaaacatct
301 agttcagaca atggaacgtg ttacccagga gatttcatcg attatgagga gctaagagag
361 caattgagct cagtgtcatc atttgaaagg tttgagatat tccccaagac aagttcatgg
421 cccaatcatg actcgaacaa aggtgtaacg gcagcatgtc ctcatgctgg agcaaaaagc
481 ttctacaaaa atttaatatg gctagttaaa aaaggaaatt catacccaaa gctcagcaaa
541 tcctacatta atgataaagg gaaagaagtc ctcgtgctat ggggcattca ccatccatct
601 actagtgctg accaacaaag tctctatcag aatgcagatg catatgtttt tgtggggtca
661 tcaagataca gcaagaagtt caagccggaa atagcaataa gacccaaagt gagggatcaa
721 gaagggagaa tgaactatta ctggacacta gtagagccgg gagacaaaat aacattcgaa
781 gcaactggaa atctagtggt accgagatat gcattcgcaa tggaaagaaa tgctggatct
841 ggtattatca tttcagatac accagtccac gattgcaata caacttgtca gacacccaag
901 ggtgctataa acaccagcct cccatttcag aatatacatc cgatcacaat tggaaaatgt
961 ccaaaatatg taaaaagcac aaaattgaga ctggccacag gattgaggaa tgtcccgtct
1021 attcaatcta gaggcctatt tggggccatt gccggtttca ttgaaggggg gtggacaggg
1081 atggtagatg gatggtacgg ttatcaccat caaaatgagc aggggtcagg atatgcagcc
1141 gacctgaaga gcacacagaa tgccattgac gaaattacta acaaagtaaa ttctgttatt
1201 gaaaagatga atacacagtt cacagcagta ggtaaagagt tcaaccacct ggaaaaaaga
1261 atagagaatt taaataaaaa agttgatgat ggtttcctgg acatttggac ttacaatgcc
1321 gaactgttgg ttctattgga aaatgaaaga actttggact accacgattc aaatgtgaag
1381 aacttatatg aaaaggtaag aagccagcta aaaaacaatg ccaaggaaat tggaaacggc
1441 tgctttgaat tttaccacaa atgcgataac acgtgcatgg aaagtgtcaa aaatgggact
1501 tatgactacc caaaatactc agaggaagca aaattaaaca gagaagaaat agatggggta
1561 aaactggaat caacaaggat ttaccagatt ttggcgatct attcaactgt cgccagttca
1621 ttggtactgg tagtctccct gggggcaatc agtttctgga tgtgctctaa tgggtctcta
1681 cagtgtagaa tatgtattta a
Amazing what a few As, Cs, Gs and Ts can do.... (Via Common Knowledge.)
One of the many disgraceful aspects about the disgraceful ID card programme is the reluctance of the UK government to make key documents available. For such a momentous change in the relationship of government to governed, it is critically important that a full debate about all the issues be conducted; but without key details of the scheme, that is made more difficult – which is presumably why the UK government has resisted the publication of the so-called “Gateway reviews” so long.
Finally, though, we have gained the right to see these somewhat outdated documents. Despite their age, and the unnecessary redactions, some useful new information has come to light, which more than justifies the long battle to gain access.
On Open Enterprise blog.
This is clearly getting serious:Katherine Aull's laboratory in Cambridge, Massachusetts, lacks a few mod cons. "Down here I have a thermocycler I bought on eBay for 59 bucks," she says, pulling out a large, box-shaped device she uses to copy short strands of DNA. "The rest is just home brew," she adds, pointing to a centrifuge made out of a power drill and plastic food container, and a styrofoam incubator warmed with a heating pad normally used in terrariums.
In fact, Aull's lab is a closet less than 1 square metre in size in the shared apartment she lives in. Yet amid the piles of clothes she recently concocted vials of an entirely new genetically modified organism.
There's no stopping this now; great and terrible things will come of this....
Follow me on Twitter @glynmoody
I wrote about this in Digital Code of Life, four years ago:
The Switzerland-based company says they can use a $199 DNA test (compare to $1,000 for 23andMe) to help you find your perfect match, statistically speaking. They’ve analyzed “hundreds of couples” and have determined the genetic patterns found in successful relationships. Based on their algorithm and your DNA, they’ll determine the probability for a satisfying and long-lasting relationship between two people.
OK, for certain diseases this is wise; for most - and certainly for relationships - it is not, if you think about the deeper implications of what's going on (see book for more....)
Posts
All Comments
To the extent possible under law,
glyn moody
has waived all copyright and related or neighbouring rights to
this work.
This work is published from:
United Kingdom.
