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Programming Worms
No, not as in malware – a program that replicates itself as it moves from machine to machine – but as in an actual dirt-loving, squirming-about, icky-spaghetti worm.
This link comes off of Boing Boing. The project is called OpenWorm, and it self-describes as:
OpenWorm is an open source project dedicated to creating the world’s first virtual organism in a computer, a C.elegans nematode. We plan to achieve this goal by 1) bringing together highly motivated scientists and engineers 2) pushing away all the red tape 3) fostering growth of a completely open computational biology community.
So, its not building a real worm – a virtual worm. The worm they are hoping to replicate – Caenorhabditis elegans – is a nematode worm about 1 mm long; there’s about 1,000 cells in each one of these tiny critters.
How is this being done? Hard to say. The project milestones are here … here’s an example:
Muscle Cell model output closely matches that of real data
We will show that we have built a model of C. elegans muscle cell that matches data recorded from the nematode muscle cell. In part, we will use techniques of model optimization to fill in gaps in the model parameter space (deduce unmeasured parameters). The main technical challenge is tuning muscle cell passive properties and building a larger data set (more cell recordings). Mike Vella will take the lead on this.
Do we need virtual worms? No, not as such – but we need these types of projects, that’s is what science is, right? There’s too much of the attitude these days that all R & D needs to be dedicated to obvious needs. I for one think we need more scientia gratia scientiae.
Seeds of Innovation?
The New York Times reports on a suit coming to the US Supreme Court. The suit is brought by Monsanto against 75 year old Indiana farmer Vernon Hugh Bowman. The matter at hand is Monsanto’s “Round-up ready” soybean seeds. Roundup-ready is a gene, developed by Monsanto, that they insert into various plant genomes. It confers immunity against the herbicide Roundup – after planting these seeds, farmers can douse their fields with Roundup, which kills all weeds but leaves the immune crops alone.
Farmer Bowman is a Monsanto customer and has been using Roundup-ready soybean seeds for a number of years. What offense does Monsanto allege? That Bowman did not sell or use all of his grown crop, but instead – as farmers have done since agriculture was invented – held back some of his crop to plant next year. This, Monsanto alleges, is illegal “copying” of their patented organism. The bottom-line is Monsanto wants farmers to buy seeds every year, instead of buying them once and “growing their own”, as it were.
I am not against genetically engineered foods (GEF), per se. Like any technology GEF should be judged on its real merits and risks. As you can read here, there’s significant evidence that Roundup-ready crops are actually inferior products. Also as it turns out weeds are developing resistance to Roundup, so who knows how long the technology will remain even superficially useful.
The pros/cons of GEF are not what interested me here, it is more the what this case says about the state of IP law. In their brief, Monsanto alleges:
Without reasonable license restrictions prohibiting the replanting of second- and later-generation soybeans, Monsanto’s ability to protect its patented technology would effectively be lost as soon as the first generation of the product was introduced into the market.
The Monsanto license does in fact prohibit any use of 2nd-generation seeds other than selling “… the harvested crop through customary distribution channels as a commodity, or for use as animal feed.”
SCOTUS will in part rule on whether such a license is “reasonable” and should be enforced. There’s also a lot to be considered in the method of these “inventions”. While the gene-insertion method does seem like an actual invention to me, the way the actual Roundup-ready gene was created was more like observation – expose plants to the herbicide and examine the genes of those that are resistant. Observations, no matter how arduous or costly, cannot be patented.
Without going through the twists and turns of IP law on this, my thinking comes down on the side of Farmer Bowman. Yes, Monsanto created a better seed. They should charge more for it and let the marketplace decide on its merits. But it is still a seed. I don’t see that Monsanto’s activities warrant any change in the 1,000s of years-old practices of agriculture and the normal use of seeds.
I find it troubling that the Business Software Alliance has filed a friend-of-the-court brief in this case. In it they contend:
A legal rule eliminating patent protection for “self-replicating” seeds that had the same result with respect to temporary copies of software programs would facilitate software piracy on a broad scale.
The BSA of course is concerned about licensing and doesn’t want anything to interfere with current software industry practices, where you don’t actually buy software, you license it. I went through the brief – it is quite vague, and calls for “balance” as if they were Jedi knights and not corporate executives. Essentially the BSA hates copies of software and resale of software. Now, the chances of Bowman vs. Monsanto being relevant to software are low. Soybeans are self-replicating, and right now the only meaningful category of self-replicating software is the computer virus I guess the BSA wants to keep the door open for Microsoft to create a useful virus and to charge everyone who ever gets infected.
Alas, in all this customers are rarely mentioned. Everything is about protecting industries – farmers, who exert massive effort and resources growing those 2nd generation contraband soybeans, are never mentioned. Nor are software users, who sadly often spend more time working on their software than the software spends working for them.
On the plant front seems to me there’s a lot of innovation happening with heirloom seeds – breeds that have been re-discovered, either on farms or in the wild. Finding, cataloging, assessing, distributing – all that is innovative and, frankly, looks pretty tasty too.
Fernando Salazar 