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.
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.
Wife Kim sent me a link to an interesting site, Data Stories (India). This is the blog of Avinash Celestine, a journalist with India’s The Economic Times. The idea of Data Stories is it shows interactive visualizations of different types of Indian economic and socio-metric data.
What sort of thing is Data Stories showing? The map below shows ownership of TV, Computer, Phone and Vehicle (either 2- or 4-wheeler). The darker the color the higher the percentage of households who own all those things in that area:
Where I live in Pune about 18% of households have all these things. The message here is how wealth in India is concentrated in a small number of urban centers.
These maps show worldwide per-capita income from perspective of both India (on the left) and China, on the right:
India and China are represented by flat lines in their respective graphs. The other lines represent the relative proportion of that country or region’s per capita income to the base country at that point in time.
In 1975 USA per-capita income was about 18 times that in India, and maybe 19 times that of China. But notice how in the China chart the USA line starts sloping down steeply starting in around 1977? By 2005 the USA:China ratio has dropped from 19:1 to 6:1, but in India with its more gently sloping line, the ratio has not dropped much, from 18:1 to 12:1.
What to make of these visual presentations? I’ll leave the public policy aspects of these to the side and just say: We need more of this stuff. Thinking I might make my own geographic visualization I did some quick Googles on the topic. Conclusion: There’s not that much out there that can do this quickly. Microsoft sells an add-on for Excel called MapPoint that looks quite powerful, but at $300 list for the North America edition, it’s not going to get my vote. There’s some Flash- and/or web-based tools out there, like StatPlanet and BatchGeo, but tools like these definitely have a learning curve. Isn’t there something easier?
<shameless-plug>My employer IBM has an answer, ManyEyes.</shameless-plug> ManyEyes is a free system where you can create visualizations from existing data-sets, or upload and visualize data-sets of your own. I found many India-related visualizations there, like this one:
Note to self: Government of India has many data-sets available online. Try to find a likely one and then make a ManyEyes visualization of it.
Here’s some tips tip for those contemplating a stint as an ex-pat: #1, Plan to immerse yourself in local culture, food, shopping, sightseeing, travel, meeting and conversing with new people. Don’t be isolated – connect.
Tip #2: Get some video games.
Seriously, you and your family won’t be able to do the cultural ambassador thing 24 x 7. You need some downtime, some alone with your family time – you need games.
The game that has swept the Salazar household this past weekend is Dragon Island, free for iPad. This game is like Pokemon … turn based combat, with really cool monsters organized into the traditional air-water-earth-fire model. There’s a role-playing aspect as your hero character – a “monster trainer” – travels around doing the bidding of the Trainers’ Guild and piecing together the also-traditional story of a lost father and mysterious doings at the highest levels of something or other.
Who cares? It’s the planning and the combat that make this game. Seriously, once you start it is hard to stop. First, the monsters are very clever – thus far among the enemies I’ve faced are Bitewings, Mutations, Giant Crabs, King Penguins, Cult priests, Blood Priests, Baby Nessie, plus something called an “Abomination” that is animated as a fat opera singer. Second, your own monsters gain new abilities fairly quickly, and even “evolve” into new forms – for example, a “Fairy”, an innocuous Tinkerbell-like thing that puts 1 enemy monster to sleep, evolves into a “Fairy Queen” which puts many monsters to sleep, and is, shall we say, very attractively rendered.
Here’s another look at the combat screen:
There’s just the right amount of animation here, the enemies slowly floating up and down, with animated question-marks, or ZZs to indicate different conditions, and slashes or explosions to mark each attack. All this is squarely in the Dragon Quest style. and takes about 30 seconds to figure out.
Finally, this game is very forgiving. You lose lots of battles, but there’s no effect on your progress in the game. You just re-spawn in the last town you visited, your battalion of little horrors all healed-up and ready to try again. If you can’t get past a certain boss fight, no problem: Just wander around, level up your monsters, maybe capture some more, then after a while go back and try again.
Net-net: Dragon Island for iPad, super-game, get it. Now sorry, have to go – need to find out what my 20th level Bat Fiend is evolving into …
The issue now isn’t what fancy car the teenager plans to buy with his millions. The real question is whether Summly, and now Yahoo, can take news stories from around the Web, present altered versions of them, and not run afoul of copyright law.
The precedent here – that GoogleNews uses, for example – is that search or aggregation services can display article titles and lead sentences – that is deemed fair-use. Content creators *want* such services to do this because it ultimately drives traffic to their sites.
However Summly does more than show a title. Through its wondrous algorithms it creates a 400-word news summary that is supposed to contain the essence of the source news item. While I haven’t directly experienced Summly (and probably never will) it seems clear to me that this will take traffic away from content creators – why read the original 1,000 word news item on Kim Kardashian when Summly can quickly give you the 400 words with the tastiest bits?
A US Court has already ruled, in Meltwater vs. A.P., that this type of abstraction goes beyond fair-use. A key part of the evidence there was the contention that a lede – the key summary paragraph of a news story – takes substantial skill and effort to craft, and that Meltwater’s summary services was taking ledes and offering them separate from the original content. Certainly sounds wrong to me.
I’m sure Summly will continue to make the rounds another day or two … the world will then get back to cat pictures and Boromir memes. Meanwhile the winner of cleverest Summly headline so far goes to Reuters:
A “genetic algorithm” that “thinks like I do” and that “helps” me find the news I need on my mobile phone, faster than ever. All devised by a 17 year-old Harry Potter-like whiz kid entrepreneur who made a cool video with Stephen Fry and has now sold his company to Yahoo for $30 million.
This is just more rampant “solutionism” – the mind-set of arbitrarily declaring something a problem, then selling you an “innovative” solution for it. And if the solution provides you with monopoly power over a much-needed basic service, well, that’s the price of progress I suppose. Clearly Summly aims to be the conduit that feeds you news and by doing so, will no doubt employ your personal settings for tuning these algorithms into other, I’m sure purely innocent, needs. All this magic was in part evolved by SRI International, some legitimately clever people with a hand in creating “the Internet”, ultrasound diagnostics, robotic surgery but also – alas – Siri, that service which has enabled an entire industry devoted to stupid things it says.
For my part, here’s the news I need to have reach me on my mobile phone:
Daughter’s school ending early today.
Regional tsunami approaching.
Timing of immanent life-ending asteroid strikes.
Nuclear launch codes mistakenly left in Silicon Valley Red Robin being found by Dick Cheney.
I’m pretty much covered on #’s 1- 3. If someone writes an app for 4, maybe I’ll actually buy that – but meanwhile I will pass on Summly.
Stephen Fry, as to your role in all this I can only say (with the added bonus of being confident no one in existence has ever written this combination of words before):
I know you must pay the mortgage, but next time choose a means that would not so obviously raise the gorge of a hippopotamus to levels not seen since Noah decided the dinosaurs could very well swim for it.
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.
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.
Recently a Facebook friend posted a question on miracles: What were they, and could they be verified. I don’t believe in the traditional definition, loaves, fishes, all that. But I do agree with the poster who said that it is really the unfolding of the natural world by science that deserves the label “miraculous”.
What better proof than the video above. Home Sapiens … sometimes we get it right.
Just to clarify, “smaht” is Massachusetts-ese for “smart”, as in when Tommie tells Kevin on This Old House, “Ainchu the smaht one?”
All across the Connect 2013 show you see and hear stuff that is “smart”: Smarter Commerce, Smarter Workforce, Smarter Cities, and more. When I first came across these “smarter” products I confess I was skeptical. I mean, Agent 86 had a “smart shoe”, that wasn’t actually very smart, right?
But a message coming through loud and clear for me here at the show is smarter is where we need to go. Let’s face it: The fundamentals of collaboration are the same today as they were 20 years ago at the first Lotusphere: Saving information and sharing information with people and teams. A Connections community is logically pretty much the same as a circa-1999 Notes teamroom.
There is a difference though – the community is smarter. It sends notifications and makes recommendations, just to name the top 2 clever things a community can do. These are individually small things, but their cumulative effect makes a major difference.
But I have to say the smartest thing I’ve seen at Connect 2013 so far was They Might Be Giants in the OGS:
After 30 years these guys still have it. They did this number for us, one of my faves:
Leaving out the whistles and bells … all time greatest – and smartest – song about a nightlight, ever. Well done, OGS!
I’m at IBM Connect 2013 … was a long trip from India, but here now and getting into the familiar flow of going to talks, meeting people, and hikes twixt Dolphin, Swan and elsewhere.
The first talk I’m at … seen above … is all about Kenexa, IBM’s new acquisition of Smarter Workforce technology. The topic of Smarter Workforce has a lot of synergy with the Connect show (Lotusphere of years past). Kenexa let’s you improve your workforce, by finding the right people, developing them, assigning them and improving them. The majority of worldwide CEOs in IBM’s CEO Survey recognize that developing talent is the top need for maintaining and increasing competiveness. It’s the old idea on “our people are our greatest asset”, but in the modern world, where physical resources and assets can be anywhere and become less important, it really is quality of people that makes the difference.
And the Connect show? What else is it about, but people? On the web today we can learn whatever we want, whenever we want. Coming to a place and seeing others F2F, we do that because a connection with someone else you make when you see and hear each other is so much more valuable than a purely virtual one.
Will try to do more blogging while I’m here. But hopefully I’ll be doing a lot of old fashioned sit down and talk sessions.
What you see here is my new, Microtek DoublePOWER 800VA UPS – an uninterruptible power supply. Here in India electrical service is not consistent. Brown-outs and outages are common. For example back when I first arrived in Pune and was recording my lease at the Registrar’s office, power went down there and for a few blocks around, at which point civic work halted and we collectively went out for tea. Power was restored in a few hours and my lease was eventually duly recorded.
Buildings like mine have their own generators which pick up when mainline power fails. However there is anywhere from a 10 to 30 second failover time when that happens – way more than enough to power down my wireless router, not a great thing to have happen when you are in the middle of, say, online banking. So I got this UPS in the hopes that when these brief outages occur I can at least keep internet going for a while. Kim tells me that today we had a short outage and all seemed to work as planned. Bahuta acchā!
An amusing thing about the delivery of this unit … Saturday I received a call. Was hard to make out what the other party was saying, but I eventually understood that there was a parcel for me at the local post office and that I needed to come by and pick it up. So Monday myself and driver Rupesh make our way there and indeed it is the UPS. Rupesh asked, why was the package not delivered to the address? For answer they indicated this label on the package:
So, from a spirit of diligence they decided that “transporting” the package to my flat was forbidden.
I forebore from asking what miraculous agency had gotten the package to the post office in the first place …
