Monday, January 16, 2006

Art imitates life

Since I can no longer engineer animals in 'real life', I've been devoting some time to one of my hobbies, engineering life 'in silico'... in this case, 3D modelling of animals using the 3D modelling program Povray.

Despite their complexity, organisms are built up from a series of simple rules... and in theory, by applying these rules in a script, we can generate a diverse array of computer images that closely resemble living organisms without having to do a whole lot of fine-tuning and careful editing. This is most easily demonstrated in plants... new cells in plants are generated at the growing tips of roots and branches, and get information on what they should become (leaf, stem, branch point) based on where they are in a hormone gradient generated from the last stem branch point or leaf node. Thus, you can expect a new leaf every X number of inches from the last, and a new stem branching off every Y from the previous branch... and when a new branch point is generated, the new stem (or leaf rib, rootlet) will diverge at a fixed angle from the old one rather than a random angle. This allows a complex branching organism to form from a set of very simple rules governing node spacing and divergence angle - the sort of simple rules that can be easily translated into computer graphics. Indeed, there are quite a few 'plant generators' based on this principle available for 3d graphic imaging... ranging from freeware scripts for Povray to commercial packages such as XFrog. The only difference is the amount of 'polish'... texturing, extra details, etc. which add realism to the image.

Modelling animals is a bit more challenging... unlike plants, animal patterns involve more (and more complex) rules due to their very different method of development and specialized appendages. Yet in principle, with a bit of extra coding it should be possible to create a series of scripts for rapidly generating realistic animals in the same way that plants can be easily generated. In practice, the main limitation isn't the animals structure, but rather the limits of povray itself. Objects in povray are assembled from primitives (balls, tubes, cones, blobs, etc) that don't lend themselves easily to realistic animal structures... at least, not in a way that can be easily put together from scripts (animals in povray generally require quite a bit of tinkering to create a truly organic looking creature, rather than something that appears to be cones and balls stuck together).

My interest is in scripts to model invertebrates... not simply to generate a realistic looking invertebrate, but to quickly generate diverse invertebrates by plugging in a few simple parameters and letting the program use simple rules to do the rest. I've chosen invertebrates for two reasons. Many phyla are clearly externally modular, and much better suited for this approach than vertebrates (which are also modular in places, but internally where it doesn't do me any good). Secondly, everyone is VERY familiar with what a vertebrate should or should not look like, and will quickly note a flaw in leg position, body proportions, etc. Many invertebrates (true worms, insects, etc.) are both extremely diverse in nature and fairly unfamiliar to us.... this allows a greater degree of 'artistic license' in the final product.

I'll talk a bit more about the details in later posts, but just to throw up some examples of Cnidarians I've been working on:

An early test concentrating on ways to generate realistic tentacles.

A much more realistic jellyfish, giving an idea of what I am going for in the final product (the small image doesn't do it justice... click on the image to get the full size picture, in better resolution).

More later.

Wednesday, January 11, 2006


One thing you can't fault the Norwegians for is their sense of community. People in Norway grow up, live, and die in the same towns and neighborhoods. They may leave for a few years, returning with a husband or wife in tow, but they do return. Sure, it makes them xenophobic, insular, a bit conservative, but it also lies at the root of their extensive network of social support and the dedication of their oil wealth to the people, rather than to private profits. Norwegians feel a need to help their neighbors, and by extension their fellow countrymen. Health care in Norway may not be the greatest, but its definately there... from your local doctor to the neighborhood legevakt (walk-in clinic) up to the regional hospital. Crime really is low, and community care is present for the sick, elderly, and those with mental health problems or drug addiction.

In England, the Blair government has been on a seven year spree of dismantling communities in favor of centralization. The police forces are being centralized, the hospitals have been centralized, education has been removed from local control, and large retail corporations have been favoured at the expense of small local business. As communities have broken down and the crime rate jumped, Blairs response has been to boost law enforcement, rather than try to rebuild the institutions that support the community. The result has been new laws, new punishments, and fewer civil liberties. Now we have 'Respect'... Blairs latest response to increased petty crime.... a hodge podge of police quick-fixes (more Asbos, parenting orders, and summary convictions) with a dash of short-term, underfunded programs that will be de-funded and forgotten by the end of the year. No attempt to tackle the root causes of antisocial behavior, and an explicit rejection of poverty (which is increasing in England) as an underlying cause. An outside observer can't help but wonder if this is a 'get-tough-on-crime' attempt to boost popularity, rather than a serious attempt to deal with community problems. Perhaps someone should remind Tony that 'Respect' is something he still has to earn?

Friday, January 06, 2006

DIY data-mining

Want to do your part for God and Country? Curious if there are subversives in your neighbourhood that need rooting out? In the old days you had to guess who was with us and who was against us, and then go through the annoying leg-work of rooting through garbage for suspicious sales slips, opening peoples mail for subversive literature, or installing wiretaps to monitor their conversations.

No longer. The strategy for the new millenium is to identify subversive ideas and topics, and then prowl databases for information connecting these ideas to individuals. But why let the NSA have all the fun? With a set of simple scripts, Tom at Applefritter describes how you can be a junior G-man and prowl the publically available Amazon wishlist database to find out what people are reading, then use Google maps to track them down. Send your results to the Department of homeland security (202-282-8000 or through their webpage contact), open a brewski, and relax in the knowledge that you have done your part! Hunting the terrorists has never been easier!

Wednesday, January 04, 2006

From Korea with Stem Cells

For the past few weeks I've been following the gradual unravelling of that breakthrough stem cell research published last May by a Korean team led by Woo Suk Hwang. For those who don't follow stem cell research (probably most people), Woo Suk Hwang claimed that he had created 11 stem cell lines from patients suffering from various diseases... the first step in being able to use a patients own stem cells as a cure.

No one has been able to repeat their findings, and now allegations have come forward that photos have been reused, data has been fabricated, and DNA tests to match the cells to their donors are being called into question. Hwang admits that mistakes were made in the lab, but claims that his results are still valid, only that there were procedural problems.... the duplicated photos were the result of accidental submission of the wrong photo set, for example, while fungal contamination has conveniently destroyed several of the cell lines.

I can understand the occasional mistake... valuable cell lines do get contaminated and figures can be mislabeled (the most common mistake I have seen is scientists with little statistical background confusing standard error, standard deviation, and 95% confidence level when labeling graphs), but the picture coming out of Hwang's lab is one of extremely poor and confused procedures... and thats putting it in the best light.

I don't like to out-and-out call someone a fraud... its a very serious charge, and not one to be tossed about lightly. Science is a tough field to cheat in, since everyone is trying to replicate everyone elses results. A charitable interpretation is that equivocal results were interpreted as positive results, and that after prematurely announcing their success Hwang and his team cut corners to 'prove' their claim (since I suspect, they had trouble replicating their own results). It is also possible that Hwang honestly feels he was successful and that subordinates supplied him with the data he wanted to see, either out of a desire to please or as a result of pressure to produce a success. For the sake of all those people suffering from congenital illness or spinal cord damage I want to hope that Hwang was genuinely successful but is the victim of a very slopply lab environment... but I'm not holding out much hope.

Tuesday, January 03, 2006

Hey Tony, George, howyadoing?

My little break from the internet (a consequence of entrusting my computer system to the tender mercies of the British and Norwegian mail services) has spared me the bulk of the discussion on George 'W for wiretap'Bush and his desire to listen in on the private conversations of ordinary Americans.

However, it has had me wondering if England is any improvement. I've always been under the impression that England has less of a tradition of championing individual liberties.... from what I've seen so far (cameras on every street, plans in the works to track everyones car trips, extrajudicial executions on the London Underground) I'm not confident. Blair seems to be on the same powertrip as 'King' George, tempered only by the fact that the US is a superpower and Englands power has been declining since the second world war.

Happy New Year...

... in a new country.

Will post more very soon.