Recommend me a good web host

I need a new web host. My current one, Interland is not good. They are sloppy about a good many things, but the worst is that I am regularly unable to edit my blog because of some sort of CGI budget that I’m topping out. I get a message that says (effectively) “Can’t help you now. Try again in five minutes. :-)” When I complain about this, they don’t offer to help me understand or monitor the problem (Why is this happening? What can I do about it?), they just want to upgrade my plan to a more expensive one with a bigger CGI budget.

Upgrade this: I’m using your computers to advertise the fact that you stink.

A barbarian in China

My nephew Ben (I hosted his high school salutatory address on this site) has graduated college and moved to China for a while to teach English in Guangdong province. He has already been asked to be a model for commercials. Without being absolutely certain, I believe this is the first time Ben has been asked to be a model in his life. But even better than being asked to be a model in China, he has also taken a blog-pen in hand and will be posting to http://hairybarbarian.blogspot.com/ under the name Barbarian at the Gates. At the rate they’re going, the Chinese will soon be running everything, so I’m glad to have a family member who can help coach me through new New World Order.

Hacking life

Why is molecular biology so different from engineering?

Engineers build things using well-understood systems, the details of which, while sometimes complex, were originally specified and documented by other engineers. Molecular biologists, on the other hand, are uncovering the bizarre workings of an almost impossibly remote alien world hidden from all but the most obsessively persistent observers.

By great contrast, a field like software can be up-ended with lightning speed by a clever teenager, because the tools are smaller, cheaper, easier to wield, and also because people need only download and run software to understand its value. The next Netscape, Napster, or Google might be right around the corner.

Biologists, on the other hand, devote endless hours to coaxing new information out of living cells. It can take years of lab-bound tedium to reach a result which may, after all, turn out to be inconclusive. Results, once published, may take years to verify. Consequently, biologists tend to move in conservative, reputation-oriented packs. When biologists publish, they know it is critical to publish in a journal that has “impact factor”, since findings can be so easily questioned. Reputation is the currency that can validate their findings. In many ways, biologists function more like the members of a medieval guild than the participants of a fast-moving twenty-first century knowledge industry.

Nevertheless, biology is changing. It must, and it will, move from its current mode into more of an engineering mode. Industrial-scale genomics and systems biology are the beginning of this transition. What is coming? Here’s a short list:

  • cheap, fast experiments
  • easy, accurate simulation
  • easily verified results
  • an information-sharing “hacker” culture

All these things are common in the engineering world. Of this list, the last item is the most important and will certainly be the slowest to change. In biology, the toys have been too expensive, the results too dear to be profligate in giving them away. If you devote your entire career to a single protein, for example, how likely are you to be generous with what you find? So biology culture has moved slowly on the backs of laboring grad students. One of the great turning points in bio-engineering came when Craig Venter ushered in the era of industrial genomics. Up to that point, the cost of decoding a genome was dominated by human labor. The attitude was essentially: “What’s the rush? There’ll always be more grad students to finish this in another decade or so.” High-speed machines changed that equation forever.

I have been very happy to read dispatches from the front lines of biological research that indicate the age of the bio-hacker is upon us. The notion of a “bio-hacker” can sound alarming, I admit, but things are going to start happening extremely fast. Here are some items: Howard Salis’ synthetic biology blog has a good post on automated molecular biology that touches on these themes. Bio-IT World has a couple of exciting articles, one on a breakthrough genome sequencing product and another on whole-genome synthesis entitled “Pimp My Genome”.

Pimp my genome. Heh.

Now that’s what I’m talking about.

Update. Over at Nodalpoint, the bioinformatics weblog, Pedro Beltrao just made a very similar point: “Open source software comes to mind as one of the best examples of what you can achieve by getting interested people together in a virtual space. Why can’t we do the same for scientific research?”

Badge button builder

I came across Luca Zappa’s clever button maker by way of some del.icio.us popularity list somewhere. I was going to dismiss it quickly, but then I thought: maybe I’ll try to make just one. Once you start playing around with it, it’s hard to stop. This is a nice little tool for making those ubiquitous badge buttons you see all over the place.

The badges are exactly 80×15 pixels, and they use Jason Kottke’s Silkscreen font.

Almost as good as playing around with the badge maker was learning about Luca Zappa on his 49 “100 Things About Me” page. He is not related to Frank Zappa.

Confusing mythos and logos

In a recent issue of New Scientist magazine, I came across a book review by religious chronicler Karen Armstrong about a book on Creationism by Michael Ruse. In her review, Armstrong does a remarkably compact job of summing up much of the religious vertigo we face in modern times. Here’s a long quote from her review (the online review is locked behind a subscription barrier at New Scientist).

In the pre-modern world, it was generally understood that there were two ways of arriving at truth. Plato called them mythos and logos. Neither was superior to the other. Logos (reason; science) was exact, practical and essential to human life. To be effective, it had to correspond to external reality. Myth expressed the more elusive, puzzling aspects of human experience. It has often been called a primitive form of psychology, which helped people negotiate their inner world…

Myth could not help you create efficient technology or run your society. But logos had its limits too. If you became a refugee or witnessed a terrible natural catastrophe, you did not simply want a logical explanation; you also wanted myth to show you how to manage your grief. With the advent of our scientific modernity, however, logos achieved such spectacular results that myth was discredited, and now, in popular parlance a myth is something that did not happen, that is untrue. But some religious people also began to read religious myths as though they were logos.

The conflict between science and faith has thus been based on a misunderstanding of the nature of scriptural discourse. Many people, including those who are religious, find it difficult to think mythically, because our education and society is fuelled entirely by logos. This has made religion impossible for many people in the west, and it could be argued that much of the stridency of Christian fundamentalism is based on a buried fear of creeping unbelief.

In the pre-modern world, it was considered dangerous to mix mythos and logos, because each had a different sphere of competence. Much of the heat could be taken out of the evolution versus creation struggle if it were admitted that to read the first chapter of Genesis as though it were an exact account of the origins of life is not only bad science; it is also bad religion.

One observation that she makes in light of these comments is that fundamentalism is a modern phenomenon. I had heard this said about the Islamic extremists, but the same thing is true of religious fundamentalists of all stripes. The concept of a literally inerrant “history” specified by the bible is a modern construct. It would not have occurred to people before the Enlightenment to dissect the scriptures in such an awkward way. Fundamentalism was enabled by science. The weird scenes pictured by religious historicism (Where exactly was Eden? Is Noah’s ark still wedged in Mt. Ararat?) first needed the framework of historicism to build upon. Mythos is based on dream logic, and dream logic is not Logos.

The Dalai Lama has said “If science proves facts that conflict with Buddhist understanding, Buddhism must change accordingly. We should always adopt a view that accords with the facts.” This sounds like a capitulation, but it is nothing more than a well-drawn line between Logos and Mythos. “You stay over there,” says the Dalai Lama in effect, “and I’ll stay over here. But I still have something valuable to tell you. You’ll see.”

Breaking spaghetti

Lots of everyday phenomena puzzle most of us. How do radio waves magically transmit voices through the air? Where does bellybutton lint come from? Who buys the head cheese at the grocery store? But we don’t have time to waste contemplating mysteries like these, and besides, some physicist somewhere understands it all. Why bother?

Only that last part isn’t always true. We have been culturally imprinted with the idea that Scientists Understand Everything. Except they don’t. Take spaghetti, for example. If you bend an uncooked piece of spaghetti until it breaks, it will snap into not two pieces, as you might expect, but three or more. Why? This frivolous kitchen experiment was deeply puzzling to none other than Nobel-prizewinning physicist Richard Feynman. He never figured it out, but perhaps Feynman’s frustration justified in some small way the amount of effort a team in France has put into solving this puzzle once and for all.

I first saw this in the Economist, but I believe they demand a subscription before you can see their stuff. Here’s the official site in France: Breaking spaghetti. It’s loaded with movies, pictures, and simulated animations. Just goes to show, there’s magic everywhere. For those of you who don’t believe in magic, here’s the official word: “The multiple breaking of bent rods, like dry spaghetti pasta, can then be understood as a cascade of releases (loss of cohesion upon breakings) followed by stress increases leading to new cracks.”