Thursday, March 24, 2005

"On Genetics"

I have always been interested in the nature of genetic information, including its expression, transmission and change. After five months of intermittent blogging, it occurs to me that it would be useful to separate my personal diaries, opinions and recollections from commentary on genetics and genomics that might be of interest to students and colleagues. For that reason, I'm creating a new blog, On Genetics," which is devoted to my comments on scientific matters related to genetics, genomics and gene expression. I will continue to post my views on more personal or political matters here.

Sunday, March 20, 2005

"Burned Over" held over off Broadway

Six flights above 8th Ave., off of 47th St., in a building that seemed like a residential building (and probably is) we saw "Burned Over", a thoughtful new play written, produced and performed by a group of twenty-somethings. Timeless religious debates are given life and tied to feminist issues. We see a graduate student writing emails to her major professor juxtaposed with her ancestors living in the same house exchanging letters sealed with wax. Implicit in this play is the important question of who has the right to tell history. The expertise of writer Fortenberry and director Osborne are beautifully exhibited in a soliloquy on Martha and Mary near the end of the play. This is a substantial work. The run has been extended. If you're in New York this week, try to see it.

(written with Janet and posted from Sheila's kitchen with the generous assitance of the anonymously donated NETGEAR wireless service)

Saturday, March 19, 2005

Samsung's obscure menu for text entry

I'm playing with my new phone and one of the first things I wanted to do was send pictures to the real world. The 169 page Samsung a670 user's guide is silent on this subject. Verizon's FAQ page says
Can I send pictures/videos to an e-mail address?
Yes. All you have to do is type the email address on the addressing screen of your picture/video messaging phone.
However, I could not figure out how to add letters to the address field (which is designed for phone numbers). I found the answer online (in a column called "Mobile Tech News") which said
Update: Good news! One of our readers cracked the code on entering an email address via "ABC."

Steve Eschenberg says, "In order to enter an address via "ABC," push the left soft key/option button, scroll down one notch to "123", then hit the right navigation key (next to "OK"). The deal is that you can scroll left to right within the options that you scroll up and down to get to!

This is truly amazing. To get "ABC" I have to select "123" and then activate a menu that is not shown by hitting the right navigation key!

I now have picture taken with my phone on my computer.

Thank you Steve Eschenberg!


Wednesday, March 16, 2005

The Heart of Darkness

Janet is teaching a course entitled "The Amazon Through Film" this semester, and it's been a pleasure previewing films with her. Especially prominent is the Herzog film "Fitzcarraldo" and the Les Blank Film "The Burden of Dreams," which is about the making of "Fitzcarraldo." (Actually, we've been having something of a Herzog Blank film festival for months). By chance "The Burden of Dreams" was shown at AFI last Friday night, including an appearance by Les Blank. We arrived an hour late (by design — Janet has seen “The Burden of Dreams” many times and was there to see Les Blank, who was to take questions after the film). I went into the theatre and watched the second half of the movie. Janet stayed outside for what must have been 20 minutes. It turns out that she was talking to Les Blank, who she found setting up a table to sell videos and t-shirts.

Like most Americans (most Westerners, I suppose) I was exposed to the idea of a journey into the heart of darkness early in life. I recall seeing the 1960 film “The Lost World” on TV as a child of 4 or 5, jumping up and down with excitement about the prospect of seeing dinosaurs. Only when I saw the film again at the age of 9 or 10 — and when I read the Conan Doyle book in high school — did I clearly understand the plot line involving travel upriver, away from civilization and back in time, into the heart of darkness. When I first learned where Janet did her field work I quipped that this was no doubt very close to the plateau on which the dinosaurs were found in “The Lost World.” The same myth is most clearly delineated in Conrad's “Heart of Darkness” which I read as an adult, in a single sitting, on a transcontinental flight and “Apocalypse Now,” which I have seen many times and consider one of the very best films of all time (“Apocalypse Now Redux” being the definitive, and improved, version). There are also “Hearts of Darkness” (about the making of "Apocalypse Now") and Ken Good’s book “Into the Heart: One Man's Pursuit of Love and Knowledge Among the Yanomami” about his (ultimately failed) marriage to a Yanomami woman.

Whether it is the Congo, the Amazon or the Mekong, these works all refer to a fundamental myth of our culture. It is about nature, about colonialism, about the illusion of enlightenment and about the other. Janet tells me (her source being "King Leopold's Ghost") that the origins probably lie with the Stanley's accounts of his search for Livingstone, and the later writings by William Sheppard and Edmund Dene Morel about the horrors of colonial exploitation in the Congo.

"Fitzcarraldo" is about a foolhardy attempt to move a boat over a small ridge connecting two river basins during the Amazonian rubber boom. It is a great film, and "Burden of Dreams" does a good job of showing the parallels with Herzog's own efforts during the making of the film. Sitting in AFI on Friday I watched Herzog voice his answer to the immortal words of Conrad's Kurtz ("The horror! The horror!"):

[Klaus] Kinski [the lead actor, who plays Fitzcarraldo] says [the rainforest] is full of erotic elements. I don’t see it so much erotic. I see it more full of obscenity. It’s just … and nature here is vile and base. I wouldn’t see anything erotical here. I would see fornication and asphyxiation and choking and fighting for survival and growing and just rotting away.… Of course, there is a lot of misery but it is the same misery that is all around us. The trees here are in misery and the birds are in misery. I don’t think they sing, they just screech in pain. It is an unfinished country. It’s still prehistorical. The only thing lacking is the dinosaurs here. It’s like a curse weighing on the entire landscape, and whoever goes too deep into this has his share of that curse. So we are cursed with what we are doing here. A land where God, if he exists, has created in anger. It’s the only land where … where creation is unfinished yet.

The audience, appropriately, laughed at his words. Through Les Blank, Herzog was making two films at once and he knew that the script called for horror, but I think that he confused his discomfort at being away from civilization as he knew it with the horrors of exploitation. I don't think that he was the first to do so.

Monday, March 14, 2005

What you can do with a dozen genomes

I really enjoyed the ISR Distinguished Lecture by Eric Green on Wednesday. It reinforced my excitement about the idea that having a dozen genomes will allow us to obtain qualitatively different information than we’ve been able to obtain from a single genome. In addition to the alignment-based methods he described, there is the (rather amazing) possibility of reconstructing the ancestral sequence (see Blanchette et al. 2004, a very nice paper by an all-star cast) and methods of assigning gene function based on patterns of duplication and loss (e.g. the recent paper by Li, Pellegrini and Eisenberg in Nature Biotechnology). It strikes me that with 20-30 appropriately related genomes one could deduce whether individual nucleotides within a conserved block are under selection, an incredibly powerful tool (of course, I’m thinking about ESEs). I suspect that, like many new methods, comparative genomics will yield insights in ways that will not be fully appreciated until the data are at hand. It is exciting, and it reminds me of the excitement we all felt during the late 70s, when the first sequences were being obtained.

Sunday, March 13, 2005

Verizon wireless: The best of service, the worst of service

When Janet and I got cell phones a few years ago we selected Sprint because of their true nationwide calling plan (no roaming charges). Janet was still in Miami and we knew that we would both be originating calls from a variety of places around the country often. However, the service to key spots, like my office, is not good. Calls are of poor quality, or the phone doesn't ring at all.

So we're switching to Verizon. Unfortunately, it looks like service is going to be terrible in another sense. Last Saturday, we spent an hour at their store on Wisconsin Ave. without speaking to a sales person. There were two people whose job it was to take our names and control access of customers to the sales staff. These people seemed to have little else to do. To avoid wasting time again we decided to order phones and sign up over the web, and seem to have successfully done so. However, it was hard to get information. At one point, we got a salesman on the phone but he hung up on us when he learned that we weren't going to place our order with him ("I work for commissions," he said). It's clear that Verizon has no idea how to run a business when it comes to customer service or sales. This is reminiscent of trouble I've seen at AT&T and USAir. I fear the worst but there is no good alternative. With any luck Verizon wireless will be bought out sooner rather than later and the company that acquires their transmission system will treat us better!