February 2004 Archive



Sunday, 29 February
too much politics, not enough poetry

Acorn is an independent journal of haiku-in-English founded and edited by AC Missias, whose own haiku were among the first "international haiku" (viz., haiku not written in Japanese) I remember reading:

father's kimono
fluttering empty
still protects his yard


spring chill --
rounded sparrows cling
to bare branches


far from land
waiting for sunrise
-- the creaking of ropes

Subscription is less than USD12/year. I'd happily pay that much for just one good poem.
logolepsy | sennoma | 29 Feb, 2004 | |
snippets

scissors icon Why would Mel Gibson make a movie about the ancient Middle East and fill it with white people? William Rivers Pitt answers at length and with restraint. Me, I think Gibson is a bigot; end of story. And if you think I'm going to go see his grubby little porn flick, think again. (via Eliot)


scissors icon Orgnet.com (heh) has a nice simple introduction to social network analysis and interesting examples of the method in action. I particularly liked the analysis of book buying habits (2003 version here) and viral spread. (link-fu props to John Q at Crooked Timber)


scissors icon I bloody knew it. It's the same everywhere, and don't let the bastards tell you otherwise.


scissors icon Pix Populi is a Los Angeles photoblog by Neil Baylis. I like.


scissors icon (via Boing Boing) How to make matchstick rockets. You know I'm going to have to try this.


scissors icon These look like heaps of fun: for example, watch some of these quicktime movies. Sadly, they seem mainly to be available through unethical suppliers like Wal-Mart. They are manufactured by Swiss toy company ACTIVE PEOPLE, who don't say where their factories are, and distributed in the US by the icky-looking Body Time Wellness.


scissors icon Leuschke points to this review of this book, which I have added to my predictive model of things I will like in the future.


scissors icon Tolerance.org has some fun tests aimed at uncovering hidden biases. According to the one I just took, I have little or no automatic preference for or against a particular body type (thin or fat). (Being on the chunky side myself, I'd have expected to be somewhat pro-fat.)

snippets | sennoma | 29 Feb, 2004 | |


Friday, 27 February
brilliant

the playpump in action Oh, this is wonderful. The Playpump uses a children's playground toy to pump water to a holding tank, dramatically reducing the workload of poor women in South Africa. Advertising on two sides of the tank pays for installation and upkeep, and the other two sides are reserved for public health messages like the one in the picture at right. Via Rivka, who provides lots more detail; go read about it, it will cheer you up no end. diagram showing how the playpump works

social justice | sennoma | 27 Feb, 2004 | |
add your pebbles to the avalanche

Tolerance.org has been following the gay marriage debate, and links (scroll down) to further coverage and activism by the Human Rights Campaign and GLAAD.

HRC offers excellent background on the issue, the arguments and the politics, including a clickable map of relevant US State laws and statistics. Right now, you can join me (and, at time of writing, 326683 others) in signing the Million for Marriage petition (it will sign you up for an email newsletter, which is annoying but you can unsub). If the media are your thing, GLAAD is keeping an eye on them and offers a variety of ways to take action.

Update: Natalie Davis would like you to sign the Million for Marriage petition, too. Really, go do it.

Portland Communique continues to cover the local angle, and quotes this OPB story in which "County Counsel Agnes Sowle says any day now a same sex couple could ask for a marriage license in Portland, just like in San Francisco". So it's "cousel", not "council"! I'm a tool. b!X also points to gay marriage polls by KPTV, KATU and Basic Rights Oregon (whose homepage is still useless); go vote, because media polls can have a real effect on public perceptions. There was a KGW poll but it's disappeared; I did find this story on the flowers.

In the good news department, Mayor Jason West of New Paltz, NY will marry a small number of same sex couples today. Said Mayor West:

The people who would forbid gays from marrying in this country are those who would have made Rosa Parks sit in the back of the bus.

On a lighter note, George Wallace is a dab hand with a double dactyl; here's the first of a series of six entitled Epithalamion:

I

Hymen, Hymenaeus!
Gay men and lesbians
Flock to the City Hall,
Follow their bliss,

Purchase their licenses,
Swear to their permanence,
Pose for the camera crews
Sharing a kiss.


Update -- poll results:

KPTV: "Do you think gay marriage should be unconstitutional?"

yes 54%
no 42%
not sure 4%
n = not specified

KATU: "Do you agree with President Bush's stance on gay marriage?"

yes 63%
no 37%
n = 2608

Basic Rights Oregon: "Do you support a constitutional amendment banning gay marriage rights?"

yes 4%
no 86%
not sure 9%
n = 337

KGW (using "previous results" link): " Do you support a constitutional amendment to ban gay marriage?"

yes 50%
no 49%
not sure 2%
n = 5626

KGW earlier poll: "Should gay marriage be legal?"

yes 52%
no 47%
not sure 1%
n = 9771

Update: Atrios wants you to torture Lou via his CNN poll: "What offends you most?"

Howard Stern 5%
Corporate pornography 11%
Government standards of decency 26%
Gay marriage 12%
Opposition to gay marriage 45%
n = 12134



Wednesday, 25 February
people change. not often; not often enough; but they do change.

Hazel Bryan and Elizabeth Eckford in 1957Hazel Bryan Massery and Elizabeth Eckford in 1997On the left, fifteen-year-old Hazel Bryan screams unthinking hatred at Elizabeth Eckford during the racial integration of Central High School in Little Rock, Arkansas in 1957. Five years later, Bryan sought out Eckford to apologize, and in 1997 they were photographed together again (right) and have since become friends. Commenter Naomi brought this story up in the comments on this post by John Scalzi; for which my thanks. Pictures from this CNN story, photo credit Will Counts.

(This has a particular resonance for me, as I too have had to resect prejudices that were grafted onto me while I wasn't paying attention. Anaesthetic is contraindicated for that operation, and there is something of the zeal of the convert in my interest in social justice; and that's all I have to say about that.)

nowt so queer | sennoma | 25 Feb, 2004 | |
go! go now!

From billmon via Kip: spend Shifty George's ill-gotten campaign funds for him with this astroturf tool from georgewbush.com. You type in your zip code and up comes a list of local newspapers, helpfully grouped by circulation and proximity; check the ones you want to write to, cut and paste some predigested GOP propaganda write your own message into the form, and with a single click your letter is on its way to dozens of editors.

Do this. Do it now, do it tomorrow, do it as often as you can think of something to say about the state of the nation.

[P.S. billmon warns that the tool sets a cookie so you might want to nuke that little fucker after each session.]



Tuesday, 24 February
flower power

If you've been reading Rafe Colburn's blog for long, you surely have the same impression that I do, of a reasonable, thoughtful and well intentioned individual. So when Rafe says this:

You know, my views on the gay marriage issue have really polarized over the past few weeks. I've never been opposed to gay marriage, but I also didn't feel particularly zealous about opening the option of marriage to gay people either. I have thought it's a right they should have for a long time, but I was OK with civil unions as an alternative, because I was focused on the legal rights that married couples have. Then a few things happened. My views started changing when the Massachusetts Supreme Court said that legislation providing separate but equal civil unions would not suffice to meet their requirements, because separate but equal usually isn't. I found that argument persuasive.

What really changed my attitude, though, was the marriage licenses being granted in San Francisco. Most people have seen the pictures of jubilant couples who are getting married after decades of waiting in vain. After seeing those couples, I'm ready to grant the right to marry nationwide, right now. Getting married was the best decision I ever made, period. Seeing other people joyfully getting married reminds me of how much joy marriage has brought to my life. I no longer have the energy to see the issue in a politically safe manner -- we need to grant this right to same sex couples in every state immediately.

it makes me think: firstly, that the flowers were a good idea; and secondly, that an avalanche of gay marriages is an even better idea. Spousal unit and I are perfectly happy if the flowers we sent did nothing but brighten a random couple's wedding day, but I can't help but think that the flower sending "campaign" contributed to the visibility and feel-good-factor of the San Fran weddings. Rafe's comment makes me believe more than ever that those weddings are important, and that A MILLION GAY MARRIAGES IN THE NEXT MONTH (ahem, sorry) could swing public opinion so far, and create so nearly accompli a fait that begrudging bastards like Bush will not be able to enshrine their grubby prejudices in law (or worse, the constitution). Happy wedding pictures everywhere, and then married gay couples are your neighbours, doctors, teachers, colleagues -- and the world doesn't end, no one riots, and nobody's hetero marriage is altered one whit. Sounds like a step in the right direction to me.

So I thought I'd have a dig around in the Oregon constitution and law. In neither 2003 nor 2002 were the relevant statutes altered in any way that concerns my question, and the 2001 version reads:

106.010 Marriage as civil contract; age of parties. Marriage is a civil contract entered into in person by males at least 17 years of age and females at least 17 years of age, who are otherwise capable, and solemnized in accordance with ORS 106.150.
Spousal unit pointed out that the wording does not rule out same sex marriage by defining it as a contract between one male and one female. Furthermore, the restrictive interpretation of that statute would seem to me to contravene the State constitution; to wit, Article 1 section 20:
Section 20. Equality of privileges and immunities of citizens. No law shall be passed granting to any citizen or class of citizens privileges, or immunities, which, upon the same terms, shall not equally belong to all citizens.—
As per my earlier entry, I called the Multnomah Co Marriage License Section this morning. My question -- "Will Multnomah Co grant a marriage license to a same sex couple?" has been passed on to the County Council, and they -- whoever they are, I can't find any mention of them on the homepage -- will phone me back. They'd better not take too long, or I'm going to start pestering the judges who authorise marriages.

There hasn't been much in the local media on this issue, but Ashbel Green at the Oregonian has filed two stories, the first of which contains a good brief history of gay marriage legal issues in the US and these encouraging observations:

Of any state, though, Oregon is perhaps the most likely to recognize gay and lesbian marriages, and extend the myriad health, tax and other benefits that go with them, several observers and scholars agree.

Although Oregon law defines marriage as being between a man and a woman, the state is one of 12 that did not adopt a law prohibiting recognition of gay marriages from other states.

And perhaps more significantly, Oregon is just one of three states where the courts have recognized the rights of gays and lesbians to be treated equally.

The other two are Vermont, which, through its civil union law, extends all marital benefits to gay and lesbian couples, and Massachusetts.

"We are ripe," said George Eighmey, a former Oregon legislator and chairman of the state's Gay and Lesbian Law Association. "Oregon is definitely at the eye of the hurricane when it comes to this particular issue."

nowt so queer | sennoma | 24 Feb, 2004 | |
snippets

scissors iconAnimals on the underground: London tube map as constellation-riddled sky. I wonder if anyone's tried this with LA or NY? (via the indispensible Boing Boing)


scissors icon(also from BB) John Ashcroft is barking mad. (I think Mike must have typed this Vanity Fair article in by hand, a prodigious effort.)


scissors iconStuart of DoublePlusUngood issues a challenge. I'm going to do it; so should you.


scissors iconTwo posts from the Pagan Prattle indicating that Scotland the not only Brave but also Sensible is preparing to jettison state funding for faith schools.


scissors iconAlso from PP, something I want to follow up: apparently right-wing psychofundy "Christian" bigmouth Pat Robertson recently said

I think George Bush is going to win in a walk. I'm hearing from the Lord that it's going to be a blowout.
so when (think positive!) Shifty George loses, I want to Pat to tell me: was God wrong, or did He lie to you?


scissors icon(via Jerry Kindall) I know someone who would love this: Enigma-E, a kit with which to build yourself an electronic version of the Enigma coding machine. If that's too much trouble, PBS has a virtual Enigma you can play with.


scissors iconJerry got that link from spurl.net, which is a neato keen bookmarking and recommendation service. I like it better than del.icio.us, which I joined and never got around to using much.


scissors iconCrooked Timber features a bunch of overeducated liberals, posting and commenting. I like that in a website. Also, Belle likes Sesame Street, and even caught them out in a James Joyce allusion. Criticisms about "preparing kids for sound-bite consumer culture" are valid I suppose, but the last word for my money goes to commenter mike: Name a single other entertainment entity that over a quarter century threw up occasional bits of disorienting depth with so much good humor and so little mean-spiritedness.


scissors iconAnother great books thread; in this one, Ed wants to know which five science and technology books you would have every (university) student read. Good stuff.

snippets | sennoma | 24 Feb, 2004 | |
EMI can kiss my ass

I think the Beatles were crap and I can't stand hip-hop (the music, not the culture), so it's not surprising that I think DJ Danger Mouse's Grey Album is shite. That's not the point, though. From greytuesday.org:

DJ Danger Mouse created a remix of Jay-Z's the Black Album and the Beatles White Album, and called it the Grey Album. Jay-Z's record label, Roc-A-Fella, released an a capella version of his Black Album specifically to encourage remixes like this one. But despite praise from music fans and major media outlets... EMI has sent cease and desist letters demanding that stores destroy their copies of the album and websites remove them from their site. EMI claims copyright control of the Beatles 1968 White Album.
Hence Grey Tuesday, a day of online civil disobedience on which sites all over the web will be turning grey in support of artistic freedom from greedy corporate pirates and offering the Grey Album in mp3 format. I couldn't turn this site grey if my life depended on it (html is a dialect of Martian, right?), and I frankly don't have the stones to host the mp3s. My immigration status is somewhat delicate and I just don't need the kind of legal aggravation that bastards with deep pockets and squads of attack lawyers like EMI could give me. Linkage is the best I can do for now. Waxy first made me aware of the issue; mathowie and 6foot6 both have the album and a great, thoughtful post to go with it; and greytuesday.org is the official site and has lists of all participating sites.



Monday, 23 February
why do you care; or, if you don't, why not?

Joi Ito, in one of his thinking-out-loud style posts, wondered about what it is that makes people care:

What is really striking to me and something that I'm trying understand is the process that people go through to reach a higher level of caring for human beings outside of their immediate circle. I think that this process holds the key for some of the important contributions that technologies can make.
This struck me as being a fundamental question. It seems utterly -- viscerally -- obvious to me that human need on the other side of the world, or down the block, matters to me; that it affects me, that I must respond to it. By way of rational explanation, I offer two observations. One, I've been up and down a bit through my life, and it's not hard for me to see myself in pretty much any lousy situation; and I know that it's all too easy to end up in the shite through no fault of your own, and fault doesn't matter much anyway when you just need a hand. Two, I am always better off if those around me, whether next door or across the world, are better off: it means they are more able and more likely to lend me a hand if I should need one, and less likely to try to elevate their situation by climbing over me. In the long term, over many generations, sharing is the only real security. In the short term, over one lifetime say, that doesn't really hold. There are plenty of assholes living well on other people's sweat, and since I don't believe in any form of life after death I don't believe they will ever pay any material price for that. The price they pay, though, is in quality of life. I don't believe you can be happy without awareness, and once aware you cannot escape empathy. Or to put it another way: like Honest Abe, I feel good when I do good things, and that's my religion; and I don't see how anyone can be really happy any other way. Money and power and all the trappings thereof are no substitute; not even close.

I didn't always see the world that way, though, and it got me to wondering how I came to have the Weltanschauung I now do. About then, kevin of bastish.net joined the conversation with a careful exposition of his own journey into caring. It neatly describes my own, and so I reproduce it here with his permission:

1. Ignorance
----Blissfully unaware of problems and plights of both neighbors and those thousands of miles away.

2. Awareness
----Heard something on the news. Know it's not good. Think "Someone should do something about that."

3. Superficial action
----Start making easy changes, that don't affect my lifestyle. Requesting paper bags instead of plastic. Recycle bottles. "Adopt" a poor kid in Columbia. Begin to feel "I am good", yet continue with my own irresponsible patterns of consumption, make decisions based on my own wants, rather than how they will affect other people.

My Tipping Point
3.5 Relatively satisfied with own economic / social condition
----Realize that I don't need to be rich, that my "quality of life" is not based on how much money I have, that I don't need to own what TV, movies, and blogs tell me I do. Begin to have less-quantitative values. Spend less time trying to get richer, begin to have more time to read about both local and global issues.

4. Deeper awareness
----Aware of how my life-style decisions are effecting other people in a negative way. Begin to seriously think about global / local inequalities and what it really means.

4.5 Dissatisfied with own condition as an irresponsible-consumer.
----Realize that my superficial actions are worthless, no matter how many times I re-use a plastic bag, it doesn't help if I am using it buy sweat-shop goods at Wal-Mart. In order to make change, I have to change my lifestyle first, because it is my lifestyle that promotes global inequality.

5. Despair
----Overwhelmed with the enormity of the situation, and the impossibility of changing my behavior, yet remaining a member of a society that doesn't share my values, and puts enormous pressure to put myself first.

6. Find examples / community
----Begin reading, searching, eventually find a community and examples of people who share my values.

7. Resolution / Search for answers
----If they can do it, I can do it too. Resolve that I will make consumer decisions based on a "first, do no harm" approach.
Research, research, research. What are the effects of my decisions? How much do I need to consume? What should I avoid? What can I cut out? What can I use as a substitute?

8. Implementation on a personal level
----Live own life according to the information I am finding. Strive to make good decisions. This is a semi-active approach. While I am actively changing my own lifestyle, placing my wallet vote, I am not doing anything to actively influence others to make large scale changes.

9. Despair
----Plagued with increased awareness, filled with despair that for every good choice or sacrifice I make, there are hundreds of thousands of individuals who don't care, who are working against a sustainable, equitable earth, who can nullify a years worth of my sacrifices, with a single trip to the mall.

10. Implementation on a local level
----Activism on a local level. First, setting an example to those around you by living in a way that promotes your ideals. Devoting time and money to help local institutions influence local policy.

11. Implementation on a global level
While I am not there yet, I have recently applied to a couple graduate programs regarding policy making for sustainability and global equity, in the hopes that I can use what I learn there to implement more wide-spread changes and influence more than my friends and family.

I'm just starting on #10. On a global scale I'm not sure what I can do, besides supporting worldwide charities and being politically active here in the US (Anyone But Bush '04!); but that's a start, and perhaps other opportunities will present themselves.

So to return to the point of this post, I'd like to hear from anyone reading this: do you care? If so, why; if not, why not? Answers on a postcard in Joi's comment thread, of course.

viral targeting of tumour cells

cryoelectron microscopy map of Sinbis virusResearchers at NYU School of Medicine have found that Sindbis virus, a Togavirus that causes cold-like symptoms in humans, can systemically and specifically target tumour cells in mice. The press release is here, and the original paper in Nature Biotech is here. The virus enters mammalian cells by binding to the 67kDa high-affinity laminin receptor (LAMR), which makes it highly selective for tumour cells. Relative to healthy cells, the vast majority of tumour cells express greatly increased numbers of LAMR on their surfaces, and (again, unlike healthy cells) the majority of those receptors are unoccupied. (Normal LAMR function is involved in interaction with the extracellular matrix.)

Tseng and colleagues showed that Sindbis virus could infect tumours without infecting surrounding normal tissue and cause significant reduction in tumour mass (up to complete regression in some models) whether they induced the tumours subcutaneously or in the surface topology model of Sindbis viruspancreas, lungs or peritoneum of immunocompromised mice using human cancer cells, or subcutaneously in immunocompetent mice using mouse cancer cells. This indicates that the results are not species specific and that a working immune system does not interfere with the anti-tumour activity despite repeated treatments with the virus. They also showed that the virus could infect and reduce spontaneous tumours in a cancer-prone mouse breed, decreasing the likelihood that the anti-tumour activity depended in some way on the manner in which the tumours were induced.

The virus was injected intraperitoneally or intravenously at as great a remove from the tumor sites as possible, which means that the virus targeted the tumours after being disseminated in the blood. This is great news, because it indicates that we can build a tumour-seeking virus missile that will find metastatic tumours no pathologist or surgeon could detect. It's also important to note that Sindbis is not a retrovirus (and so does not integrate its genome into the host cell's) and is highly lethal, so it kills virtually any cell it enters well before that cell could become a Sindbis-induced cancer itself. The virus used in this study was created in such a way that it cannot package itself into new particles after infecting a cell: it is replication incompetent, and cannot spread on its own through the patient's body. (Barring frankenviral recombination events, it only gives you a cold anyway.)

The images are from a different paper entirely (Zhang et al. J Virol vol. 76 pp. 11645-11658). Right, cryoelectron microscopy map of a partially deglycosylated Sindbis particle; left, surface topology model of same. Both pictures are to the same scale, the bar in the map represents 20 nm.

hello world

photo of me That's me, more or less. I took that shot about a week ago; the spousal unit says that if it were all you had to go on, you'd recognise me easily enough. What's left of the hair is mousy brown, the beard is reddish where it's not grey, and the eyes are blue: standard WASP-y hybrid. (Another photo here.) Born Papua New Guinea 1969, moved to Australia 1976; high school here, university here; Hons with this bloke, PhD here on vaccine candidate antigens in this disease with this bloke (photo here, works here), just before he moved to Tulane. First post-doc in HIV replication with David Harrich, to whom I owe an enormous debt and not just for all the science. Met wife online Nov 01, married Aug 02, moved to Portland OR Nov 02. Until June 2005, worked with Caroline Enns on the molecular basis of iron homeostasis in humans, with a particular emphasis on haemochromatosis. Now working with Peter Hurlin on cancer biology, specifically the roles of the Max network of transcription factors.

Anything else you want to know, just ask.

Update 041207: no one asked, but for Google juice and because I never actually meant to be anonymous (I keep the handle because it's how most of my online friends know me): Bill Hooker. Search here for "Hooker CW" to see most of my scientific publications.

heaven on earth


astronomy picture of the day for Feb 23 2004

Today's Astronomy Picture of the Day took me back to my sci-fi1 reading days: galaxy rise over Earth-beta, or something. Make sure you go look at the big version, which makes a great desktop.




1 Yeah, yeah, "skiffy" blah blah whine snivel get over it already.



Saturday, 21 February
updates on the avalanche

Boo, hiss! Scratch Sandoval County thanks to New Mexico's backwards asshole Attorney General:

The Sandoval County clerk's office granted licenses to 26 same-sex couples before New Mexico attorney general Patricia Madrid issued a late afternoon opinion saying the licenses were "invalid under state law."

The clerk's office stopped issuing licenses and told newly wed couples their licenses were invalid.

Full story here, thanks to PDP at Alas, a blog for the link.

That's not how Atrios reads the New Mexico law, by the way. Atrios also provides a reference for that New York opinion I mentioned: Lawrence C Moss, a Manhattan lawyer and chairman of the Reform Caucus of the New York State Democratic Committee in the NY Daily News.

In local news: I didn't know that Kip's Short Pier is in Portland OR; he sent mail to mayor Vera Katz and got a spineless cop-out (that's my opinion there, Kip is more gracious) in reply.

Digital prozac: the original LJ thread is full of responses from people who sent flowers, people who received flowers, and more. For the record, the name of the guy whose idea started it all is Greg Scanlan; let history remember him with favour. Speaking of names and history books, someone in the thread commented that Gavin Newsom is getting hate mail, so you might want to send him a note of thanks (I just did).

Speaking further of history books, I don't think it diminishes Mayor Newsom's achievement to point out that he is standing on the shoulders not of giants but of hundreds of unsung heroes in the long struggle for glbt rights. Pericat provided a link a while ago on the backstory of Phyllis Lyon and Del Martin, which I meant to feature at the time but forgot. I lack the background to do it, but now would be a good time for someone to write a short summary, aimed at the general public, of the history of "the other civil rights movement".


P.S. the new category is about folk, not just glbt issues!



Friday, 20 February
avalanche

Amid speculation that Chicago might follow San Francisco's lead, Sandoval County in New Mexico steps up. I read a comment somewhere to the effect that New York admits no legal impediments to the marriage of true minds either.

Obtaining a Marriage License in Multnomah County doesn't appear to be regulated according to sex. I can't seem to find a County Clerk, but the director of the Department of Business & Community Services, which issues marriage licences, is Cecilia Johnson (503-988-5880; cecilia.johnson@co.multnomah.or.us) and the Marriage License Section phone number is 503-988-3027. Hmm.


Update: I called the MLS number and got Ms Johnson's answering machine. Stay tuned for further developments.


Update the second: spousal unit writes to tell me that b!X is covering it. Four ballot initiatives have been filed that seek to prevent Oregon from recognising same-sex marriages performed in other states, all by the same three contemptible scumbags. B!X has the details.

nowt so queer | sennoma | 20 Feb, 2004 | |
snippets

scissors icon Language Hat points to "one of the most charming articles I've read in a while", If You Build a Restaurant, He Will Not Come in the New York Times. I agree; go read it. (Unlike LH, I haven't gone to any trouble about the link. Get yer own fake member account.) Use one of these. (thanks to randomWalks for the link)


scissors icon Scott J Bloch is a worthless maggot. (another registration required)


scissors iconfractal flowers, a video feedback image by Tom Holroyd (via jwz) The Ultimate Video Feedback Page. Humans make art from the strangest things. Tom Holroyd's explanation and gallery are a good starting point if, like me, you can't read Danish.


scissors iconwaterwheels.jpg (via Dave Barry) St. Petersburg inventor Tim Englert has created Water Wheels, a bicycle-mounted pump-operated squirt gun capable of directing two independent jets of water up to fifty feet. He predicts that "Water Wheels will do for bikes, squirt guns and extreme sports what Peter Fonda and the film Easy Rider did for Harley Davidson and motorcycles." After sinking twelve years and $300K into it and quitting his job to market it full-time, he'd better hope so. (photo credit: James Borchuck, St Petersburg Times)


scissors icon (also from Dave Barry) Noon, Feb 23. Yeeeeeee-haaaaa! Update: Booooooooom!


scissors icon Sisyphus Shrugged reminds me that we are all Tommy Chong now, and TalkLeft reports that the gummint has spent $12 million bringing that desperate drug fiend to justice. (The 65-year-old father of five plead guilty to a bullshit charge related to his son's business, Chong's Bongs, to shield his family from prosecution; he got nine months in jail, a $20K fine and $100K in forfeited assets.)

snippets | sennoma | 20 Feb, 2004 | |


Thursday, 19 February
with love from Portland, OR

I wish I'd thought of this:

Today a coworker of mine had a thought to send flowers to a random couple waiting in line at SF city hall.

He called a florist and they agreed to do it. He told them to deliver to any couple -- it didn't matter who -- standing in line to get married, with his blessing. The card will read simply "With love, from Minneapolis, Minnesota."

Instead, I read about it on Boing Boing, opened up my email client to write to the spousal unit and say "let's do this!", only to find that she'd already done it. Aw. *snif* I'm all teary again.

In case anyone else is thinking of doing this, it might be a good idea to spread the love among the local florists, too:

Flowers By The Bay (a Rainbow Pride business; start here, but they might be overwhelmed pretty soon)

Delicate Daisy House of Flowers

Amy Kee Floral Design

Directories of local florists: Yellow Pages, Yahoo! , Online Flowers Network, Locate-a-flower-shop.com, Florist Locators. Go on, you know you wanna.


Update: if your funds are limited, perhaps you'd like to have more lasting impact. Powazek is selling a poster ("Justly Married", heh) and donating the funds to Don't Amend, who sell neat stuff themselves (and accept donations, of course). The ACLU is also fighting the Federal Marriage Amendment.


Update the second (thanks again to Boing Boing): if you want to chip in but can't afford a bouquet on your own, Darren is collecting PayPal donations for bulk buys. At the time of writing he's up to nearly $1000.

nowt so queer | sennoma | 19 Feb, 2004 | |
Scientists Protest Bush Administration's Misuse of Science

I've been meaning to write about this issue, but the sheer scope of it has caused me to procrastinate. Now, however, someone has done the work I should have (and then some), and things appear to be coming to a head. Angry Bear at The American Street links to this story from the Union of Concerned Scientists:

...more than 60 leading scientists—including Nobel laureates, leading medical experts, former federal agency directors and university chairs and presidents—issued a statement calling for regulatory and legislative action to restore scientific integrity to federal policymaking. According to the scientists, the Bush administration has, among other abuses, suppressed and distorted scientific analysis from federal agencies, and taken actions that have undermined the quality of scientific advisory panels.
As AB notes, the place to go for coverage of this issue is Chris Mooney's blog; his take on the statement is here. See also the "politics" category at Pharyngula for some bracingly bilious background on the Bush administration's hostility to science.

You can read the statement here, see a list of heavyweight signatories here, and if you're a scientist you can add your mark here (yes, I signed it). The statement itself is part of a wider campaign in which I urge everyone to get involved. One of the focal points of the campaign and the force behind the signed public statement is a report entitled Scientific Integrity in Policymaking: An Investigation into the Bush Administration's Misuse of Science; you can download the full report or executive summary as pdf files from here. You should read the whole thing, but here are the basic findings:

1. There is a well-established pattern of suppression and distortion of scientific findings by high-ranking Bush administration political appointees across numerous federal agencies.

2. There is strong documentation of a wideranging effort to manipulate the government’s scientific advisory system to prevent the appearance of advice that might run counter to the administration’s political agenda.

3. There is evidence that the administration often imposes restrictions on what government scientists can say or write about “sensitive” topics.

4. There is significant evidence that the scope and scale of the manipulation, suppression, and misrepresentation of science by the Bush administration is unprecedented.

Remember how the media kept calling Howard Dean "angry"? Listen: if you're not angry, you haven't been paying attention.



Tuesday, 17 February
snippets

8< If you haven't been reading Henry Raddick's Amazon reviews, you're in for a treat.


8< Ever wonder what happened to HMS Beagle of Charles-Darwin-goes-to-the-Galapagos fame? Never occurred to me until now, but marine archaeologist Robert Prescott thinks he's found her under 12 feet of Essex mud. Early indications are that the ship, whoever she is, is pretty much intact; and wouldn't the Beagle make a superb museum, though? (via Samizdata.net)


8< (via Boing Boing) In the video of his arrest, Dudley Hiibel seems kind of obnoxious to me, but you can't (yet) be sent to jail for being an asshole. I think most citizens should cooperate with most cops most of the time, but no law that I know of says they have to. Predictably, I'm on the side of the assholes here.


8< This is a fascinating and deeply unsatisfying story. For about a week, a glitch at amazon.com's Canadian site displayed the real names of anonymous reviewers, but no one seems to have really dug into the wealth of information thus revealed. I'm not so interested in writers pushing their own books as in those who claim to be fighting back against unfair anonymous reviewers:

The suspicion that [...] the Underground Literary Alliance had anonymously attacked his friend Heidi Julavits prompted the novelist Dave Eggers to write a review last August calling Ms. Julavits's first novel "one of the best books of the year."
So why didn't Eggers, or the writer of the NYT piece I linked, check to see who wrote the attacks? Gah.


8< Eliot points to a Morning News article by Mighty Girl Margaret Berry: ten charities who know the value of ten dollars.


8< Do you know anything about Leonora O'Reilly, Mary Breckinridge, Dorothy Kenyon or Patty Andrews? Neither did I, but keeping up with bean's series ejumacated me.

snippets | sennoma | 17 Feb, 2004 | |


Monday, 16 February
can't have too many watchdogs

Here's an update to two earlier entries on places to go to get away from the spin and find some facts, this time with a focus on electronic voting.

For the Record points to a post by Jeanne D'arc at Body and Soul about voting machines and the importance of a paper trail; if you haven't been keeping up, those two posts are a good starting point. This is a vital issue for all Americans. (A commenter in the BaS thread recommended absentee voting as a way to force a hand-count of your vote, and I could not agree more.)

FtR also links to Verified Voting, a watchdog site concerned with "transparent, reliable, and publicly verifiable elections in the United States". They say they have been operating for the last 8 months without funding from anyone but their core group of volunteers, but now that they are registered as a 501(c)(4) non-profit (can engage in political activity, donations not tax-deductible) they are beginning fundraising. No word on whose money they will or won't take. Of particular note, they have a good background on the Voter Confidence and Increased Accessibility Act and accompanying Senate bill which require require a voter-verifiable audit trail on every voting system.

Verified Voting links to Votewatch, "a nonprofit non-partisan organization of citizen volunteers, statisticians, lawyers, technologists, journalists and election officials who monitor public elections in the U.S.A., analyze patterns, and make their findings public prior to the certification of the election". It looks to be mainly exit polling plus a forum for citizen reporting on individual elections. When you follow the money, things get a bit fuzzy:

As of October 7th, 2003, Votewatch has been internally funded through the generosity of its team members and the good will of its partners. Votewatch is embarking on an external funding plan that will target foundations of all ideologies, the general public, organizations and philanthropists.
There's also the matter of partnership with for-profit research firm Aguirre International.


While I'm on the topic, Marylaine Block's Neat New Stuff links to the Center for Public Integrity, a "nonprofit, nonpartisan, tax-exempt organization" founded by Charles Lewis which "does not accept contributions from anonymous donors or from corporations, labor unions or governments" and lists donors over $500 in the last year, with a contact address for more information. The Center was founded in 1989, has a full-time staff of 40 and has "issued more than 200 investigative reports, including 12 books", and its "findings or perspective have appeared in roughly 8,000 news media stories". For an idea of what they do, check out this story on the windfalls of war:

More than 70 American companies and individuals have won up to $8 billion in contracts for work in postwar Iraq and Afghanistan over the last two years, according to a new study by the Center for Public Integrity. Those companies donated more money to the presidential campaigns of George W. Bush—a little over $500,000—than to any other politician over the last dozen years [...]


Update: just looked through my saved folder and found this post on the electronic voting issue from Ruminate This. Jack K provides more solid background and, in the process, links to Black Box Voting. This seems to be a blog associated with the book (also available free in pdf format at the site) of the same name by Bev Harris. No information on who pays for what, though.



Friday, 13 February
and many happy returns

Peter GabrielHappy Birthday Peter Gabriel, and thanks for all the music.

music | sennoma | 13 Feb, 2004 | |


Tuesday, 10 February
and that's a great name for a blog, too

If you like stimulating conversation, you should be reading Crooked Timber. These are just from the last few days:

How will history judge? Micah picks up on this post at En Banc and asks, What will the America of 2104 think of the America of 2004?


In this post, philosopher Brian Weatherson points with sensible trepidation to Peter Singer's new book, The President of Good and Evil: The Convenient Ethics of George W. Bush. Given the timing of its release, I honestly suspect the book is aimed more at getting Singer back on TV than anything else. Nonetheless, Brian raises interesting questions that he'd like to see Singer tackle, and the comment thread has some interesting back-and-forth about Singer's most famous ideas regarding abortion and infanticide.


Speaking of books, this post is a must-read. Harry wants to know of "two books you think every educated person should have read, published 1970 or later". On another blog, this topic could be tiresome, but on CT I can almost guarantee that you'll get some great reading recommendations out of it. For me, so far:

The History and Geography of Human Genes - Luigi Luca Cavalli-Sforza
In Search of Lost Time - Marcel Proust
Feynman�s Lectures on Physics
Maus - Art Spiegelman
Development as Freedom - Amartya Sen
Love in the Time of Cholera - Marquez
The Drowned and the Saved - Primo Levi
The Eighth Day of Creation - Horace Judson
Understanding Media - Marshall McLuhan
An Artist in the Floating World, Remains of the Day - Kazuo Ishiguro
Sometimes a Great Notion - Ken Kesey
The Sheltering Sky - Paul Bowles


Finally, this post is a quick pointer to a book review, but the comments thread finds its way to the question "what is science?", which I find endlessly interesting. Commenter Keith M Ellis does a bang-up job of making Kuhnians (Kuhnites? Kuhnts?) look ridiculous.

Update: that remark was unfair, the more so since I keep comments off on posts highlighting conversations on other blogs. My apologies to Mr Ellis; see the thread (in the next day or so; I'm really busy) for a more substantive contribution from me.

Update: see also here.


lost art | sennoma | 10 Feb, 2004 | |
well, shit.

Like pretty much everyone, I've been using Tris-based buffers for nucleic acid electrophoresis since I started doing it. Turns out that the buffering capacity of the solution makes no real difference, and what you really want is a solution that doesn't carry so much current (and therefore doesn't generate as much heat; I've melted TAE/agarose gels before). I guess something was lost in translation between the interview and the article, because "carries a voltage" is meaningless to me. Also, I note that Kern and Brody have "filed for a provisional patent on the sodium boric acid solution" -- bwahahahaha! Good luck enforcing that. (In defence of the researchers, I suspect that beancounting shitbags at Johns Hopkins have made such idiocy mandatory.)

What's great about this is that everyone has been doing it the same way for thirty years, not bothering to think about improving the method since it worked well enough and, you know, that's the way everyone does it. Now these guys come along and deliver a smack-your-forehead moment to every molecular biologist in the world. *smacks self in forehead*

What's bad about this is that my one burning scientific ambition is to get a methods paper like this published, and I'm insanely envious. Why didn't I think of this? (Don't answer that.)

random stuff

photo of Porpidia sp., an Alaskan lichenPorpidia flavocaerulescens, orange boulder lichen, photographed in Alaska by Steve and Sylvia Sharnoff, whose beautiful lichen sampler and gallery are taken from their book, Lichens of North America. (thanks to Anne Galloway for the link)






03Brit2.jpg I never thought too much about the old adage that you can't fold a piece of paper in half more than 7 times; I tried with a couple of different pieces of paper, couldn't do it, and stopped there, except for a vague idea that I could do better with a much bigger piece of paper. Not Britney Gallivan, whose elbows you see there on a piece of paper folded 11 times (she's since managed 12). She derived expressions to describe the folding limits for one direction (L = (π.t/6)(2n + 4)(2n - 1), where L = length and t = thickness of the material and n is the number of folds) and alternating directions (roughly W = π.t.23(n-1)/2), then demonstrated the validity of her equations with gold foil and then with paper. Another approach is described here on Math Forum, or you can buy Ms Gallivan's booklet. I wish I'd had her chutzpah, not to mention her smarts, when I was in high school.



Monday, 09 February
snippets

8<Education is about as important as an issue gets, if not quite so pressing as poverty or disease, and science education is, for obvious reasons, my thing. For this reason, and as part of an ongoing program of becoming more involved in the various communities (geographic, scientific, etc.) to which I belong, I've applied to be a judge at the Intel International Science and Engineering Fair. Besides, it's gonna be fun.

8<(via Language Hat) Ever wonder what was up with the odd names for those new superheavy elements? William Drenttel explains that they're placeholders, just the atomic numbers rendered in Latin, for use until their existence is confirmed and someone comes up with a real name.

8<(via Rebecca Blood) Washington State Supreme Court Justice Faith Ireland won her second national powerlifting championship last weekend. The 130-pound judge squat lifted 198 pounds, bench pressed 133 pounds and deadlifted 253 pounds. Oh yeah -- she's sixty-one. Makes me feel kinda, eh, flabby.

8<(via Leuschke) This is a great short story.

8<Over at Language Log, John McWhorter is engaged in some utterly fascinating cross-disciplinary detective work. It's a bit complex to compress, so just go read it. Trust me, you'll be glad you did.

8<(Joi Ito) Eisbrecher's self-titled debut album is being released with two blank CD-ROMs, because "We are of the opinion that the music buyers are criminalized enough and have been made responsible for the wretched state in the music industry. We are giving them the chance to make 2 legal copies for private use with 'official blanks'. It can't always be that the end users have to take the blame for something that international corporations have arranged with their artist-burning methods." Kudos.

8<(via Slashdot) Stephen Wolfram's much-hyped book A New Kind Of Science is available free online. I still won't understand it, but at least I won't waste fifty bucks on being reminded how dumb I am.

8< Eliot takes a smack at that talentless idiot Lileks so I don't have to.

snippets | sennoma | 09 Feb, 2004 | |


Saturday, 07 February
critterama

Notiosorex cockrumi, a new shrew speciesNew Shrew: Texas Tech University professor Robert Baker has named Notiosorex cockrumi after his PhD supervisor. Baker discovered the shrew in 1966, but only recently confirmed that it is not the same species as N. crawfordi , which shares its home range in Arizona's Santa Rita mountains. Cute little sucker (but don't let that fool you: shrews are savage). Photo credit: Robert Baker, Arizona University.



mountain bongoBeleaguered Bongo Being Brought Back By Biologists: the last wild mountain bongo is thought to have died on Mt Kenya in 1994, but the species is not extinct thanks to hunter-turned-conservationist Don Hunt. Between 1970 and 1980, Hunt established a breeding program in the US that saw the captive population climb from the 20 he caught to around 400. On January 20, 18 bongo from the US joined 17 others at the Mt Kenya Game Ranch, where it is hoped that they will establish a semi-tame breeding pool with which to re-establish a wild population. If this story doesn't bring a lump to your throat, you're a serious hardass. Sniff. Photo credit: Mount Kenya Animal Orphanage.


Missing Monkey May Still Survive: no picture, sadly, as Miss Waldron's red colobus (Procolobus badius waldroni) is just too damn rare. Anthropologist Scott McGraw and colleagues declared it "probably extinct" in 2000, but shreds of evidence have rekindled hope that the species may survive in remote corners of the Ivory Coast. McGraw has a photograph, a skin and a tail, all of them collected in the last few years. Hunting and destruction of habitat have brought the Miss Waldron's to the brink; if they have in fact pushed it over, it will be the first recorded primate extinction in 200 years. Apart from being a shitty thing to do, that's a bad sign for the region because primates are extraordinarily adaptable, and the local ecology would have to be in really bad shape to have killed one off.


oceanic whitetip sharkSeveral Species in Shark Decline: once the most commonly caught sharks in the region, oceanic whitetip and silky sharks have almost vanished from the Gulf of Mexico, according to biologists Julia K. Baum and Ransom A. Myers. Their study (Ecology Letters Feb 2004: vol. 7 pp. 135-145) compared 1950s and 1990s catch rates data and concluded that the whitetip, silky and mako shark populations in the Gulf of Mexico have declined by 99, 90 and 79 percent, respectively. The study has drawn extensive criticism; oddly enough, the critics cited work for the National Marine Fisheries Service and the Blue Water Fishermen's Association. The photo shows an oceanic whitetip (credit: Monterey Bay Aquarium).


sea otter, Enhydra lutrisSomeone Otter Do Something: for reasons that remain unclear, the northern sea otter (Enhydra lutris) population of southwest Alaska has declined to the point where the United States Fish and Wildlife Service is listing it as "threatened", one step away from "endangered" under the Endangered Species Act. The Alaskan population was nearly eliminated by 1911, when an international treaty banned hunting; by the 1980's almost half of the world's northern sea otter population lived in southwest Alaska. Since then, the population has declined by somewhere between 50 and 70 percent. Photo credit: Friends of the Sea Otter; more info available from biologicaldiversity.org.



Friday, 06 February
nader nader nader

It seems that Ralph Nader's recent announcement that he is considering running for Preznit again has stirred up controversy in the blogosphere. Max has this to say, and Lawrence Lessig this; the comments threads on both are good. A while back, Patrick said this, which also begat a commentfest that I meant to feature.

The Nader issue is interesting to me because it highlights two potentially very different approaches to politics. Is your vote a tactical weapon in the struggle to improve society, or an expression of your political and ethical worldview? Is politics the art of the possible, or the arena in which different moral systems do unflinching battle? I'm something of a utilitarian and very much a meliorist, so I think you should write or paint or flash a boob on national TV if you want to express yourself; when you vote, do the most good you can and leave your ego out of it. (I should add: that's not to say that even swing-state Nader 2000 voters were simply indulging their ego; it seems to me that it would have been possible, before the excesses of Gee-Dub and the Corporate Welfare Tribe, to be willing to risk electing Bush II in order to promote a strong progressive voice and a third party.)

(An aside: I note with pleasure that Max's trackback window says "Continuing the discussion...". As always, comments off on this entry; the conversation is happening at the end of those links.)

lost art | sennoma | 06 Feb, 2004 | |


Thursday, 05 February
i'm just here for the food

headshot of Alton BrownI sure like Alton Brown. I don't watch his cooking show Good Eats as often as I might, because the wacky/zany stuff feels forced to me, and gets in the way of the information (which is excellent), but Mr Brown seems like someone whose company I would really enjoy. His website is entertaining, informative and well designed, and gives me the sense of a complex and curious mind. He even has a blog:

Georgia state school Superintendent Kathy Cox has decided that the word “evolution” is “…a buzzword that causes a lot of negative reaction” and should be replaced in all Georgia school curriculum with the phrase “biological changes over time”.

I agree. I hate buzzwords, don’t you? That’s why I think we should go one further and replace the phrase “slack-jawed backwater ignoramus” with the phrase “Kathy Cox”.

He also has lots of fans, and it's my guess that they skew cerebral as a demographic; you can even build your own Good Eats Geek Code. (Picture by Pelosi&Chambers stolen from Channel Guide Magazine.)

a welcome voice in any medium

(via BoingBoing) I don't think this quite qualifies as a blog, but Jimmy Carter will be sending regular reports to be posted at the Carter Center as he travels through West Africa as part of a program aimed at eradicating Guinea worm and in order to launch the Development and Cooperation Initiative in Mali. In any case, I am always glad to hear from the best ex-President the US has ever had, and that down there is just about my favourite combination of categories.

Update: There were complaints ("Bastard, I nearly hurled!"), so I moved the pictures of Guinea worm infection below the fold.

more...


Wednesday, 04 February
snippets

8< "Open Reading Frame" would have been another good name for this blog. I didn't think of it until after the spousal unit built me a site and a logo that I like too much to change, so mol biol geeks feel free to steal that idea.


8< (via Jared) A big ol' collection of record labels on the web.


8< Like photoblogs? Photoblogs.org is your one-stop shop (3,273 photoblogs in 54 countries and 25 languages as I write this). If that's too much, just try Eliot Shepard's slower.net, which is consistently wonderful.


8< (via BoingBoing) It had to happen sometime, I guess: geek names son version 2.0.


8< Super Size Me wins Documentary Directing Award at Sundance. I want to see this film, in which madman Morgan Spurlock documents the terrible things that a month-long diet of nothing but McFood does to his body.

science news

Insights into HIV-1 RNA dimerization: two RNA genomes are packaged in every infectious HIV particle, and they are joined by a specific mechanism at specific sites along the molecules. Researchers at NIST and CARB have shown that specific protonation of the dimerization initiation sequence loop residue A272 may be involved in dimer maturation. Read the abstract and, if you have access, get the PNAS preprint from here. If confirmed in vivo, this will be a novel role for protonation in RNA structure modulation.


vitE.jpgNew antioxidants: by chopping off its tail and substituting nitrogen into the two rings, Derek Pratt and colleages at Vanderbilt University have turned alpha-tocopherol (the most active in humans of 8 tocopherols that make up "vitamin E"; pictured at right) into a novel compound with about 90-fold greater antioxidant activity. Even if the new compound does not prove biologically useful, it will still probably find a home in the manufacture of oxidation sensitive products like plastics, rubber, lubricants and cosmetics. (image from Wikipedia.de)


growth inhibition of Micrococcus luteus by Penicillium notatum Potential new antibiotics: chemists at the University of Illinois at Urbana-Champaign have demonstrated that a single enzyme is capable of processing the precursor LctA all the way to the lantibiotic lacticin 481 (abstract from Science vol. 303 pp. 679-81 here). Lantibiotics are small secreted microbicidal peptides that contain the modified amino acid lanthionine, and are particularly attractive as antibacterial agents because they inhibit cell wall synthesis and disrupt the cell membrane. This dual attack makes the development of resistance less likely than with agents that have a single target; for instance, the lantibiotic nisin has been used as a food preservative for more than 50 years in more than 40 countries without resistance related problems. Nisin is produced by certain strains of Lactococcus lactis, occurs naturally in a variety of cheeses and is classified GRAS (generally recognised as safe) by the USFDA. What's cool about this is that the biosynthesis of most antibiotics is so complex that it is virtually impossible to tweak it, but this system offers the possiblity of designer lantibiotics. By modifying LctA or offering other substrates to LctM, we may be able to generate a whole range of new lantibiotics. (The image, from The Microbial World, is just for decoration, and actually shows growth inhibition of Micrococcus luteus by Penicillium notatum.)


bdello.jpg Killer bugs: but not from Outer Space. Bdellovibrio are bacterial predators which actively hunt and kill other bacteria. They are chemotactic, meaning that they can follow concentration gradients of substances likely to lead to prey, and have an impressive arsenal of lytic enzymes with which to enter the target cell and then, essentially, eat it from the inside. Researchers at the Max Planck Institute for Developmental Biology have sequenced the entire genome of Bdellovibrio bacteriovorus, and are looking forward to a smorgasbord of novel enzymatic activities. From the press release:

The researchers will attempt to identify the targets in the prey cell that have proven to be successful points of attack in this million-year-old prey-predator relationship. The lytic enzymes acting on cellular systems that are not targeted by conventional chemical antibiotics are thereby especially interesting.

Far reaching anti-microbial strategies aim at using Bdellovibrio as a "living antibiotic". This seems feasible, as Bdellovibrio is not capable of infecting eukaryotic cells, in particular mammalian cells. Moreover, it was shown in animal experiments that Bdellovibrio only has a weakly immunogenic surface, which does not produce serious life threatening reactions in test animals. These attributes, together with the facts that certain Bdellovibrio strains show a very narrow prey spectrum and are capable of penetrating the same tissues as many human pathogens, gives promise to the development of novel anti-microbial strategies.

The photomicrograph, which I swiped from here, shows B. bacteriovorus (I circled a couple) attacking Spirillum serpens (arrow). The white bar shows 1 millionth of a meter.


reversine.jpg De-differentiation of adult cells is an alternative to the use of embryonic stem cells as a source of pluripotent cells that could be induced to form specific tissues in order to heal wounds, replace organs, and so on. Researchers at the Scripps Institute have used a library screening approach to look for small molecules (read: drugs) which can reverse muscle cell differentiation and allow re-differentiation along a bone cell lineage. While many questions remain, they have come up with a compound which they call "reversine" (pictured at left; pic from J. Am. Chem. Soc. vol. 126 pp. 410 -411) which appears to have the properties they are looking for.


xrayhelix.jpg Computer program speeds up x-ray data analysis:

Scientists are finding a computer program called Elves to be a nearly magical solution to the tedious and time-consuming task of determining the 3-D shape of proteins ... the first time anyone has reported a computer generating a protein structure by itself ... Elves decreases the time and training needed for researchers to interpret X-ray crystallographic data
The big deal here is that 3-D protein structures are the keys to solving an enormous range of biological puzzles, particularly those involving drug design, and this program has made the time from x-ray data to solved structure much shorter (good primers on x-ray crystallography here and here). That's good news not only in the immediate time-saving sense but also in the larger sense that it enables meta-analysis. By reducing analysis times from days/weeks to minutes, the new software will enable side-by-side analysis of, and comparisons between, much larger data sets. For instance,
Holton is taking a second look at X-ray diffraction data that other scientists have given up working on. He hopes to find out what characterizes the nine out of 10 data sets that fail to produce good structural data.
The image at right shows x-ray crystallographic data of considerable historical impact and interest: it was collected by Dr Rosalind Franklin in 1952 and from it was deduced the double-helical structure of DNA. (Incidentally, if you're interested in that famous story, rather than listen to that egregious prick Watson, read this excellent version told from the perspective of Linus Pauling.)



Sunday, 01 February
citrus fhtagn!

photo of Buddha's Hand citron photo of Buddha's Hand citron Great Old Citrus: that thing is a citron, Citrus medica var. sarcodactylus. Spouse and I couldn't resist it when we saw it at Whole Foods. It's indigenous to the lower Himalayas and has been known for centuries throughout Asia. According to Julia F Morton's Fruits of Warm Climates, it's called fu shou in China, bushukon in Japan, limau jari, jeruk tangan and limau kerat lingtang in Malaya, djerook tangan in Indonesia, som-mu in Thailand and phât thu in Vietnam. The most common English name is Buddha's Hand. It has abundant pith and little or no flesh inside, and is mostly valued for the thick, soft rind, which can be candied or grated and used like lemon zest, and for its decorative value and strong lemony perfume. There's even a Buddha's Hand citron flavoured vodka available. Yum.

cthulhufruit3.jpgUpdate: there's the innards of the thing, with a medium sized apple for scale. I think this was about an average sized Cthulhu Fruit, although there was one in the shop at least twice as big.
Update the second: I don't know where I got the idea the rind was thick; as you can see in the picture, it's thinner than a lemon's.

serious grab bag

Blake at American Footprint reminds everyone about Tibet, the forgotten cause. He links to a story in the Times of Tibet and asks why we aren't seeing articles like that in the New York Times.

Cory Doctorow links to a story on homelessness in Columbus, OH:

When Tom Bingham describes his new apartment, a slow smile creeps across his face.

The place is small - 402 square feet - squeaky clean, and bare. A metal-frame twin bed sits in one corner, a large, worn purple chair in another. But it has one thing that Mr. Bingham, an older man, has never known: privacy.

"It's the first time I've been by myself," he says, relishing the words. "You come from a family of 10 kids, like I did, and you're never by yourself. In the shelter I was with 120 other guys.... Now, I'm getting used to peace and quiet."

The program is based on providing permanent supportive housing for the long-term homeless, and after a five-year trial signs are good that it has been a success, not only for the direct participants but also for shorter-term users of homeless resources.

Amp reports on a modern medical horror story. Amber Marlowe checked out against medical advice from Wilkes-Barre General Hospital because they insisted she have a C-section, which she did not want. About the same time she was giving birth (vaginally, without incident) at Moses Taylor Hospital, attorneys representing WBGH sought and obtained a court order forbidding her to refuse the surgery. If you'd asked me beforehand, I'd have said I didn't think it possible in this day and age.

Prometheus6 gives a nod to Steve Kerr, who referred to Yao Ming by an ethnic slur but then made a sincere apology without making excuses; you can read his letter to Ming here. I'm linking this because Kerr did wrong, but it took cojones to face the facts the way he did, and I think that sort of response should be encouraged.

Also from Prometheus6, the last Tuskegee airman died about a month ago. A quick google finds stories in all the usual places, but it wasn't exactly splashed across their front pages. The University of Virginia has a good background here if you're not familiar with the story.


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