Monthly Archives: October 2004

huh?

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I must be missing something here. EurekAlert reports on a letter to Science by Richards Palmer and Lewontin review by Richard Palmer, thus:

Genetics aren’t the only triggers for the traits a species develops, according to findings from a University of Alberta professor. The research challenges the classical Darwinian theory of evolution as being the sole explanation for how new life forms arise.
“Variations that do not initially have a genetic basis can still be important for evolution. They are 35 to 50 per cent as common as genetic variation, at least when it comes to the evolution of asymmetric forms” Dr. Palmer said. He was able to synthesize published evidence showing that the current ‘genotype-precedes-phenotype’ theory of evolution only explains about half of the examples he studied.
He came to his conclusions after reviewing more than 200 research papers from around the world, including a study on asymmetry (the difference between the left and right sides of the body) that was conducted using lobsters. Baby lobsters are born with two same-sized claws, but somehow, only one of the claws transforms into a larger crusher claw as the lobster grows. “The genetic program that makes a crusher claw is triggered by one claw being used more than the other. But if one side isn’t stimulated enough, the program that makes a crusher claw never gets started. It’s a clear example of how environment in some sense causes difference in form,” Dr. Palmer said.
Further, studies on many other plant and animal species with both right-sided and left-sided forms showed that if two of the same ‘handedness’ were mated, half their offspring would be left-sided and half would be right-sided. “Genetics made no difference in the direction of asymmetry. It’s a trait strictly determined by environment. From an evolutionary perspective, this means form arises first and the genes follow.”
These observations have some parallels with modern medical research, Palmer said. “You can’t say all diseases are gene-based. Consider cancer caused by asbestos exposure, or skin cancer. If you only study genetics, you would not learn much about environmentally-induced diseases.”

What on earth? I can’t get to the letter from home, so perhaps that will clear up my confusion when I read it at work tomorrow, but I’m not seeing anything there that conflicts with the standard model of evolution or indicates that “genes follow form”. That last smacks of Lamarckism to me. The lobster inherited the genetic basis on which one or the other claw hypertrophies, and it’s not hard to see how that would convey a selective advantage. The right- and left-sided forms inherited the basis of those forms; that the asymmetry distributes evenly among offspring of same-sided parents implies that the environmental triggers did not alter the genotype. Skin cancer and mesothelioma, when they are induced by environmental insult, arise from environmentally induced mutation: phenotype follows genotype. I’m looking forward to reading that letter.
Update: the letter from Palmer and response from Lewontin were a red herring, I just didn’t see the review article when viewing the site without paid access. The EurekAlert article refers to this review by Palmer that appears to be, at least in part, bunk. Here’s the abstract:

Because of its simplicity, the binary-switch nature of left-right asymmetry permits meaningful comparisons among many different organisms. Phylogenetic analyses of asymmetry variation, inheritance, and molecular mechanisms reveal unexpected insights into how development evolves. First, directional asymmetry, an evolutionary novelty, arose from nonheritable origins almost as often as from mutations, implying that genetic assimilation (“phenotype precedes genotype”) is a common mode of evolution. Second, the molecular pathway directing hearts leftward

cards on the table

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I admit I never paid a lot of attention to Derek Lowe’s In The Pipeline, but I had good intentions of doing so. It seemed like a good way to get a look at the pharmaceutical industry from the inside. Now, however, Lowe has laid his political cards on the table, and in so doing revealed himself to be someone I cannot take seriously. He is going to vote for Bush. It seems that a dollar in his pocket trumps a thousand American and countless thousands of Iraqi casualties in an indefensible, illegal, immoral, inadequately planned and poorly executed war, and that the fear inspired in him by Kerry’s “constant hammering on the drug companies” (that he will be “tossed out in the street”, no less) overrides the deliberate erosion of civil liberties and democratic processes, the lavish and corrupt catering to the superwealthy at the expense of the middle and lower classes, the degradation of the education system, an undeclared war on women and an open war on the glbt. I don’t buy Lowe’s claim that his biggest argument with Kerry is on foreign policy: he (Lowe) does not seem stupid (which one would have to be in order really to believe that Kerry would be worse than Bush in re: foreign policy) so I take this to be merely a cover for Lowe’s intention to vote on the basis of an exaggerated fear for his own bank balance. I won’t waste my time reading the weblog of someone so intellectually dishonest — particularly not when I want a balanced view of the pharmaceutical industry! — so Lowe is off the blogroll.

Anthony Hecht

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The Vow
In the third month, a sudden flow of blood.
The mirth of tabrets ceaseth, and the joy
Also of the harp. The frail image of God
Lay spilled and formless. Neither girl nor boy,
But yet blood of my blood, nearly my child.
All that long day
Her pale face turned to the window’s mild
Featureless grey.
And for some nights she whimpered as she dreamed
The dead thing spoke, saying: “Do not recall
Pleasure at my conception. I am redeemed
From pain and sorrow. Mourn rather for all
Who breathlessly issue from the bone gates,
The gates of horn,
For truly it is best of all the fates
Not to be born.
“Mother, a child lay gasping for bare breath
On Christmas Eve when Santa Claus had set
Death in the stocking, and the lights of death
Flamed in the tree. O, if you can, forget
You were the child, turn to my father’s lips
Against the time
When his cold hand puts forth its fingertips
Of jointed lime.”
Doctors of Science, what is man that he
Should hope to come to a good end? The best
Is not to have been born. And could it be
That Jewish diligence and Irish jest
The consent of flesh and a midwinter storm
Had reconciled,
Was yet too bold a mixture to inform
A simple child?
Even as gold is tried, Gentile and Jew.
If that ghost was a girl’s, I swear to it:
Your mother shall be far more blessed than you.
And if a boy’s, I swear: The flames are lit
That shall refine us; they shall not destroy
A living hair.
Your younger brothers shall confirm in joy
That this I swear.

Giant Tortoise
I am related to stones
The slow accretion of moss where dirt is wedged
Long waxy hair that can split boulders.
Events are not important.
I live in my bone
Recalling the hour of my death.
It takes more toughness than most have got.
Or a saintliness.
Strength of a certain kind, anyway.
Bald toothless clumsy perhaps
With all the indignity of old age
But age is not important.
There is nothing worth remembering
But the silver glint in the muck
The thickening of great trees
The hard crust getting harder.

“It Out-Herods Herod. Pray You, Avoid It.”
Tonight my children hunch
Toward their Western, and are glad
As, with a Sunday punch,
The Good casts out the Bad.
And in their fairy tales
The warty giant and witch
Get sealed in doorless jails
And the match-girl strikes it rich.
I’ve made myself a drink.
The giant and witch are set
To bust out of the clink
When my children have gone to bed.
All frequencies are loud
With signals of despair;
In flash and morse they crowd
The rondure of the air.
For the wicked have grown strong,
Their numbers mock at death,
Their cow brings forth its young,
Their bull engendereth.
Their very fund of strength,
Satan, bestrides the Globe;
He stalks its breadth and length
And finds out even Job.
Yet by quite other laws
My children make their case;
Half God, half Santa Claus,
But with my voice and face,
A hero comes to save
The poorman, beggarman, thief,
And make the world behave
And put an end to grief.
And that their sleep be sound
I say this childermas
Who could not, at one time,
Have saved them from the gas.

“More Light! More Light!”
for Heinrich Blücher and Hannah Arendt
Composed in the Tower before his execution
These moving verses, and being brought at that time
Painfully to the stake, submitted, declaring thus:
“I implore my God to witness that I have made no crime.”
Nor was he forsaken of courage, but the death was horrible,
The sack of gunpowder failing to ignite.
His legs were blistered sticks on which the black sap
Bubbled and burst as he howled for the Kindly Light.
And that was but one, and by no means one of the worst;
Permitted at least his pitiful dignity;
And such as were by made prayers in the name of Christ
That shall judge all men, for his soul’s tranquility.
We move now to outside a German wood.
Three men are there commanded to dig a hole
In which the two Jews are ordered to lie down
And be buried alive by the third, who is a Pole.
Not light from the shrine at Weimar beyond the hill
Nor light from heaven appeared. But he did refuse.
A Lüger settled back deeply in its glove.
He was ordered to change places with the Jews.
Much casual death had drained away their souls.
The thick dirt mounted to the quivering chin.
When only the head was exposed the order came
To dig him out again and get back in.
No light, no light in the blue Polish eye.
When he finished a riding boot packed down the earth.
The Lüger hovered lightly in its glove.
He was shot in the belly and in three hours bled to death.
No prayers or incense rose up in those hours
Which grew to be years, and every day came mute
Ghosts from the ovens, sifting through crisp air,
And settled upon his eyes in a black soot.

poetry news

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pamayres.jpg The good news: Pam Ayres has got an MBE. I’ve been a fan of Pam Ayres’ unpretentious light verse since I first heard her reading it in her distinctive West Country burr about twenty years ago. My favourite is still Clamp the Mighty Limpet, which begins

I am Clamp the Mighty Limpet
I am solid, I am stuck
I am welded to the rockface
With my superhuman suck.

When I get home this evening I’ll transcribe the rest of it, and a couple of others. (Update: apparently I forgot to steal the Pam Ayres books from my parents last time I visited, so I’ll make a separate entry when I’ve bought myself new copies.) I think Ms Ayres should be Poet Laureate instead of professional boring git Andrew Motion. Seriously, and if I had the time I could make a scholarly argument for the idea on the basis that light verse of a certain kind is the last (and perhaps the first and only) distinctively British mode of poetry. (photo lifted from the jacket cover of her latest book)
anthonyhecht.jpg The sad news: Anthony Hecht is dead much too soon at 81. Hecht was a formalist whose poetry merited with unusual frequency both of the overused adjectives “beautiful” and “melancholy”. He also (with John Hollander) invented the double dactyl, a light form that’s considerably harder than it looks. This, for instance, reads like one but isn’t:

Higgledy piggledy
Anthony Hecht is dead,
terrible news for all
lovers of verse:
assholes like me will be
doubledactylically
obituarizing him; what
could be worse?

You can read some of his work at the links above, and I’ll transcribe some more tonight. (photo swiped from Auburn U Dept of English) (both items from the excellent dumbfoundry)

kerry 57 bush 43

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kerry.jpg Children’s television network Nickelodeon has correctly predicted the winner of the last four presidential elections by polling their viewers. Since this year’s poll shows Kerry a handy winner, I’m inclined to say things like “children are a clear window on the revealed preferences of their parents” and “400,000 is a lot of votes”. Let’s hope the rugrats are right. (via Leiter; Kerry cartoon swiped from nick.com)

one great idea, two lousy implementations

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I’d link to del.icio.us, which is an online bookmarks manager that I’ve been playing with and quite liking, only there’d be no point. It fails to load at least as often as it works. My guess is that their server/s is/are badly overloaded. What good is a bookmark service that works half the time?
Next I’m going to try spurl, which even allows you to interface with del.icio.us (when it’s working, that is). It doesn’t seem to be much more reliable at first glance though. Right now it’s churning away trying to load in the next browser tab, but not getting anywhere. Oh wait — it’s finally loaded. Well, better that than timing out like del.icio.us, but it’s still not much use if I just want to grab a bookmark and move on without having to wait for something else to load.
Dammit, until I played with these things I didn’t even know I wanted an online bookmarks manager. Bah.

i’ve been wondering who would step up

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I keep wondering, where is all the alternative energy research and development? I’m far from an expert on the subject, but I can’t help feeling that the West is not pursuing the subject with appropriate vigour. When I visited Kuwait in 2002, it struck me that here was a country with buckets of oil money and not much else — except, you know, wind, tides, sunlight and vast empty spaces. If I were Kuwait, I thought at the time, I’d be working and investing my ass off in order to own energy production once the oil starts to run out.
What brought this to mind was the concurrence of a story about an exhibition of ecofriendly cars in Shanghai (google “Habo Shanghai” after that yahoo link dies) and this entry on WorldChanging about a meeting between Kofi Annan and Lu Yongxiang, the president of the Chinese Academy of Sciences:

…this would be of only passing interest except for the comment from an unnamed Chinese official:
“China will send experts to train local technicians in African countries, and will also host training classes and sponsor African experts to learn in China about agriculture, water power and renewable energies“. (Emphasis mine.)
China is clearly making renewable energy technologies a big part of its thrust to be a global power. Africa and other poor areas are terrific test-beds for Chinese renewable R&D, as system which would not be competitive in western markets can still find eager users. As Chinese renewable technologies get better, expect to see their target audience move from African aid to global consumers.

It seems a bit unscrupulous to be using poor nations as testing grounds, but then if the new tech is provided as aid any benefit it brings is a net plus. The strategy makes sense, and also makes me wonder how the world’s power balance will start to shift once dwindling supplies finally force us all off the fossil fuel teat.

please subvert our political system

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Today’s Guardian has two ideas, one good and one not so good, on how you might influence the outcome of the upcoming US election if you’re not a US citizen. Love it or hate it (and after two years here, I’ve learned to do both), the US is the 800 pound gorilla of international politics, and what happens here affects all the world. So is it reasonable to expect the rest of the world to sit meekly by and hope we get it right? In one sense, it certainly is — this is our country, after all. (Note the pronouns; I’ll be a citizen in two years, and I consider myself an American now. There’s more to love than to hate, despite ShrubCo’s best efforts.) That’s why I think the Guardian idea of getting their readers to write personal letters to strangers in swing counties is a mostly bad idea, more likely to generate resentment than anything. Their other idea, though, is much better: foreign donations to campaigns or explicitly partisan organisations are illegal, but there are other places to send money which will influence the outcome. In particular, if you want to send Smirky McKillemall back to the arse-end of Texas where he belongs, donate to the NAACP. Says Nathaniel Persily, a Pennsylvania university expert on election law: “It’s quite clear that if there was 100% African American turnout in Ohio, Pennsylvania and Florida, John Kerry would win this election running away.” The links go to NAACP offices in those states; other local offices can be found here. Black Americans are disproportionately affected by poverty, which tends to reduce voter turnout, and by felony disenfranchisement. Blacks have also been the target of deliberate malfeasance, because they are an easily identified group which votes largely Democrat. The NAACP runs a voter empowerment program which aims to “register, educate and get (African American) voters to the polls on Election Day”.
The Guardian story concludes:

…much of the law banning foreign contributions has never been tested in court and, argues Michael Dorf at Columbia, may even be unconstitutional on grounds of free speech. “If a group calling itself Europeans for Truth wants to run ads giving their view of the truth,” Dorf says, “it’s hard to draw a principled distinction between that and a British newspaper available at a US newsstand that has an editorial calling Bush and Blair liars.”

I’m not sure how I feel about that. I don’t think I want you damn forriners meddling in my country’s affairs that much.

this is just neat

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light microscopy image of Walsby's square archaon Walsby’s square archaon has finally been isolated in pure culture, 25 years after its discovery in a pond near the Red Sea. This is a square microorganism (not a bacterium! you’d think news@Nature would get that right) found in hypersaline environments; the pure culture was isolated in medium containing 33% saline, which is about twice as salty as soy sauce. The trick was to use dilution culture to find a range of nutrient and salt concentrations in which the square archaon would out-compete contaminating species. Other square Archaea are known, but this one has eludedelectron micrograph of Walsby's square archaon culture for so long, despite frequently being the dominant member of the halophile communities in which it’s found, that its eventual “capture” is big news to a certain specialized group of microbiologists. Me, I just liked the pictures. Both belong to Mike Dyall-Smith, who led the group that isolated the elusive microcritter and has more information and images here. The top picture is a light microscope image (epifluorescence using acridine orange stain) and the bottom picture is an electron micrograph (bar = 1 micron, GV = gas vacuole, PHB = polyhydroxybutyrate).
Update: I forgot to mention that these things are not only square, they’re very thin — like teeny living tiles. I couldn’t think why they would take that shape, so I asked Mike D-S (ain’t email wonderful? I’m just some chump with a website, and I can bug a senior scientist half a world away — and he takes time out to answer me). He says they contain bacteriorhodopsin, which is a light-driven proton pump that other Archaea use to harness the energy in sunlight. If this organism is doing the same thing, the shape makes sense as a way to maximise not only surface but also interior exposure to the sun. The gas vacuoles, then, might be a way of maintaining position at or near the water surface. (update 041018, stupid error fixed: s/photon/proton)

adios superman

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superman.jpg Christopher Reeve is dead (NYT obit) at 52, nine years after he broke his neck in a riding accident. He went from a charmed life to quadriplegia in the blink of an eye, but he never lost hope. He turned his personal tragedy into a new purpose, becoming a spokesman for the disabled, an activist and lobbyist on behalf of spinal cord research and an inspiration to all. I was looking forward to watching him walk again, dammit. If you can spare it, may I suggest a small donation in his memory?

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