Friday, September 28, 2007


Organism of the Week

Okay, so it's time to write about something besides the hypocrisy of the Bush administration. Is there really any need to continue on about that after all this time? I try to resist, but sometimes it's just so breathtaking that I can't help myself.

Instead, I'm inaugurating a new feature that I hope to make a regular part of this weblog (not that there's anybody reading it, but what does that matter?), where I will describe and discuss some of the interesting features of an unusual, offbeat organism that I have come across in my work as a molecular biologist. Given that a lot of my work is in the field of DNA repair, it makes sense to start with the undisputed champion of putting a broken genome back together - Deinococcus radiodurans. It's a bacterium that can survive doses of ionizing radiation (the kind given off by radioactive decay and nuclear blasts) and ultraviolet radiation (the kind that gives you a sunburn) 500 times greater than those that would kill or severely injure a human being. Because natural sources of such high doses of radiation are exceedingly rare on earth, it's thought that these capabilities evolved not to counter the effects of radiation but rather to deal with extreme dehydration, which can also cause massive damage to DNA.

A new paper was published this week that describes some of the genetic features that make this organism so resistant to forces that cause severe damage to its DNA. For a long time, it was suspected that these organisms had unusual or highly efficient systems for DNA repair, or that the presence of multiple complete copies of the genome (usually more than four) present in the cell allowed for stitching the whole mess back together somehow after damage. But now, a consensus is developing that high manganese (Mn) levels in the cell, and correspondingly low levels of iron (Fe) serve to protect the regular DNA repair enzymes themselves from being damaged by reactive oxygen species (free radicals, e.g.) created by severe stresses such as high doses of radiation or extreme dehydration. The exact mechanism by which manganese helps protect proteins from damage remains to be investigated, but the new research on radiodurans makes it clear that it's not the damage to DNA itself that causes sensitivity to radiation, but rather damage to the proteins that are responsible for DNA repair, an unexpected and exciting finding.

Thursday, September 27, 2007


Most Favored Tyrants

Alright, so I've beaten this dead horse beyond recognition and I promise to bring it to a close with this post, but my ears almost started bleeding when I heard news reports about Bush's UN speech yesterday:
US President George W. Bush yesterday urged UN members to join him in a "mission of liberation", denouncing tyrants in Belarus, Burma, Iran, North Korea, Syria and Zimbabwe.

Speaking before world leaders at the 192-nation UN General Assembly, Mr Bush called on the world body to go back to its guiding principles under the Universal Declaration of Human Rights to defend freedom and battle hunger and disease.

"When innocent people are trapped in a life of murder and fear, the declaration is not being upheld," he said.

Mr Bush urged "civilised nations" to help people suffering under dictatorships.
So let me see, tyrants in Belarus, Burma, Iran, etc. BAD. I got no problem with that. But for some reason he left out a few of the worst dictatorships including Pakistan, Saudi Arabia, Uzbekistan and my new favorite whipping boy, Turkmenistan, whose president was actively courted by Secretary of State Rice at the same UN meeting where Bush called for a "mission of liberation" from dictatorship. Let's see, what do all these brutal dictatorships that Bush failed to mention have in common? They couldn't all be close US allies, because that would mean that his speech was a fraud. Oh, wait....

Tuesday, September 25, 2007


Dueling Despots

One despot is the subject of well-deserved protests, official hysteria, and comparisons to Hitler. The other one (described at length in my previous post) is wooed by the US Secretary of State:
American officials, striving to weaken the grip of Gazprom, Russia's state-owned energy monopoly, in energy-rich Central Asia, are forcefully wooing the president of Turkmenistan on his first visit to the United States.

The president, Gurbanguly Berdymukhammedov, in the first trip by a Turkmen leader to the United States since 1998, went to New York to attend activities Wednesday related to the opening of the United Nations General Assembly. He met Tuesday with Secretary of State Condoleezza Rice at the United Nations.

U.S. officials say they want Berdymukhammedov to come away with the understanding that he has other options for developing extensive natural gas deposits and for shipping the fuel to market.
That'll teach him to respect his people's rights and liberties! Way to go, Condi! You couldn't possibly have given us a better demonstration of the negotiability of US principles.

Monday, September 24, 2007


Demonize This!

The highly politicized process by which the US picks its demons is always remarkable, but never has it been more clearly displayed than in the loud tempest over Mahmoud Ahmadinejad's visit to NYC during the opening session of the UN general assembly and in particular his participation in the World Leaders Forum at Columbia University. The best evidence of the narrow-mindedness of the furor over Iran's president is the fact that the keynote speaker at the Forum is Gurbanguly Berdymukhammedov, President of Turkmenistan, whose human rights record rivals that of any Iranian thug or cleric. Has anybody heard a peep out of the US media or its self-appointed defenders of high moral principles over the participation of the Turkmenistani President in this forum? Here's a summary of the human and political rights situation in Turkmenistan according to the latest survey from Freedom House, a conservative human rights organization which gives the country its lowest possible ratings for both political rights and civil liberties:

* Turkmenistan is not an electoral democracy. President Saparmurat Niyazov enjoyed virtually absolute power over all branches and levels of government. While the extent to which Niyazov’s successor, Gurbanguly Berdymukhammedov, would be able to consolidate his own power remained unclear by the end of 2006, the legacy of absolute presidential power is likely to prove difficult to overcome.

* The country has two parliamentary bodies, neither of which enjoys genuine independence from the executive branch

* None of the country’s legislative elections have been free or fair.

* Corruption is widespread, with public officials often forced to bribe their way into their positions. The authorities have used anticorruption campaigns as a way to remove potential rivals.

* Freedom of speech and the press is severely restricted by the government, which controls all radio and television broadcasts and print media. Reports of dissenting political views are banned, as are even mild forms of criticism of the president. Subscriptions to foreign newspapers and magazines are forbidden, and foreign journalists have few opportunities to visit Turkmenistan

* The government restricts freedom of religion, and independent religious groups continue to face persecution.

* The government places significant restrictions on academic freedom, with schools increasingly being used to indoctrinate, rather than educate, students.

* The state security services regularly monitor the activities of citizens and foreign nationals, limiting open and free private discussion.

* Turkmenistan remains a smuggling corridor for drugs from neighboring Afghanistan.

* Employment and educational opportunities for ethnic minorities are limited by the government’s policy of promoting Turkmen national identity and its discrimination against those who are not ethnic Turkmen.

* The government restricts various personal social freedoms, including the wearing of long hair or beards by men.

* Freedom of movement, particularly overseas, is severely restricted.

What do you have to do to get a little criticism around here? This guy generates no protests, no outcry, no long-winded diatribes about endorsing his actions by allowing him to speak. In fact, Columbia apparently decided let's make him the keynote and see if anybody cares? Will CU President Lee Bollinger be there to take this guy to task?

Sunday, September 23, 2007


Perils of Aging

Well, clearly my presbyopia has struck again. "Hail, Lurid Gun Pol" is not actually an anagram for Rudolph Giuliani, but "Hail, Lurid Gun Poi" is. Now, I know I like to make weird connections, but even I am unable to make a joke out of combining Giuliani and a Polynesian food made from taro. So this is my confession, and I'm leaving the title as is because "Hail, Lurid Gun Pol" is close to an anagram and in blogging, as in horseshoes and hand grenades, close is good enough.

Saturday, September 22, 2007


Hail, Lurid Gun Pol

Has there ever been a more craven instance of opportunistic political pandering than this?
Rudolph W. Giuliani yesterday sought to persuade members of the National Rifle Association to look past his lengthy record of pushing for tougher gun control by saying that his views on this issue had been changed by the terrorist attacks of Sept. 11, 2001.

The attacks on New York and the Pentagon put "a whole different emphasis on the things America needs to do to protect itself, and maybe even a renewed emphasis on the Second Amendment," Giuliani told the roughly 500 NRA members gathered at a Washington hotel.

This caps off a pretty impressive week for Giuliani, with courageous stances against right-wing bugbear and against a proposed visit to ground zero by the neocons' favorite nut-of-the-moment, Iranian president Ahmadinejad.

Rudy's well-known (to New Yorkers, at least) bizarre side also came to the fore as he ostentatiously answered his cell-phone during his NRA speech and cooed "I love you" to his wife, a transparent ploy clearly designed to make him seem like a human being with actual emotions. But what does it say about your humanity when you're reduced to these sorts of pathetic tactics, or when you're convinced that anyone will buy it? As for anyone who votes for this guy for president, they can't say they weren't warned.

(believe it or not, the title is actually an anagram for "Rudolph Giuliani". I shit you not. A major tip of the chapeau to the always reliable internet anagram server!)

Thursday, September 20, 2007


The Culture of Fear

A frightened population is a docile, submissive population. Nobody knows this better than politicians, who use fear to push policies that serve powerful constituencies but are against the interests of the general population; and mass media, who know that a frightened public is riveted to stories about predators, terrorists, and natural disasters, creating a self-perpetuating cycle of fear upon fear.

The success of this strategy is nowhere more evident than in a recent poll (pdf) conducted by the NYC Office of Emergency Management in which NYC residents were asked about the likelihood of certain events happening in the city in the next ten years. The answers to questions about terrorism were not surprising, but what really stuck out is the fact that 27% of the residents of NYC felt that an earthquake was likely to strike New York in the next ten years and 37% expect there to be a fire in the building in which they reside. These fears are so exaggerated that they can only reflect a general sense of fear that is so pervasive that it almost doesn't matter what you ask - people are scared shitless of the world around them.

If this were simply a socio-cultural phenomenon, it would be sad, but these fears are being exploited every day to expand surveillance and to restrict fundamental constitutional rights in ways that a confident, optimistic population would never tolerate. Frightening indeed!

Sunday, September 02, 2007


Magic Bus

I've noticed recently that new bus stops are going up around NYC with an LED display that tells you when the next bus will arrive. Being skeptical by nature, I assumed that the reported arrival time was when the next bus was scheduled to arrive, not when it actually would. I'm friends with two bus dispatchers so I asked them what's up with the new signs and I got a shocker. All NYC buses (at least that's the plan) are fitted with GPS devices that report their exact location, so somehow the bus's distance from the stop is used to calculate an arrival time that's displayed on the bus stop. The long range plan, I'm told, is that all buses will be controlled and dispatched from a central location (like the subways are already) and computer models will be used to identify problem areas to which the central dispatcher will respond. Remarkable.

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