Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide

Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) is a DinB homolog that belongs to the recently described Y-family of DNA polymerases, which are best characterized by their low-fidelity synthesis on undamaged DNA templates and propensity to traverse normally replication-blocking lesions.

By Bathsheba

WPA2 vulnerable

It seems the WPA2 encryption system used by most WiFi networks is badly broken:

This follows recent breaks in core security technologies like SSLStrip and Heartbleed.

People with good security practices like defence in depth and compartmentalization of sensitive information might not be too threatened by this. Those relying exclusively on the integrity of WPA2 may be in big trouble.

What are you sharing on your wireless network? Any file servers, cameras, or other sensitive systems?

Do you run your internet traffic through a second layer of encryption like a VPN and stick to HTTPS/TLS for sensitive websites?

End of the Cassini mission

After a 20-year mission, and to avoid any risk of contaminating Saturnian moons with microorganisms from Earth, the Cassini space probe was deliberately crashed into Saturn’s atmosphere today.

The science it has returned has been stimulating and the imagery spectacular. The watery moon Enceladus now joins Europa among the solar system’s most intriguing life-compatible bodies.

Every kakapo sequenced

New Zealand’s kakapo parrot is equally rare and bizarre: critically endangered, with 154 survivors living on three protected predator-free islands, the birds can’t survive the presence of rats, cats, and other potentially-carniverous mammals, can’t fly, and reproduce slowly and strangely.

The chapter about them is perhaps the most memorable part of Douglas Adams’ excellent non-fiction book Last Chance to See.

Now, the DNA of every living kakapo is being sequenced, with 81 done already.

History’s unpredictable paths

Columbus could not have foreseen the results of his search for piperine, Magellan was unaware of the long-term effects of his quest for isoeugenol, and Schönbein would surely have been astonished that the nitrocellulose he made from his wife’s apron was the start of great industries as diverse as explosives and textiles. Perkin could not have anticipated that his small experiment would eventually lead not only to a huge synthetic dye trade but also to the development of antibiotics and pharmaceuticals. Marker, Nobel, Chardonnet, Carothers, Lister, Baekeland, Goodyear, Hofmann, Leblanc, the Solvay brothers, Harrison, Midgley, and all the others whose stories we have told had little idea of the historical importance of their discoveries. So we are perhaps in good company if we hesitate to try to predict whether today there already exists an unsuspected molecule that will eventually have such a profound and unanticipated effect on life as we know it that our descendants will say, “This changed the world.”

Le Couteur, Penny and Jay Burreson. Napoleon’s Buttons: 17 Molecules that Changed History. Penguin, 2004.

Related: Learning and teaching

Alcohol’s societal role

In many ways, the treatment of ethanol in societies like Canada is exceptional.

It’s the only powerfully psychoactive drug top-end hotels and restaurants will provide you in unlimited quantities as long as you can pay. It’s the only drug that large groups of strangers routinely use to the point of inebriation together, in contexts ranging from weddings to club meetings to fancy dinners at universities. In places like Ontario where it is sold by the government, the government actively advertises it, while simultaneously notionally trying to prevent unhealthy use (which is probably any use, despite self-serving studies that purport to show health benefits from moderate consumption of this known carcinogen).

The societal burden of ethanol is spectacular. The Economist notes:

Between 2006 and 2010, an average of 106,765 Americans died each year from alcohol-related causes such as liver disease, alcohol poisoning and drunk driving—more than twice the number of overdoses from all drugs and more than triple the number of opioid overdoses in 2015… The percentage of Americans who met the criteria for alcohol-use disorder (AUD) in the DSM-IV—a psychiatric handbook that uses questions such as, “In the past year, have you found that drinking—or being sick from drinking—often interfered with taking care of your home or family?” to diagnose alcoholism—jumped from 8.5% of Americans in 2001-02 to 13% in 2012-13, or nearly 30m people. By comparison, 2.6m are estimated to have prescription-opioid and heroin addictions… Analysis by Phillip Cook, a professor at Duke University’s Sanford School of Public Policy, published in 2007 suggested that whereas 30% of Americans did not drink at all in 2001-02, 10% of Americans—or about 24m—had an average of ten drinks a day. He believes such habits would not look different today.

The Washington Post reported recently on a study which concluded that one in eight Americans meets the diagnostic criteria for alcohol use disorder, adding: “Stunningly, nearly 1 in 4 adults under age 30 (23.4 percent) met the diagnostic criteria for alcoholism.”

I think a few responses to this are prudent:

  1. Alcohol advertising should be banned in areas including billboards, print media, and television
  2. Plain packaging requirements like those used for tobacco may be prudent to try
  3. Alcohol corporations should pay a significant share of the cost of treatment for alcohol dependence and alcohol-induced chronic health conditions, and treatment availability should be greatly expanded
  4. Alcohol licenses should be experimented with, which could be revoked for those imposing risk or harm on others
  5. We should support research into less damaging substances which could play a similar social role, like the alcohol-replacing benzodiazepine David Nutt is searching for
  6. Combat the ideological dogmatism in the treatment system, including the idea that total abstinence is the only goal to pursue or that AA-style 12-step programs should be a mandatory part of treatment

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