Sunday, January 24, 2010

When radiation misfires...literally

The New York Times has a rather chilling account of how radiation overdose in the treatment of some cancer patients caused deadly side effects leading to death. The entire sobering article deserves to be read. In one case a man's tongue was going to be selectively irradiated; instead his whole face received a blast of radiation that led to a horrible, slow death. His story makes for very painful reading. In another case, misguided radiation beams literally cut out a hole in a woman's chest that gradually killed her.

And all this mainly because of computer errors that were not detected by human beings, errors that caused the radiation to be overdosed or misdirected. Seems like one of those classic "technology is a double-edged sword" kind of scenarios with the whole system just becoming too complex for human understanding. In one instance, a wedge in a linear accelerator delivering the radiation was supposed to focus the beam in the "in" position. But the computer that used Varian software- the same software that I used in grad school for operating the NMR spectrometer built by the same company- made a mistake and instead pivoted the wedge to the "out" position, removing the radiation shielding. The mistake was not detected 27 times, leading to acute radiation overdoses in the wrong parts of the body. In the case of the man whose tongue was supposed to be treated, an error in the software failed to save the critical settings for the accelerator which would have focused the radiation to the right parts.

The statistics unearthed by the Times are startling. From 2001 to 2009, more than 600 cases of improper radiation treatment were reported. Out of those, 255 were related to an overdose, while 284 were related to the wrong parts of the body being exposed to radiation. Even in its idealized form radiation has side-effects, so one would assume that doctors and technicians would be deathly serious about operating these protocols. These statistics were collected for New York State, which is apparently supposed to have some of the strictest radiation standards in the country.

What is even more shocking is the lack of transparency due to "privacy laws". Names of the culprits have been withheld, and some of them seem to have been let off the hook with a simple reprimand. Some doctors who have participated in the treatments refused to talk to the journalists. There also does not seem to be a single agency responsible for these radiation safeguards. On top of it all there seem to be scant ways for patients to pick beforehand which hospital they would like to receive radiation treatment in, since records of mistakes are not available to the public. The whole shebang sounds appalling.

Now I understand that 600 cases in 8 years is probably peanuts compared to the total number of cases in which radiation has worked successfully. Nonetheless, the factors responsible for the lapses and the horrendous consequences deserve scrutiny (seriously, death due to "computer error" sounds like something out of a bad science fiction horror movie). For something as serious as radiation treatment for cancer, one would assume that the same kinds of safeguards, fail-safe mechanisms and backup checks would be in place as are used in nuclear reactor safety. Yet it seems that shoddy training, computer error, and lack of accountability are dealing out death and enormous physical and psychological suffering to patients and their families.

Labels: , ,

Friday, January 22, 2010

Is a book refund a "bribe"?

So here's an experience I had with an Amazon used book seller named "Booxygen". I had ordered a book from him and the book arrived on time. However the book's spine was detached about halfway down the middle. Problems with the spine constitute probably the most serious problems you can encounter with a book. So I wrote a lukewarm review on Amazon in the "seller feedback" section complaining about the spine.

About two days later I get an email from Booxygen. While they apologize for the problem, they also make me an intriguing offer. They say that they will refund the price of the book if I take back my negative review and either write a positive review or no review at all.

Now I know this sounds reasonable and is probably the norm for most book sellers, but in my view, such an offer clearly constitutes a "bribe" for a simple reason. Reviews are supposed to attest to the quality of a particular bookseller. Consider what happens if I accept Booxygen's offer. While my money is refunded, because I don't write a negative review, future buyers like me who are planning to buy from Booxygen never get to know that I was shipped a defective item. The whole purpose of reviews is to accurately represent the quality of a bookseller's service, warts and all. A failure to write an unfavorable review or the misrepresentation of such a review clearly misleads future buyers.

Thus, while it sounded reasonable, I regarded Booxygen's offer as a bribe. My reply somehow got buried in the drafts section of my email. I discovered it three months later and emailed Booxygen a deal which to me sounds much more honest; mail me a good copy of the same book and I will gladly take back my review and write a new favorable review for the book. Regrettably, Booxygen sent me a very rude reply saying that they refuse my suggestion and that I should not do business with them again. I am glad they said this themselves because I am pretty sure I won't feel the need to buy from them again. In addition I am quite sure I am not going to accept such a bribe from other booksellers; if you want good reviews, sell me good quality products. It's that simple.

Labels: , ,

Friday, January 15, 2010

Haiti

I am planning to donate money to the earthquake relief effort in Haiti. As usual I want to make sure the money is actually used promptly and through the right channels. Any thoughts on which organization it would be best to donate to? Candidates include Partners in Health, the American Red Cross, Doctors without Borders, the White House and musician Wyclef Jean (in many of these cases you can simply donate by texting; the amount will be added to your mobile phone bill)

Labels:

Thursday, January 14, 2010

Book reviews: A hawk, a dove and the missile man of America

Two books on the Cold War

1. The Hawk and the Dove: Paul Nitze, George Kennan, and the History of the Cold War - Nicholas Thompson

In this book, Nicholas Thompson provides a fascinating account of the life, times and work of probably the two most important American diplomats of the Cold War. George Kennan and Paul Nitze were starkly opposite in many respects, yet both provided immensely important direction to American geopolitics through their advice to many Presidents and shaped the Cold War more than any other two American policy makers.

Of the two Kennan is the more famous and is regarded by many as the most important American diplomat of the twentieth century (he passed away in 2005 at the ripe age of 101 and was known for the resplendent prose in his many books which I could strongly recommend). Kennan is mainly known for a famous 1946 telegram that he sent from the Soviet Union. At this time Americans were still trying to understand the looming Soviet menace and Kennan was probably the most knowledgeable Soviet expert in the country. He rightly understood Stalin's bluster and sent a telegram describing the intentions and nature of the Soviet state. The telegram instantly catapulted him to recognition and set in place the official policy of "containment" which Kennan's name became synonymous with. In the telegram Kennan indicated that the Soviets would respond to only strength and not reconciliation and weakness. In his book on the hydrogen bomb, Richard Rhodes says that it was this telegram along with Churchill's "Iron Curtain" speech and Stalin's rousing speech in Moscow that inaugurated the Cold War.

However Kennan did not advocate necessarily employing military strength. This was advocated by Paul Nitze, a man who may not be as famous as Kennan but who was no less important. Nitze is regarded by many as the "father of threat inflation". As a measure of his influence as a hawk, it suffices to realize that many of the neo-conservatives in the Bush administration were either Nitze acolytes or acolytes of Nitze's proteges. Just like Kennan Nitze also became famous for a secret 1950 document called NSC-68 that advocated the use of preemptive force against the Soviets and exaggerated their military might. This was a pattern that Nitze and his growing band of followers (among them in various ways were Albert Wohlstetter, Richard Pipes, Richard Perle, Paul Wolfowitz and Donald Rumsfeld) would consistently pursue; whenever they thought that liberals were trying to be too reconciliatory toward the Soviet Union, they would prepare documents and advocate polices exaggerating Soviet military potential and intentions. Their policies frequently worked and became especially influential during the Reagan administration (formerly they did a good job of portraying Carter as being weak on the Soviets). To some extent they were responsible for the dangerous arms race between the two nations.

Needless to say, such hawkish views radically differed from those of Kennan the dove whose more measured opinions fell somewhat out of favor in later years. Yet the book does an outstanding job of showing that the agendas of both men were more subtle and complicated. Occasionally when it was necessary Nitze would take a softer approach, and during the later Reagan years he joined the President in pressing for open disarmament and reconciliation when many of his followers continued to take a hard line. In his later life Nitze mellowed down, and in 1999 went so far as to write a New York Times op-ed recommending unilateral nuclear disarmament for the US. Although Nitze rightly perceived the work that he had done to be very important in dictating Cold War policy, it is tragic that unlike him, others did not have the sense to see the shortcomings and detrimental effects of these policies in a post Cold War world (Nitze and the accompanying rise of the neo-cons are very well-documented in J. Peter Scoblic's
"Us vs Them: How a Half-Century of Conservatism Has Undermined America's Security").

With such differing perspectives one would think that Nitze and Kennan would have been mortal enemies. But remarkably, through several decades of acute differences and disagreements, the two men remained close personal friends. As Thompson who is Nitze's grandson shows, it is a mark of the character of both men that they managed to rise above their political differences no matter how severe these were. Thompson shows in this highly readable volume, the tremendous impact on US foreign policy that the work of Nitze and Kennan had. He bring both of them to life and sensitively and wisely dissects their personalities, thoughts and lives. Very strongly recommended for foreign policy/Cold War enthusiasts.

2. A Fiery Peace in a Cold War: Bernard Schriever and the Ultimate Weapon- Neil Sheehan

Neil Sheehan apparently spent 15 years writing this account of a little known Air Force General, Bernard Schriever, and the time he spent on the man shows in this comprehensive account. He has performed a very valuable service in bringing this rather obscure character to life and driving home the importance of his accomplishments. Schriever was one of the individuals most responsible for jump starting the US's missile program, especially shepherding the development of the ICBM. Sheehan does a great job bringing to life all the characters that Schriever was associated with, from his mentors in flight school (including General "Hap" Arnold) to his bete noir, the notorious Curtis LeMay, to his contact with brilliant scientists John von Neumann and Edward Teller whose contributions were critical for America's missile and atomic bomb programs.

Sheehan provides ample background and little known tidbits of Schriever's life and times. For instance I was not aware that the US Air Force was a rather inefficient backwater organization till the mid-1930s, easily outclassed by its European counterparts. Apparently at one point, pilots were asked to deliver the mail in the wake of a post office scandal. Their inexperience in flying and the loss of life that resulted galvanized FDR and others to issue directives for a modern Air Force that would become among the best in the world.

The main problem I have is that while Sheehan's digressions (for instance on the atomic bomb project and Soviet espionage) are fascinating and reflect the most up-to-date information, they are too many and too frequent. An editor who could have shaved off a few pages and encouraged a tighter narrative would have definitely helped. The digressions draw your attention from direct information about General Schriever. To be fair the book is not supposed to be just about him, but a little less meandering would have been a boon.

In spite of this deficiency, the book will be fascinating for Cold War enthusiasts who want to know about the development of the US Air Force and its atomic and missile arsenals during the early Cold War. There is also a fair amount of technical detail about missiles explained in relatively plain and accurate language. After JFK came to power Schriever's influence waned and the latter part of the book is not as interesting. Nevertheless, Sheehan has done a valuable and outstanding job in bringing a little known individual to life and telling us about his enormous contributions during a critical period of American history.

Labels: , ,

Tuesday, January 12, 2010

Particle or nuclear?

This is interesting. A Tehran University physics professor has been killed by a bomb planted outside his home. There is speculation whether this could be the work of outsiders, especially from Israel or the US.

To me the accusation that this was an Israeli operation seems anything but far fetched. After all there has been ample talk of the Israelis bombing Iran's nuclear facilities the way they did with Iraq's Osirak nuclear reactor in 1980. But any such action would likely cause immense international outrage and political problems for Israel, not to mention added Arab animosity. Thus from their perspective the next best option would be to do something like this, assassinate someone who was playing a key role in the nuclear program with the hope that it would at least slow down Iran's plans and intimidate them.

The trouble is that until now the specialty and role of the assassinated professor is not known. As the NYT reports,
There was some dispute about his field of scientific specialization.

The English-language Press TV said he taught neutron physics at Tehran University, although it was not clear whether he was part of Iran's contentious nuclear enrichment program.

The broadcaster called the professor a ?staunch supporter of the Islamic Revolution? of 1979 that overthrew the Shah and initiated three decades of theocratic rule.

But two Iranian academics, who spoke in return for anonymity because of the sensitivity of the issue, said in telephone interviews that he was not a nuclear physicist and had specialized in particle and theoretical physics. The Web site of Tehran University lists him as a professor of elementary particle physics.
Now that's silly. A professor who teaches neutron physics would likely know a lot about nuclear reactors and bombs; in 1939, the greatest expert in neutron physics in the world was Enrico Fermi, probably the most important physicist working on nuclear energy. Everyone should know that it does not matter much whether the dead professor's field of specialty is "nuclear" or "theoretical and particle" physics since it is quite easy for a particle physicist to learn nuclear physics and vice versa (even the movies seem to have understood this; in the George Clooney-Nicole Kidman blockbuster "The Peacemaker", the scientist working for the bad guys is an astrophysics PhD.)

Thus the unfortunate man's specialty by itself does not at all preclude him from working on the nuclear program. Only time will tell what his exact role was.

Labels: , ,

Friday, January 08, 2010

A biochemical parody of Bryan Adams

For some reason when I was in high school Bryan Adams was big, and we used to listen to his songs all the time. These days I find many of his songs too sappy, but I still love some of the melodies and find myself going nostalgically down memory lane when "Summer of '69" or "Everything I Do" or "Cloud Number Nine" wafts on to the air from somewhere.

So yesterday I happened to be looking at a particularly ravishing picture of dihydrofolate reductase (DHFR) and Adams's "Have You Ever Really Loved A Woman" randomly started playing on my iPod and Bam! The two topics meshed together in an ungodly union. So here is my tribute to Bryan Adams with profound apologies...an ode to that perfect protein which we can only covet. Chemically inclined folk will appreciate this more but others should also be able to smack their forehead. The original version is copied first to mitigate the trauma that will follow.

HAVE YOU EVER REALLY LOVED A WOMAN

To really love a woman
To understand her - you gotta know it deep inside
Hear every thought - see every dream
N' give her wings - when she wants to fly
Then when you find yourself lyin' helpless in her arms
You know you really love a woman

When you love a woman you tell her
that she's really wanted
When you love a woman you tell her
that she's the one
she needs somebody to tell her
that it's gonna last forever
So tell me have you ever really
- really really ever loved a woman?

To really love a woman
Let her hold you -
til ya know how she needs to be touched
You've gotta breathe her - really taste her
Til you can feel her in your blood
N' when you can see your unborn children in her eyes
You know you really love a woman

When you love a woman
you tell her that she's really wanted
When you love a woman
you tell her that she's the one
she needs somebody to tell her
that you'll always be together
So tell me have you ever really -
really really ever loved a woman?

You got to give her some faith - hold her tight
A little tenderness - gotta treat her right
She will be there for you, takin' good care of you
Ya really gotta love your woman...

Then when you find yourself lyin' helpless in her arms
You know you really love a woman
When you love a woman you tell her
that she's really wanted
When you love a woman
you tell her that she's the one
she needs somebody to tell her
that it's gonna last forever
So tell me have you ever really
- really really ever loved a woman?

Just tell me have you ever really,
really, really, ever loved a woman? You got to tell me
Just tell me have you ever really,
really, really, ever loved a woman?


HAVE YOU EVER REALLY LOVED A PROTEIN

To really love a protein
To understand her - you gotta know her deep inside
Hear every helix - see every sheet
N' give her energy - when she wants to jiggle
Then when you find yourself staring helpless at her domains
You know you really love a protein

When you love a protein you tell her
that she's really conformationally correct
When you love a protein you tell her
that she's catalytically perfect
she needs somebody to tell her
that her half-life?s gonna last forever
So tell me have you ever really
- really really ever loved a protein?

To really love a protein
Let her hold your high-affinity binders-
til ya know how she needs to be crystallized
You've gotta mass spec her - really sequence her
Til you can feel her atoms in your spectrometer
N' when you can see the unformed hydrogen bonds in her pockets
You know you really love a protein

When you love a protein
you tell her that she's really evolutionarily conserved
When you love a protein you tell her that she's peptidase-digestion preserved
she needs somebody to tell her
that her fold will always hold together
So tell me have you ever really -
really really ever loved a protein?

You got to give her some metal ions - hold her co-factors
A little pH-control - gotta treat her ionization state right
She will be there for you, takin' good care of your ligands
Ya really gotta love your protein...

Then when you find yourself staring helpless at her PDB coordinates
You know you really love a protein
When you love a protein you tell her
that she's really conformationally correct
When you love a protein you tell her
that she's catalytically perfect
she needs somebody to tell her
that her half-life?s gonna last forever
So tell me have you ever really
- really really ever loved a protein?

Just tell me have you ever really,
really, really, ever loved a protein? You got to tell me
Just tell me have you ever really,
really, really, ever loved (that helical, sheety, hydrogen bondalacious) protein?

Labels: , , ,

Thursday, January 07, 2010

Barbara Crossette is a computer (and she almost fails the Turing test)

That is the delightful conclusion I have drawn after having read her appalling "critique" of India in "Foreign Policy". Crossette seems to have been assigned a rather easy task fit for a search engine- trawl the internet and gather as many negative statements about India as can fit in a two page writeup. Even in this endeavor her failure seems to be laughably transparent.

Both Manasi and Nitin do excellent short work of the article so there's not much I can add. Among Crossette's most egregious transgressions are accusing India of being something of a rogue nuclear power who has not signed the NPT. Crossette blithely ignores India's impeccable non-proliferation record, its highly admirable success in the peaceful uses of atomic energy (India's thorium program has been praised by nuclear analysts worldwide) and the structural problems that have kept the NPT from being definitive and effective since its conception. And of course, with North Korea and Pakistan around, India should be a meek footnote when it comes to nuclear proliferation in South Asia. Perhaps Crossette conveniently forgets (or more probably ignores since it does not fit into her assumptions) that India has not been part of the China-North Korea-Pakistan club, members of which have regularly slapped quality control stamps on each others' missiles and bombs and in addition exported them.

Nor does Crossette's article hold even nanoliters of water when she accuses India of meddling in climate change legislation. As noted, India's emissions profile is significantly below the world average and it has made a commitment (non-binding perhaps but commitment nonetheless) to 20-25 percent reductions. Plus, India's achievements in nuclear power can have a very positive impact on reducing emissions. And of course the US is never out of practice when hypocritically preaching to the rest of the world to reduce greenhouse emissions while flying high on its own.

Crossette's criticism that India is "hardly a liberal democratic paradise" seems to be an exercise in making pithy, simplistic, misleading statements. Sure, incidents like the banning of James Laine's book on Shivaji sound discouraging, but these incidents are few and far in between compared to the big picture. In the bigger picture, India has survived probably the greatest assault of diversity, chaos and disagreement among its politicians and citizens of any country to remain a successful democracy, notwithstanding the serious flaws. The press in India is among the freest in the world (so free in fact that we have to berate journalists for being loose cannons who could endanger national security), the internet and other public forums in India are vigorously argumentative and even though taking offense to trivial things has become a fashion in our country, everyone is free in turn to take offense to taking offense and vociferously voice their opinions. One would be hard pressed to find a developing country where such robust and cantankerous debate exists amidst so much diversity and flared tempers.

Did Crossette sleep-walk through her tenure as a New York Times journalist in Delhi? Maybe it is another growing sign of the New York Times's waning days and their increasingly shoddy journalistic standards.

With such a fanfare of cherry picking and misleading statements, Crossette claims that India is the "elephant in the room". She needs to think twice if she plans to assault it with a spear, since if she does so she is almost certainly going to run straight through this invisible entity and smack her head on the wall. That should give her the "headache" which she thinks India is.

Labels: ,

Saturday, January 02, 2010

Almost back

I have been in Tasmania for the last three weeks visiting family, enjoying sunny weather while my home in the northeast faced the wrath of the Norse gods. Back next week for a new year of bloggity bloggings.

Happy New Year