28 May 2011

People who are not in our league VII

Jin8 plays tetris. So fast is he that being able to see the blocks already on the board appears to be just extraneous. That hypothesis is confirmed when the blocks turn invisible (at 5 minutes in) and he just keeps on playing.

People who are not in our league VI

Fabrice Bellard wrote jslinux, Javascript that emulates an x86 processor and boots a working Linux kernel.

As if that weren't impressive enough, the hosted filesystem includes a C compiler... that he wrote himself... and a partial emacs clone... that he wrote himself.

Bellard was also responsible for ffmpeg, QEMU, and what was (at the time that it was released) the fastest known algorithm for computing digits of pi.

Movie roundup

Recent movies, in descending order of enjoyableness:

Ip Man. Semi-biographical account of the life of Ip Man, the grandmaster of the Wing Chun form of martial arts who taught Bruce Lee. Donnie Yen is pretty much the embodiment of unadulterated badassery. Excellent fight scenes. Recommended.

Source Code. Not only an entertaining thriller but also somewhat moving (which I did not expect). Don't take the science seriously and you will enjoy the movie a lot more for it. It's well executed and the characters and their interplay are very likable. Recommended.

In The Shadow of the Moon. Documentary about the Apollo missions, as told by the Apollo astronauts. Really brings to life the political and social climate of the time. I watched the JFK footage and I could not tell if he was a visionary, or insane. Also, sometimes we forget that, yes, some astronauts did die so that we could go to the moon. Recommended.

The Rock. Classic action movie, and one with heart.

Contact. It does have its moments of awe, but the cheesiness is way overdone.

Con Air. Everyone in this movie seems to play a caricature of himself, which gets tiring very quickly.

District 13: Ultimatum. I enjoyed the original District 13 (the parkour scenes are something to behold), and had been looking forward to the sequel. Unfortunately Ultimatum is just ridiculous and nonsensical in alternation.

The Taking of Pelham 123 (2009). Empty and unexciting.

27 May 2011

The Immortal Life of Henrietta Lacks

The Immortal Life of Henrietta Lacks, by Rebecca Skloot, is the biography of the poor black woman whose cancerous cells were taken from her (without her knowledge or permission) and which subsequently became the first line of human cells to be successfully grown in vitro. Lacks died in 1951 but the HeLa line of cells, descended from the cancerous cells in her cervix, live on in labs around the world.

There is some science background/history in this book, but it is primarily the story of Lacks and her family as well as a story of the history of medical ethics. Shockingly, as recently as the 1950s, doctors frequently withheld critical information (such as, oh, a diagnosis) from their patients, for fear of upsetting them. Black patients like Lacks were the least likely to be given all the facts. Given the lack of respect in the doctor-patient relationship then, it does not seem quite so surprising that when Lacks went to Johns Hopkins for cancer treatment, doctors dared to take and store samples from her tumor for use in experiments without even asking for her consent.

The discovery that HeLa cells were actually capable of reproducing in culture medium (outside of the body) sparked a revolution in medicine. Suddenly you could perform experiments on human cells without having to perform experiments on a human. HeLa became part of the standard arsenal for research studies involving human cells. HeLa cells were used to test the first polio vaccine; they have been used to test the effects of carcinogens, drugs, zero-g environments, and more on human cells. By 2009, research done on HeLa had led to the publication of some 60,000 research articles.

And yet, for about twenty years after Lacks's cells were taken from her, by which time they were already routinely in use in labs around the world, Lacks's children had no idea that any of that was happening. Understandably, they became quite upset and paranoid when they finally learned what was going on. The irony of this story is that while Henrietta Lacks's cells have produced scientific research of untold aggregate value, her descendants are still too poor to afford decent health care.

In researching for this book, Skloot definitely crossed the traditional boundary between author and subject. She worked closely with Henrietta's youngest daughter, Deborah, and helped her to learn about her family's history, unravel what it was that had actually happened to her "mother cells," and assuage many of her concerns. Lacks's descendants were relatively poor and uneducated, and this book could easily have crossed the line into sounding patronizing, but it doesn't. Skloot has done an admirable job in not just identifying but creating the human story here.

This book is both thought-provoking and captivating; recommended.

Review ends here; only moderately thought-out speculation begins. IANA doctor or medical researcher.

Reading The Immortal Life of Henrietta Lacks, you can see that the medical institution has come a long way since the 1950s, but as a society we still don't have a lot of the answers for how to deal with the use of donated human biological products (tissue, usually) in medical research. One positive change is that the idea of requiring "informed consent" is now widely recognized and standardized. But patients do not have a great incentive to actually donate their biological products to research, because the vast majority of samples are worth approximately nothing, except as part of a larger collection, and donors receive no other benefits. (It doesn't help that in Moore v. Regents of the University of California the Supreme Court of California ruled that once a biological product is taken from your body, it is no longer yours; therefore, in order to profit from its use you would have to have the extraordinary foresight to come to some agreement with the hospitals/researchers before you donated the sample.)

There are a number of proposals to compensate donors of biological products, e.g. with reduced health care costs, or money paid out of a pool funded by pharmaceutical companies. I think some of those are good ideas. But what may be interesting to try here is some sort of analogue to a Creative Commons license: something drafted by lawyers, similar to all the pre-written legal documents or software licenses you can get today, that would provide various stipulations that ensure that research and IP derived from a patient's particular biological sample meet some standard of public accessibility. As Skloot points out, what many donors really want is not remuneration (especially since only an exceedingly small fraction of single biological samples are worth anything anyway) but the knowledge that the fruits of research done on their donations are available to the public and to other researchers, rather than staying in some freezer because no one is going to pay some exorbitant fee for an unknown sample. HeLa itself revolutionized medicine because it was widely distributed, and that only happened because it hadn't occurred to anyone to patent cell lines in the 1950s.

Donors are going to have to be the ones to fight for the public interest, but they don't really have any leverage unless they show strength in numbers.

24 May 2011

Mastering Regular Expressions (O'Reilly)

Many programmers use regular expressions frequently, but most of us can go for months, if not more, between the occasions when we really need to understand what the heck the regex implementation is doing.

For those times when you actually need to know, Mastering Regular Expressions, by Jeffrey Friedl (ebook version available on O'Reilly) is the book you want to have read. It does discuss various regex features, but you can usually find the same info in the API docs for the language bindings you're using; the real meat of this book is its clear discussion of regex engine implementations.

When you want to answer such questions as "Why is the regex engine matching the string P, and not the different-but-equally-valid match Q?" or "How can I make this regex code faster?", then it really helps to understand what's going on under the hood. NFAs, DFAs, state machines, and all that good stuff are covered here, but with many more practical notes than appear in your college compilers textbook.

Recommended... if you're into this sort of thing.

05 May 2011