Friday, April 27, 2012

Book Review: The Rook

It's easy to call The Rook (by Daniel O'Malley) Harry Potter for grown-ups. It is thoroughly British, about a UK institution whose job is to hide magic from the outside world, and its concealed substrate of "unreality" is just as detailed and surprising (if more dangerous and adult). Hogwarts is a school for training wizards and the Ministry of Magic is its magical bureaucracy; its counterpart in The Rook is an estate for training run by the bureaucracy of The Chequy, but it's worth noting that the school (that one, at least) isn't even given a name. This is all about running the bureaucracy, which would be mundane if it didn't deal with a constant stream of supernatural threats and powers. For those undergoing Potter Withdrawal Symptoms (who are old enough to enjoy some of the details of running an organization), this is a fine substitute.

It's worth noting where the two are different. This is about patriotism where HP was about education -- but both are best when they capture the frantic, barely controlled chaos of a "busy day at work/school." In The Rook, an adult struggles to find out who she is, while in HP the theme is finding out who you are while growing up. The Rook has more sitations that are immediate life-and-death and a far higher body count -- but it's not "about death" in the way HP is (according to JK Rowling). Rather, it may be about contingency, choice, and the power of a fresh start even in the most challenging of circumstances. People are a lot more competent in this universe (and there's nothing nonsensical like the rules of Quidditch ... ) but it's also not as wonderful and eye-widening as HP.

As for the writing, it is wonderfully chaotic sometimes and there's a surprise a page. There's some odd shifts in tone from horror to humor and back again that come across as callous, so that may be part of why it's not as endearing as Rowling's characters. So many people die that it doesn't seem to matter when they do. That said, you may be able to argue that Myfawny Thomas (the central amnesiac thrust into the day-to-day operations of The Chequy) is more of a hero than Harry Potter himself. However, there's no Hermione or Ron around to care about, and I began to miss that as well.

Fundamentally I love books like this because they give me a plausible but convoluted world to explore and imagine. I don't want to mention too much of what goes on because the surprise is part of the fun. If this is a first effort from O'Malley, there definitely should be more.

Thursday, April 19, 2012

TV News Interview on BPA

So yesterday I was asked to get up early in the morning, drive in to the local FOX news studio, and answer some questions about BPA and other plastics additives. Those are chemicals, and I'm a chemist, so I said yes. This is the result:

It's funny how much is not able to be said in that context, but I think I was able to squeak out some of the nuance to the issue. I didn't know they were going to use that particular study to open with, so what you see is my on-the-spot reaction on live TV. Hey, as long as I don't get made fun of by Joel on The Soup I think I'll be pretty happy with this result.

(By the way, the one chemical fact I really wanted to get across but didn't is that there's some good science done by Joseph Thornton in Oregon about how the hormone receptors learned to recognize their hormones, and it turns out they bind by exclusion -- that is, the estrogen receptor isn't really specific for binding estrogen, it's more that it's specific for NOT binding testosterone or cortisol or anything else -- and this gives me a little more pause that maybe BPA might be able to bind, if it's never been specifically excluded before. But I'm still only mildly cautious. We aren't all gonna die, I don't think. Well, not from BPA. The bottom line is that mechanisms of receptor development and hormone binding probably do NOT make for good TV!)

Sunday, April 15, 2012

Metal Enzymes That Multitask

Here is the heart of a metal-containing enzyme -- see how the two purple irons (marked Fe) are held in place by the network of dashed green bonds. Those iron ions are poised, waiting for a component of DNA (adenine) to bind the enzyme. When the adenine approaches, they will swiftly switch one of its protruding nitrogen atoms for an oxygen, changing the adenine into a hypoxanthine and producing nitrogen for nitrogen-needing processes.

But wait ... there's more. Some researchers (see reference below) had some trouble purifying this enzyme, and when they investigated why, they found out that it's because of an alternate activity; this enzyme does more than one thing with its iron atoms. If peroxide approaches the irons, they can neutralize it into oxygen or water by shuttling electrons around. So this enzyme converts nucleotides, and it also protects against reactive forms of oxygen. This means the enzyme has two names and two jobs: it is not just a "deaminase" (described in the first paragraph), but it's also a "catalase."

It's a useful reminder. When we ask an enzyme what its job is, we shouldn't stop when we get one answer. We should be like that kid in the Coke Zero commercial: "And ... ?" Metal ions in enzyme active sites are powerful enough to do several different things: even in the same enzyme. This is a good example of how the power of metal ions makes enzymes able to do more than we expected. What other hidden jobs are in other enzymes that we don't know yet because we haven't asked the right questions?

This also has important implications for the development of enzymes. If an enzyme can do two things at once, that gives it the freedom to tweak one of its activities while the other one keeps plugging away, earning its worth in the cell. In this way, the second activity might be able to change and do something else entirely. All because of the versatility of the iron ions at the heart of the enzyme.

Source: Kamat et al. (2011). "The catalase activity of diiron adenine deaminase." Protein Science 20:2080—2094.

Saturday, April 7, 2012

Book Review: Jesus Wars

In Jesus Wars, Philip Jenkins casts some light on a dark corner of history that has always intrigued me: the years from 400-700 AD when the Roman empire fell, the Byzantine empire continued, the creeds solidified, and Islam began to rise. This period definitely isn't Medieval -- and it definitely isn't Roman. Yet important things happened, just with a theological focus that came later to seem pedantic and hair-splitting. Of all people, Philip Jenkins is uniquely qualified to comment on this because of his work studying the development of the church in the Global South (previously reviewed here!) and the history of the rise and loss of the Eastern churches (Nestorians and Jacobites) (also previously reviewed here). The result is worthwhile to read, but a few mild disappointments keep the book from being a great one despite its desperately needed subject matter.

Much of the disappointment is an inevitable part of the accuracy of what went on: It's definitely disappointing to find the church 400 years after Jesus acting just like the church 1400 years after Jesus! Physical coercion and/or the fate of one particular ruler played major roles more than once. The theological fights turned physical. But there is some justice here. Extreme physical coercion established a "One Nature" heresy ... for two years until the Council of Chalcedon established what in my opinion was a perfectly balanced statement of theology. The result from Chalcedon is in my opinion an undeniable high point, and thought heroes are few, Pope Leo strikes me as one in originating it.

Notice the "in my opinion"s of the previous paragraph. I wish there was more of that in this book. In the final chapter I finally started to get a clear view of what Jenkins thinks about all this, but up until then the book is objective and historical, which to me is a mistake. After all, the litany of names is associated with places and heritages, sure, but also with patterns of thought, and if (as the last chapter points out) the patterns of thought are the most important thing, why don't we know more about them? This leads to some confusion on my part. The "One Will" heresy, for example, is completely opaque to me, because I can read the Garden of Gethsemane in which Jesus prays "Not my will but Thine be done." Um, I can count them there, one, two wills. I KNOW there must be more to it but it didn't make the final cut. And I wish it did.

The role of contingency is a deep question (that motivated LOST, for example!). It even shows up in sources like the science news reporting on nickel's disappearance from the oceans long ago, but when discussion of chance and history shows up in these places, it's always taken for granted that everything-runs-on-chance and life-is-fragile-and-contingent-in-an-indifferent-universe and aren't-we-lucky-to-be-here et cetera. Until the last chapter, this book adopts the prevailing attitude on contingency that is indistinguishable from the scientist who took the nickel's disappearance as a sign that life is contingent on luck and chance, or that God DOES play dice with the universe. I think Jenkins does that as a show of "professionalism" but I was constantly wishing he would take more of a different tack, like G.K. Chesterton for example. I would love to combine the accuracy of Jenkins with the big-picture, opinionated slant of Chesterton. It would definitely be more fun to be able to argue with the author! But at the very least, this book is a start. Just be warned that for the most part it's BYOI: Bring Your Own (theological) Interpretation.

Friday, April 6, 2012

O Sacrum Convivium and the Perils of Translation

The choir is singing James Biery's "O Sacrum Convivium" (words by Thomas Aquinas). It's one of those pieces that drains you: 95% of the notes for the basses are the same but to keep on pitch is like standing still in an ocean of other tones that push and pull you different ways depending on the chord. It's quite a discipline just to sing that same note! And when you're done you're physically tired from the intensity of it all. A great example of what music can do to the musician, not to mention the listener.

I'm glad we're singing it in the original Latin because the translation they offer shows the limitations of facile translation.

In Latin:
O sacrum convivium!
in quo Christus sumitur:
recolitur memoria passionis eius:
mens impletur gratia:
et futurae gloriae nobis pignus datur.

Thankfully I can't find the bad translation they had in the music itself, but it did things like eliminated the reference to the "feast", which is the whole point of the music: it's a song for when you're eating the Eucharist! But even the best translations have their limitations. Here's an average one:

Wikipedia translation:
O sacred banquet!
in which Christ is received,
the memory of his Passion is renewed,
the mind is filled with grace,
and a pledge of future glory to us is given.

There's a few things that are left out, and without knowing Latin it's very tricky. Here's what stands out to me with my half-forgotten and "intuitive" Latin translation abilities:

-- "Convivium" contains "life" (viv) within it. It is more "comes together in life" than a huge buffet line or something. With "banquet" it's easy to lapse into the same mistake the Corinthians made in making it a big party-meal (See 1 Cor. 10-11). It must involve eating -- but it's not eating to get full. It is a multiplication of life, which seems a lot simpler at heart, like the word "convivium" itself.

-- "Sumitur" means "is taken in" and has a direct connection to Eucharist and eating itself. Every bit of food is "taken in", which I think shows your involvement in the process better than the (at least in modern usage) anemic "received."

-- "Mens" is mind, yes, but is more "alive" than that. One site puts it as "the personification of thought." "Soul" in many translations fits the way we may use the word a little better, but "soul" doesn't have the rational aspect in common usage, quite the opposite, which is unfortunate. We need a word with the rationality of mind but the personality of soul. Why not just say "mens"? These "interior" words are the hardest to translate, and I'd prefer to try and sit in the way they thought than to take the way they thought and try to make it fit my categories.

-- "Pignus" is "pledge" but in my mind it always takes on a tinge of "sign" as well as "promise" (although that may be because of the "ign" in it!). I prefer thinking of it as both a promise and a sign. According to one source, it means "mortgage" as well! Obviously current promises (and mortgages) are somewhat devalued, but this is saying that the bread and the wine is the real, non-devalued promise, and the true sign pointing to the real reality of what's going on: we are feeding on the life of Christ.

Bottom line: Knowing the language allows you to see the original connotation and to think of things as "both/and" when that's appropriate and "not THAT" when that is appropriate. So learning language makes the poetry that much richer. I think Barfield's right when he says the language you use and the way you think and the way you KNOW are much more closely related than we think!

Wednesday, April 4, 2012

The Color Lecture (2012)

One of my favorite lectures of the year is when I get to talk about ANYTHING that involves biology, chemistry and physics as an introduction to a natural sciences seminar class. What to pick, what to pick ... so I pick color and talk about lots of things in a slightly revolving order. This year, topics involve:

-- Rainbows
-- Moonbows
-- Fogbows
-- The "Spectre of the Brocken"
-- Why the early stained glass makers were nanotechnologists
-- Blue people
-- Blue lobsters
-- Blue roses
-- Yellow spiders that turn purple
-- Green aphids that turn red
-- Green single-cell lasers
-- ... and to bring it full circle, protein rainbows.

Maybe next year I can do it to the tune of "My Favorite Things"?

Here it is:

Monday, April 2, 2012

Book Review: The Immortal Life of Henrietta Lacks

I've been looking for a book for biochemistry seminar that combines the issues of biochemisty and biotechnology with those of social issues and history and what it's like to be poor and sick and not understand science. I also want a book that describes science accurately and fully, makes scientists out to be real human beings (acknowledging their skill and talent while avoiding deification, or demonization, of them or their work), and also has a place for faith in the process of healing. And I'd like a book that takes an unflinching look at issues of race.

I didn't know such a book exists till I read this one. And now I know what book we'll be discussing next year in class. I don't know what scene stands out most:

-- the ingenuity of the mad scientist and practical pack-rat who first discovered that the cells from Henrietta Lacks's tumor would grow and grow and grow;

-- the harrowing descriptions of Henrietta Lacks's sickness and the toll that tumor took on her body and her family (extending years past her own death);

-- the prophetic cousin who quotes 1 Corinthians 15 and helps a worried and torn-down woman to lay down her burden with prayer and speaking in tongues (pracitcally an exorcism in the middle of a popular science book!);

-- the beautiful art of DNA that calms a man who was angry from birth;

-- the amazing power of the cells that would grow on motes of dust and invade other cultures causing millions of dollars in damage;

-- the moral murkiness of the scientists who took/stole the cells in the first place and who perhaps deserved to have millions of dollars of damage done to their work ...

... but my favorite scene must be when the white science-book author is suddenly called upon to preach in an African-American (probably AME?) church, ending up describing HeLa cells to a chorus of "amen"s and "hallelujah"s. The author is not independent from this book -- the author herself is drawn into it and changed by it.

Henrietta Lacks lives! READ THIS BOOK. It has my highest recommendation.