Tuesday, July 31, 2012

Book Review: The Colors of Hope

It's weird to review a book by the pastor you've heard preach for 500+ hours over the past decade and a half. So I approach The Colors of Hope by Richard Dahlstrom with the two sides of familiarity: sure, I've heard a lot of it before, but it's really cool to see people you know in a book! This book actually has more new stuff to me in it than Richard's first book did, mostly as expanded conversations with people in my church, which is an excellent direction to go in for a book (and should continue to bear fruit for future books). It's these extended conversations that really make this book shine, including one with the married couple who runs Seattle's Taproot Theater, and one with Richard's own dead father. It's a bit of a limb to go out onto, but it works, or perhaps I should say, it holds. Plus, I love the cover art. This book captures more of Richard's style than the last one, perhaps because it has more of other people in it? Lots of good paradox there.  

Sunday, July 29, 2012

Batman vs. The Avengers

Would everyone's reaction to this summer's movies be different if the release dates were reordered? I have some personal evidence that may be so. Finally saw The Avengers last night and The Dark Knight Rises earlier this week, so I saw them in reverse order; and I think the Batman movie is definitely the better movie, plus the better use of my money according to my Official Rule of Movie-Going (Is it worth the $10?). The hive mind that is Rotten Tomatoes thinks The Avengers is better, but of course I know I'm right.

The Avengers did everything it was supposed to, and that's part of the problem. It didn't do a single thing I didn't expect, at least not between the "not-a-submarine" moment and the shawarma joint scene (what, you didn't wait through all the credits? Tsk tsk.). All the repartee was witty, all the internal and external fights were exactly what they should have been, and there were about 500% more laughs than TDKR. The climatic battle was long but not too long. And the real moral center of the movie was Captain America, not Iron Man (was this the real "fight" of the movie?). Most importantly and most impressively, Hulk was done right, which is apparently about as hard as balancing an egg on its end.

Maybe it was this proficiency and tidiness that decides the balance for me. TDKR never hit the pervasive bone-rattling sense of dread that the previous Dark Knight did, but it didn't need to: that's what the Joker feels like, and Bane feels different. Bane as a villian has always felt messy and half-baked to me. After all, Bane's claim to fame is physical prowess, messing things up, rather than pure psychological terror. In the same way, TDKR was satisfyingly messy -- at least for a Christopher Nolan movie. It's Nolan's version of a Dickens tale, and he knew it too, because he put in all those Tale of Two Cities references (there's not really any references like that in The Avengers, beyond Tony Stark's glib name-calling).

In feel, TDKR was a touch warmer than Inception (which just means it was a few degrees above absolute zero, but it does means I could actually relate to some of the characters, like Blake) and it had a nice solidly directed sequence for the part when the Dark Knight actually rises. That and other images stick with me, most spoiled by the trailer but a few not. The Scarecrow's courtroom is just the right mix of absurd and perverse, for example. And the pacing and intercutting at the end is arguably finer filmmaking, technically, than anything found in The Avengers.

I was going to say TDKR doesn't reward thinking about it, but that's not quite right. It does indeed reward thinking about it, because finding the plot holes and imperfections has the same kind of satisfying pop as popping bubble wrap. There's lots to find, but it's kind of fun to do it, and it doesn't ruin the movie for me. Finding TDKR's flaws is part of the experience, because the flaws that are there are put there by Nolan's vision. At least Nolan is adapting someone else's mythology to his vision, and has several storyline innovations in the movie, as in how Bane maintains his power over his minions and how Batman's back is broken. (By the way, notice how Bane's mask is Batman's inverted? That's a Nolan innovation, not in the original.) Whedon follows the known Marvel Universe too closely and that may be why I wasn't surprised at all by his vision. I've already seen his movie in panels on pages.

It comes down to the fact that I'd rather have a more flawed movie that deviates from the comic universe than to have a perfect movie that fits in exactly with the comic book universe I already know. Nolan's vision is imperfect, but it's HIS vision. Whedon's vision is Marvel's familiar vision, so I was slightly bored by it, and by what it has to say.

Conclusion: if I'm the ref, Batman wins.

I wonder what this says about the Spiderman movie I haven't seen yet?

(One final note: This is nothing against Whedon, who co-wrote The Cabin in the Woods: my favorite movie I have seen in a theatre this year. I love Whedon's style, skill with characterization, and way with a one-liner, but maybe again, I'm too familiar with it already.)

Friday, July 27, 2012

The Periodic Table of TV Shows

Because I have a rule that I must post all periodic tables I find:

Thursday, July 26, 2012

The Van Gogh Painting Hidden in the Sun's Corona

Quick question: Is the sun solid, liquid, or gas? I know, trick question ... it's none of the above, mostly being composed of plasma, a fourth state of matter beyond the typical three terrestrial states. Being its own unique state of matter, scientists are going to study it, and even something as simple as watching it heat up and cool down can yield unusual beauty.

Here's a picture of how the temperature of the sun's plasma changes:

Here's a video of how they did it:

And here's links to previous entries on the blog about how an islandthe ocean and dominoes can look like Van Goghs, with various degrees of intentionality. Apparently since this is the fourth post on this kind of things, I need to create a category for "Van Gogh" in my labels section.

Wednesday, July 25, 2012

Angel's Glow, Under a Microscope

Sometimes the same science story can look very different depending on how you tell it. Instead of angels, you find worms. But that's not necessarily a bad thing.

This is what happened with "Angel's Glow." The Civil War caused a Judgment Day's worth of carnage and flesh wounds. Army doctors noticed that some soldiers' wounds glowed with a faint blue light, and that these wounds were almost always clean from infection. They called this the Angel's Glow of protection, and no doubt were thinking of angels that did it.

When science looked into the story it found no little dancers on the ends of pins, although it did find something that could dance on the end of a pin if so inclined. It found tiny "bugs," microbes that contained the glowing blue light. Science named these microbes Photorabdus luminescens, and you can find out all about them at their Microbe Wiki page (I did not know such a site existed, but it sure makes sense). That site has a nice picture of the blue glow coming from waxworms infected with Photorabdus:

Part B shows the same bacterium inside a different worm, Heterorhabditis bacteriophora. (Yes, I know it's green, not blue: they "painted" it that way with a green-glowing protein, so that shows what happens when you mix biological glows, I guess.) The interesting thing about this infection is that it's actually good for the worm. Photorabdus likes to be the only bacterium on the block, so it has developed an arsenal of potent and creative antimicrobial molecules that it lobs around the environment, taking out most other bacteria. Heterorhabditis apparently doesn't mind the antimicrobials, because they destroy bad bacteria that might infect it. So the worm has made a handshake deal with the bacterium: I'll give you a place to live (and a set of wheels to get around) IF you'll take out the other bacteria. And it seems to work very well, because Photoradbus is able to kill a lot of other things. It's an effective little bug, it just needs a worm to give it a ride.

Gardeners apparently use this worm all the time to kill ants and other insects. Now we know that this works because of the "Angel's Glow" -- the worm spreads the glowing bacteria around the garden and it goes its little glowing way, spreading insect death and destruction while sparing the life of its wormy host. Photorabdus even likes to take two forms, one of quiet little colonies inside the Heterorhabditis worm-car, but then it transforms into Superbad-Bacteria when it gets into the insect. A fascinating transformation, found in other small organisms like Malaria. I'd love to know more about how that happens at the protein level.

So how should this story be told? The blog post that first alerted me to it is titled "Worm Kills Insects by Vomiting Hulk-Like Bacteria." Well, that would work a little better if the Hulk were blue, but it was good enough to attract my attention. My thoughts on reading it is that the blog tells its story explicitly, in vivid, gross terms, dwelling on what a horrific death it must be for the insects. Ok, that's true but it's an editorial emphasis. I also found  happy gardeners, worms, and soldiers in the story. The horrific death is occurring to some organisms that have a pretty bad effect on the environment (whether they would be killing a soldier or ruining a garden given the chance). If you're pro-insect you can lobby against this process but I'm not so sure it's a bad thing for the pro-human people among us.

What this really is, is a case where the story reveals something about the storyteller. The storyteller can't help but put himself into the story. The story itself is a complex and networked mix of good and bad. It's gross but it's also beautiful, with the image of glowing wounds protected from further harm. It's something that has been harnessed by human ingenuity (and before that, by biological ingenuity) to create and maintain order. So you can talk about it with images of death and vomit, and I'll talk about it with images of well-manicured gardens and fathers who could return to their families because of a mysterious, ethereal blue glow. You may see demons-- but I see angels. It's all in the looking. (... when he looked up, he saw that the hillside around Elisha was filled with horses and chariots of fire ...)

And who's to say angels AREN'T there? After all, haven't you ever seen The Ten Commandments, with its depiction of the Angel of Death? Looks pretty familiar to me ...

Saturday, July 21, 2012

Book Review: Worlds Apart

The Owen Barfield reading tour continues with Worlds Apart, written by Barfield as a "dialogue" between several academics with different philosophies. Two are clearly anthroposophists like Barfield, and the rest represent different disciplines ranging from physics to psychology. I'm trying to decide if this book is a good entry point to Barfield or not. It does focus on science and the back-and-forth of the many objections to Barfield's ideas. The dialogue format of Worlds Apart plays to Barfield's experience as a lawyer, and about 1/3 of the way through there's an extended Socratic dialogue that may be the best entry to his philosophy that I've seen. The problems include a section of extended Steiner-worship at the end and a definite feeling that the other characters are straw men.

What I'd really like to see is an extended dialogue between Barfield and C.S. Lewis, which I know actually happened because Lewis alluded to it in his famous description of Barfield as his "second friend." There's a book of Barfield commenting on Lewis, and that may be the next stop on the tour.

One of my constant questions would be what Barfield would make of the analysis of DNA words that I'm thinking about right now to reconstruct the ancient words. On the one hand, that's exactly what he did with English words, and he argues at the end of Saving the Appearances that evolution and Christianity naturally cohere. On the other hand, English words are a way of looking at the human mind, while DNA words are not, because these words were never formed by the human mind, and there's also that little bit about Barfield saying the past "never happened." But this passage near the end of Worlds Apart finally resolves it for me:

"Brain, heart, liver, spleen have been built into your body by the world, by the whole history of the world, and if you 'study' one of them in that intensive way, you have access to the relevant period of world-history. Access, first of all, to the building that was going on before your birth and, through that, back into their remoter phylogenesis."

"You see -- or at any rate I have argued -- that if evolution has indeed been fundamentally the evolution of self-consciousness, there cannot be that sharp break between ontogenetic and phylogenetic development, which the positivist picture of evolution assumes. The one must merge gradually back into the other." (p. 195-196)

Of course, right after this high point is when the book really goes off the deep end, with too much Steiner and too little anyone else. (Maybe even too little Barfield!) However, that part is written as a collection of unconnected observations, almost like appendices, and so I think even Barfield saw some of that as outside the necessary argument he was making. I'm starting to separate the wheat from the chaff here and I think there's a way to adapt some of the ideas of Barfield in a way that takes the good and leaves the bad. In particular, I think Tolkien ultimately did that and such an adaptation accounts for some of the strength of The Lord of the Rings. Is there a way to do that with the data collected by current biology rather than the ancient Norse sagas? I'm not sure. Stay tuned.

Thursday, July 12, 2012

If a Philosophy Network is Based on Wikipedia and It Doesn't Illuminate Anything, Does It Exist?

I was excited when I saw that someone had made a graph of the influences among philosophers, but I'm a little less excited after looking at it. First, the graph, which is cool enough -- you'll have to click on it to see anything but "Plato" probably -- but then the reasons for my mild disenchantment:

This graph was constructed according to the "influenced by" section for philosophers on Wikipedia, by the method here. That's a pretty nifty (and easy) way to get a graph. But I'm not convinced the lower levels of this network have enough reliable data that they say anything. Granted, I have my own biases, but the philosophers I know anything about don't really fall in a place that illuminates anything about them. There's a distinct lack of the Christian philosophers I know best (John Calvin is way out on the edge, which I just know is wrong), so I think this graph has suffered from the biases of Wiki contributors and artificial distinctions between theology and philsophy (for some reason, Muslim theologians are more commonly classified under philosophy by Wikipedia, see the northern part of the graph). Alasdair MacIntyre by Augistine of Hippo makes sense, but what are Francis Bacon and Muhammed doing there? Ayn Rand by Richard Swinburne? I'm probably trying to stretch the graph too far, but to me that's just the point -- this graph can't be stretched very far at all. It shows interesting relationships for the top 10 names is all.

I just don't see how this really illuminates anything beyond the banal conclusion that all philosophy is connected. It should be able to say more, but it needs more effort on the back end to make it interpretable on the front end. My conclusion is that a simple analysis leads only to simple interpretation, and there's still a role for the human brain in interpreting Wikipedia!

Wednesday, July 11, 2012

The Evil Nazi Plan to Breed Pure Cows

Speaking of evil scars on the landscape: let's talk about Nazis. There's a B-movie somewhere about the evil Nazi plan to mutate cattle and breed a pure, extinct species called the Auroch that used to roam the forests of Europe, and to introduce this Nazi cow, wild and roaming free, in Poland (once those people who were already there were ... removed). Oh, wait, that's not a movie, it actually happened.

The Zookeeper's Wife by Diane Ackerman is how I first encountered this story (the Nazis were interested in the zoo for reasons related to the Auroch breeding program), but it's been covered from another angle here, in "Heavy Breeding" by Michael Wang.

What stands out about this story to me is how good Nazis were as scientists. For example, they understood the critical importance of the relationship between the environment and the organism, something that's become more obvious recently. We can now reconstruct ancestral proteins from the fragments of current genomes, and that's essentially what the Nazis were trying to do with the Aurochs, just with an organism rather than a protein. And they actually did have some measure of success in reshaping cows to become more Auroch-like, a success that can be seen today in the Heck Cattle. Early 20th-century Germany was one of the best places to do science. But that obviously is not enough. It meant that their eventual war machine was that much more formidable in both World Wars.

Some people take this kind of observation and say that because Nazis believed in evolution, therefore Darwin was wrong. That doesn't compute. The problem is deeper. It comes with the use of science, as much as with the science itself. It goes with a willingness to impose one's will on the lives and landscape of all those around you, no matter the cost, in pursuit of your vision of perfection. This vision of biological perfection is actually very intricate and, in some scientific points, correct. But that is precisely what makes the whole package so very wrong. The lie may be closer to the truth ... but all the worst lies are.

To me, it's far more important to note that the Nazis went after the handicapped and weak first than to note that they read Darwin. That's far too narrow. Their reading of Darwin aligned with and contributed to this twisted pristine vision of theirs, definitely (a point I make in third-quarter biochemistry every year, in fact), but if we're looking for the root problem we have to include other data. We have to look at their politics as well as their science, their operas as well as their breeding programs, their relationships as well as their experiments, their hearts as well as their minds. And so my ambivalent relationship with Richard Wagner's operas continues.

At the very least this story should give us pause about our own societal blinders. Now that we have more precise genetic means to pursue these ends, but we have essentially the same human will and weaknesses ... what now?

And if you want an unambiguous moral to this story: great research institutes do not a complete society make. It's the highly scientific society that can do the most evil. (GK Chesterton makes exactly this point, and warns about Germany/Prussia, in 1920's Eugenics and Other Evils -- before these horrors really began.)

The Burn Scar in Colorado

Satellite imagery of the area recently burned in Colorado.

Doesn't this burn scar just look evil? It seems to be reaching out for Colorado Springs ...

[Source link]

Tuesday, July 10, 2012

Standing Stones Before They Stood (In LEGO)

One of my favorite TV documentaries is the History of Britain series hosted by Simon Schama. It's rewarding to watch multiple times, and I hardly think that about anything on TV. But what could make it even better? That's right, LEGO.

Here's a History of Britain series (no direct relation to Schama, I don't think) done entirely in LEGO. Truly eductational toys at multiple levels. Personally, this particular one makes me think of Brave for several reasions:

Thanks once again to the Brothers Brick for the heads up.

A Music Box Made of Planets

"Natural" music doesn't often sound very musical -- except once in a blue moon. Here's some that does. This example of "natural" music works, and even makes a point. The astronomer Alex Parker put this together by assigning different tones to six different planets observed circling around a distant star (the Kepler-11 system), as explained on the YouTube notes:
Here, I’ve taken each transit seen by the observatory and assigned a pitch and volume to it. The pitch (note) is determined by the planet’s distance from its star (closer=higher), and they are drawn from a minor 11 chord. The volume is determined by the size of the planet (larger=louder).
Even my untrained ear can tell the tones never converge or coincide, they keep plinking along like raindrops, and so this music shows that the planets never come together into "orbital resonance". It's just doing it with music rather than numbers. Or numbers as music, that's more like it. I think someone should expand this and maybe combine it with DNA music. (A challenge for the next generation of composers!)

Friday, July 6, 2012

"Why Are You Putting So Many Chemicals in Your Food?"

Most chemists' pet peeve is the label on food that says "chemical-free." Last I checked, most food was made from atoms, and all food is therefore made of chemicals. Nathan Myhrvold researched chemistry and food, published the five-volume, beautiful (but inaccessibly priced) Modernist Cuisine, and in much briefer form summarizes the counterargument to the "chemical-free" label here. My favorite part is this connected article in which he opens up his pantry and tells you what chemicals are in there and why. There's a recipe for chemical-laden grilled cheese if you like.

I sense some biochem exam questions coming on ... but what do you do if you run out of sodium citrate? It's not like you can run over to your neighbor and ask for a cup ...

Thursday, July 5, 2012

New Protein Science Publication

Protein Science is one of my favorite journals, so I'm doubly excited to have a publication accepted by it. I'm also happy with the long list of student co-authors on this one; it was really an amazing team effort. The article was accepted only a short while ago and it's already online. Here's the link to the official abstract.

LEGO-Builders of Catan

So what if the cool 3-D version of Settlers of Catan costs more than $1000 if you're lucky enough to find one? Build your own out of LEGO! (Unfortunately it may cost about that much to buy all the specific bricks ... but it's still incredibly cool.)

See more detail and other photos here:

Thanks to Brothers Brick for the original link.

Wednesday, July 4, 2012

Book Review: Evolution: A View From the 21st Century

This was like going to a scientific seminar with a high-profile speaker that you knew was going to be good, and when it was over you realize it was REALLY good. (If you've never experienced that, it's one of the consolations for years of Ph.D. study, and it's a nice feeling.) James A. Shapiro wrote this book to argue that evolutionary change is not only much less gradual than many biology textbooks insist, but it's also directed by the cell and therefore has the hallmarks of intentional engineering. I am most excited about Shapiro's willingness to re-introduce teleology into evolution, and there are many threads and references he drops off that I will follow up for my own chemistry-based angle. I have a few comments, not even really criticisms: basically he ends up downplaying the single-mutation mechanisms to the point that the general reader may not even know that those exist, and he spends so much time away from the protein level that he neglects a few examples that sort of coincide with his thesis but involve the dreaded single-mutation type change (in particular, I'm thinking of Susan Lindquist's work on the way heat-shock proteins can "buffer" destabilizing mutations during normal times, allowing for more rapid change in times of stress -- if this was among the 1000+ references, I didn't see it). But honestly, this book is not for the general reader, even though Shapiro makes some faint stabs in that direction. You really need a master's degree in a related field to read this book. But I've seen biology slowly moving in Shapiro's direction, especially with the observed large changes of DNA that are not small or incremental. Another minor quibble is that he insists on going after Darwin as being wrong, when Darwin's mistakes were perfectly understandable, and, like a blurb on the back says, Darwin would have been excited by this book. It's not about Darwin, it's about role of randomness and a possible role for intentionality (and therefore order). It's about whether biology is just a branch of thermodynamics or if there might be something more to it. And it's exciting to have all of this evidence in one place, especially for a chemist like me who didn't know, for example, how plant biologists make new species (by hybridization, not small incremental change). Shapiro is definitely onto something here, and I look forward to seeing this story continue to unfold. By the way, this book is all the things The Signature of the Cell wanted to be but wasn't -- including right.

Book Review: What We Talk About When We Talk About Anne Frank

This collection by Nathan Englander may be enough to get me to regularly read short stories. Almost half of the stories were outstanding, and the rest were at worst very good. I figure a short story deserves a short review of its own, so here goes:

"What We Talk About When We Talk About Anne Frank": Starts out like the story I expected, in which four Jewish parents meet in a house and talk, but quickly turns funnier, sadder, weirder, and more meaningful than I expected, with a devastating ending. (Would make a good play.)

"Sister Hills": My favorite, jumps through time with the relationship of two women who founded a settlement in Israel, and has incredible resonance and character. I don't know of a better story that simulataneously faces the paradoxical tragedy of these settlements head-on and yet fits it into the long Jewish story. Almost Biblical. This one was so good that I was slightly disappointed with all that followed.

“How We Avenged the Blums”: Sort of run-of-the-mill growing-up-Jewish story, but it gets a lot right that Inglourious Basterds got wrong, and especially, the last line is perfect.

“Peep Show”: Outlandish and dream-like, but I'm left wondering what the point is. The setting is a stroke of brilliance.

“Everything I Know About My Family on My Mother’s Side”: This one didn't even make much of an impact on me. Maybe because it didn't translate well to audiobook.

“Camp Sundown”: This is more like it, with a bizarre set of circumstances at camp and guilt underlying the farce. A little too bizarre, actually.

"The Reader": I found this one exciting because part is set in the old Elliot Bay Bookstore, and it uses the setting very well. But otherwise it seems a bit like Englander's version of one of Stephen King's "write about being a writer" stories, and I just don't get that genre.

“Free Fruit for Young Widows”: The third outstanding story (after the first two), again with a strong historical grounding, and the one that is most directly about the Holocaust, after that tragedy is hanging around outside the windows in each of the other stories.