Tuesday, December 31, 2013

Book Review: The Miraculous Journey of Edward Tulane by Kate DiCamillo

This was an excellent read-aloud book, just taking a total of about two hours to get all the way through and telling the tale in vivid, elegant, simple language. The transformation of the characters in the story is also believable and hard-earned. The protagonist is a china rabbit doll who, unlike the toys in almost every other toy story, cannot move by himself. This is not just a good story but one that can change the reader as well, and I hope that it built some empathy and compassion in my boys as we read it together. I hope it did so for me too, come to think of it.

Friday, December 27, 2013

The Sun of Many Colors

This video combines the different colors we can see in the sun. One of them is yellow (surprise). Several of the others are colors that we can't see and sit beyond human eyesight, but reveal features like particular helium energy emissions and things like that. Each of these wavelengths was assigned a different color that we can see in the video. It's kind of mesmerizingly beautiful, like peeling layers off of the sun to see the dynamics inside.

For more information see this blog post at Discover.

Tuesday, December 17, 2013

The Middle Earth Weather Report

A few years back there was a writer from Eastern Europe or Russia who wrote a version of the Lord of the Rings from Sauron's perspective, I think it was. That "Wicked"-esque stunt didn't attract my attention as much as that writer's claim that the geography of Middle Earth doesn't fit with its climate at all. I think that last comment would have rankled Tolkien (although he almost certainly didn't actually have climate in mind when drawing the maps, so he'd be right to concede the point!). It did sort of rankle me, because if you're going to make such claims you should back it up.

Yet here is a real climatologist analyzing the climate of Middle Earth and coming up with detailed weather maps of it. Lo and behold, it all fits together with Tolkien's description. The Shire's like some parts of England, and Mordor's like the Sahara and/or Los Angeles. Yeah, that works.

What initally caught my eye are two things: high CO2 levels from Mount Doom (which fits nicely with Tolkien's anti-industrial and even anti-auto bent) and how the global map of the planet looks suspiciously like our planet, if drawn by someone with the accuracy and perspective of the sea voyagers of the 16th century. Tolkien always claimed that Middle Earth was supposed to be part of our history, and that global similarity just confirms it to me.

So there you have it. Not only did Sauron cause the enslavement of peoples and the pseudo-eugenic experimental abominations of the Uruk-Hai (along with Saruman, yes, yes), he also caused global warming in Middle Earth. I knew it.

Monday, December 16, 2013

Book Review: The Where, the Why, and the How

This idea behind this book is a simple one: for 75 questions that science has not answered (but possibly could), have a scientist write a few paragraphs on the left side of the page and have a graphic artist supply an illustration on the right side of the page. The result is a diverse book that probably bit off more than it can chew. Some of the illustrations are great (some, honestly, aren't) and a few, like the one asking how mind arises from brain, would be welcome all by themselves. But usually the promise isn't quite fulfilled and the art and the science don't quite meet. I think they got the right artists, but I'm not sure if they got the right scientists. I marked three pages (one illustration and two articles) as worth going back to in terms of ideas, but the rest was a nice exercise, signifying I'm not sure what. I wish this was better, but it too is less than the sum of its parts.

Sunday, December 15, 2013

Book Review: War in Heaven by Charles Williams

I saw the grave of Charles Williams, in a little graveyard in the heart of Oxford, before I read his novels, but I always knew I would need to get around to reading them some day. So War in Heaven is the first I've read. I expected it to be rough around the edges, because it's his first novel. I'm not sure how much of the roughness is from first-book jitters, or from the general distance in reading novels 100 years old (not composed by masters of their craft), or from something unavoidable in his writing that explains why he may be the least popular of the Inklings (well, it's probably down to him and Barfield). Is it all three?

But as I got more used to Williams's idiosyncratic voice I found sentences, character traits, and whole scenes that shone with a light that speaks of very real things, things that are normally glimpsed through a mirror darkly. This particular story has to do with the Holy Grail and Prester John and dark rites. There's something very modern and Hollywood about the subject matter, and yet the way it develops is exactly the opposite of Hollywood tendencies (and I mean that as a sincere compliment). There are moments of disturbing darkness in this but also moments of clear, illuminating light. To call it a thriller would be to emphasize not the former moments, but the latter, and that's what I found most surprising about this story. The light is thrilling. That's a very special trait in a writer.

As for what this story seems like, it's most like CS Lewis's That Hideous Strength, although I must say that I liked War in Heaven more than Lewis's novel, which always felt over-the-top and unrealistically characterized to me. Williams writes "good" characters that are both more serene and more convincingly doubtful than Lewis's characters, and "bad" characters that seem both more evil but convincingly so to me. Granted, Lewis is clearly a better writer, I'll definitely give him that. But enough about Lewis. Williams's story is also strangely like a modern movie and even has elements of Alan Moore in its use of supernatural darkness and occultism.

My advice is to get past the rough parts and odd writing and to look for the lucid moments, which are worth it when they come. I'm looking forward to the rest of Williams's novels in the future, and he's definitely a worthy member of the Inkling crowd. In fact, for some kind of people (the type who read Alan Moore comic books, and I'm looking in the mirror when I say that), Williams offers a combination of themes and characters that I have not found anywhere else.

Tuesday, November 26, 2013

Tolkien, in Nature, on Science

Nature recently published an editorial on the 50th anniversary of Doctor Who, but it was the quote at the end by J.R.R. Tolkien that really got my attention. Then I noticed that the quote was about science, and I realized I had just read my favorite Nature editorial of all time. Tolkien gives some very good advice about writing, stories, and magic:

"Perhaps the most surprising critic of such technological fixes was the great hobbitmonger himself, J. R. R. Tolkien, as revealed in his unfinished story The Notion Club Papers (published posthumously in 1992 in Sauron Defeated, edited by his son and literary executor Christopher Tolkien). Much of the story is a discussion between academics and writers on the dishonesty of using scientific-sounding MacGuffins to get one from here to there. If one insists on doing such a thing, one might as well dream oneself to Mars or wave a wizardly wand. The story centres on criticism of H. G. Wells’s The First Men in the Moon (1901), in which the protagonist, one Dr Cavor, invents a material, cavorite, that provides insulation against gravity. “Gravity can’t be treated like that,” complains one of Tolkien’s characters. “It’s fundamental. It’s a statement by the Universe of where you are in the Universe, and the Universe can’t be tricked by a surname with ite stuck on the end, nor by any such abracadabra.” Which suggests, perhaps surprisingly, that even if time travel and warp drives are impossible, the world’s best-selling fantasy author knew a thing or two about the general theory of relativity."

Friday, November 22, 2013

Book Review: Cat's Cradle by Kurt Vonnegut

With Cat's Cradle I expected a satire about science but I didn't expect religion to be an equal target, as well as island nation politics. I was pleasantly surprised. Vonnegut covers a lot of ground.

I found the science to be most entertaining and detailed of Vonnegut's targets. The idea of ice-nine is an excellent foundation for a book like this and Vonnegut's fast pace and occasional poetic interlude among the hilarious-depressing events that follow keep this book going. The visit to the American research lab set a high bar for the rest of the book, and I thought at that point that this might be one of my all-time favorites.

The more he got away from science the less I cared about the story, and the less biting his satire seemed to me. Maybe that's because there's so few writers that really stick it to scientists the way Vonnegut does, yet with a deep understanding of what science really is and (mostly) how it works. Lots of writers satirize voyages and prophets (ever since Jonah?). I have read/seen many island nation satires as well.

Now, I know in satire the characters are supposed to be a little ridiculous, but I found some of the science stereotypes (and the religion stereotypes, for that matter) to be too simplistic and the broadsides a little too broad to really illuminate the topic. I would take the real-life Oppenheimer (or Langmuir) over the fictional Hoenikker any day, and the real person is much more interesting than the caricature. For that matter, the fictional scientist Gale Boetticher in Breaking Bad is more interesting (and realistic) than Hoenikker -- he felt like someone I might meet in a lab, while Hoenikker did not.

The same for the way faith is dealt with. The people with faith that I know are more interesting than the characters in this, when I'd expect that the freedom satire provides could make them more interesting and ring more true, given the outlandish things that the author could contrive for them and their stories. From a classic beginning, the end fell a little flat for me.

The reader may start out thinking Cat's Cradle is about science, but at its heart, it's really about God. And on those grounds I do wish Vonnegut's critique had been just a touch more trenchant. The faith he's satirizing is not recognizable as faith to me, and the science, too, is close but ultimately does not resonate. Job provides a sharper critique than Vonnegut.

Both the science and religion in this book are too broadly drawn. More cutting details would have turned it from a very good book into a great book. But, again, I realize that satire is very much a matter of taste. I'm just surprised that this book wasn't more than the sum of its parts for me. Rather, it was less. Still, it's a classic, and a must-read. Just an "I liked it" rather than "I loved it" must-read.

A 3-D Supernova

The Cassiopeia A supernova remnant has been reconstructed in 3-D. It looks like a big, big explosion, with purple lines that might be "surprise lines" in a comic strip, but here must be some superheated jets of matter and radiation. If we can't travel to the stars, through astronomy we can bring the stars to us. (The rotatable version above doesn't work on IE but does work on Chrome for me.)

Tuesday, November 19, 2013

How to Hack Where's Waldo

Slate has a nice article about how to use an objective method to determine the optimal search pattern for Waldo. There are certain places where Waldo will be more than half the time, so you look there first. I can't wait to try this out on my kids. It also may be a good teaching exercise for a stats class ... or even a psychology, or design class? Are there other methods of analysis we can apply to Waldo's xy coordinates?

Monday, November 18, 2013

Flannery O'Connor's Inspiration

Marilynne Robinson reviews Flannery O'Connor's recently published journal and, as usual, makes connections that cross time and space, pointing out how the patterns of thought that gave us the Muses as literal inspiration have been lost, evoking some of Barfield's comments to my ear:

"O’Connor’s awareness of her gifts gives her a special kind of interest in them. Having concluded one early entry by asking the Lord to help her “with this life that seems so treacherous, so disappointing,” she begins the next entry: “Dear God, tonight it is not disappointing because you have given me a story. Don’t let me ever think, dear God, that I was anything but the instrument for Your story — just like the typewriter was mine.”
"... I would be curious to know what story or part of a story by O’Connor should be attributed to the Lord. It can seem self-aggrandizing or simply bizarre to ascribe any thought or work to a seemingly external source, named or unnamed. Nevertheless, ­Hesiod, Pindar and any number of poets and prophets before and after them have declared indebtedness of this kind. If they, and O’Connor, were naïve, sophistication has made language poorer."

The Periodic Table of Storytelling

Here's a periodic table that's more periodic than most, although even this could be rearranged. For example, I don't see fandom as noble gases. But the "chemicals" that make up various stories are appropriate, I'd say. (And here's where I got it.)

Thursday, November 14, 2013

Book Review: Apt Pupil

On the whole, this story comes together to be more than the sum of its parts, although at the halfway point I wasn't sure it would. What is essentially a character drama between an old Nazi war criminal in hiding and the golden boy who discovers his secrets (and keeps them secret) is an interesting start, and it's where the focus is for the first two-thirds. Near the middle the excesses of the evil spiral between the two added up to be almost too much for me -- I was ready to resign this story to the "old Stephen King" more-or-less-what-you'd-expect-from-King file rather than the "new Stephen King" surprised-by-meaning file (see: 11-23-63, Joyland, etc.). The real depth comes from the additional characters who are not caught in the descending spiral, and those don't really come out till the last third of the book. I do think some of the scenes in the middle are unnecessary but there are just some things about psychology that King and I don't agree on. Getting past those was indeed worth it.

Thursday, November 7, 2013

Book Review: Of Mice and Men

I experienced this book as an audiobook from the library, and when it came I found it was read by Gary Sinise of all people. This made for an experience that may have felt more like a movie than a book, but then again, all the interior action described so well by Steinbeck would be very difficult to put onto a screen, so it felt more like a one-act monologue than anything else. As for the story, I tried to experience it fresh, and it built slowly to a devestatingly sad series of events. It surprised me in how much it felt like Junot Diaz, not necessarily in direct topic but in indirect emotion and style.

Book Review: Both Flesh and Not by David Foster Wallace

Both Flesh and Not is a posthumous collection of essays by David Foster Wallace. This collection translates well to audiobook and, well, actually exists on audiobook, which is why I listened to/read it rather than Infinite Jest. This collection spans decades and is uneven, yet Wallace's alchemical style (in which he can take a mundane subject like an editorial introduction to a collection of essays and turn it into clear gold) makes every topic worthwhile, even the long pair of essays about tennis. Wallace's most outstanding feature is not his intelligence or breadth of interest but his underlying compassion that shows through in almost everything he writes. Don't miss the editorial introduction that is reprinted as "Deciderization 2007" -- it is the best of the bunch.

Monday, November 4, 2013

Today's Writing Quote by David Foster Wallace

Loce this quote, courtesy of David Foster Wallace in "Deciderization 2007 -- A Special Report" (this pretty much nails it as far as non-fiction is concerned; I would not know about fiction!):

"Writing-wise, fiction is scarier, but nonfiction is harder—because nonfiction’s based in reality, and today’s felt reality is overwhelmingly, circuit-blowingly huge and complex. Whereas fiction comes out of nothing. Actually, so wait: the truth is that both genres are scary; both feel like they’re executed on tightropes, over abysses—it’s the abysses that are different. Fiction’s abyss is silence, nada. Whereas nonfiction’s abyss is Total Noise, the seething static of every particular thing and experience, and one’s total freedom of infinite choice about what to choose to attend to and represent and connect, and how, and why, etc."

Monday, October 28, 2013

Book Review: On Writing by Stephen King (10th Anniversary Edition)

On a recent Facebook thread on books about writing, On Writing by Stephen King kept coming up. I agree -- it's the Fred Meyer of writing books, a one-stop shop for everything from getting ideas to getting an agent (with wonderfully specific advice on that last one that I may try out some day ... ). It is as much about Stephen King as it is about writing, and that's all right with me. The one mistake I made was starting it on an airplane after I had some sushi and we hit some turbulence. Some of King's formative experiences are vividly medical in nature and ... let's just say I put the book down for the rest of the flight and the rest of the summer. Then I came back to it and found a practical guide for the intuitive writer. Simple and effective advice. Worth the time.

Thursday, October 24, 2013

Book Review: Gone Girl

It's hard to review this book, because the reason you read it is to find out what happens at the end. Might as well start where it starts. Nick Dunne starts the narration, and soon his wife Amy goes missing -- not just not-there missing, but door-wide-open iron-left-on missing. Nick is not a reliable narrator, he leaves things out and outright lies to you when he wants. Soon after, Amy is narrating, through diary entries that were left behind. The mystery of what will happen next is sustained very nicely, although if you're one-third of the way through the book and wondering if it will be worth it -- trust me, you'll want to get halfway through because that's when it really starts to get intricate.

This book reminds me about how Stephen King is still my favorite. This plot is more intricate, and these characters are probably more interesting than King's, but they aren't as warm, and it isn't ultimately as satisfying. This plot was carefully contructed, but in the end, though it tries, it's cold as clockwork gears. Read it for the plot, and for the surprises, including some of the best twist moments I've come across. It does end up being less than the sum of its parts, but its parts alone are absorbing.

Wednesday, October 16, 2013

Another Chemistry Recruiting Scandal

Most of the sites that try to imitate The Onion are hit and miss. I think this one is a hit, although it might just be my chemistry bias showing through. (Title: "Chemistry Major On Probation After Allegations of Improper Benefits from Big Pharma Recruiters")

Wednesday, October 9, 2013

Book Review: Joyland by Stephen King

Another good historical novel by Stephen King (if something set in 1973 can be considered historical, which I think it is). It's about being 21, having a broken heart, and working at an amusement park. It's about death, injustice, and forgiveness. It's only incidentally about a ghost and a serial killer. It's also short (for King) at about 1/5 the length of 11-22-63, for example. It's not big on the surprises, really, but it's got a nice little plot. King's skill at foreshadowing comes through in this one, and he even directly addresses his views on the soul (obliquely, but it's there). All with a beautiful, simple last scene. What's impressive is that this is an average book for King. I don't know how he does it.

Wednesday, October 2, 2013

Biochemistry Lectures (2013)

Another year of lectures has begun. I always like to link to the lectures from here, so here's the link for this year. Pass it along and enjoy!

Book Review: The Ocean at the End of the Lane by Neil Gaiman

Neil Gaiman is my favorite author that I can remember the least about his books after they're done. Perhaps it's the mythic elements and the simple, powerful, but common language he tends to use. In The Ocean at the End of the Lane, forgetting the story is actually part of the story, so I have to assume part of this is what Gaiman is about. What's different about Ocean is its perspective, told as memory: it's remembered by a 40-ish year old from an experience when he was 7. Gaiman uses this perspective to enhance the mystery of what's going on and to introduce some dark, adult undercurrents very gently (for the most part, with one shocking scene that stands out all the more for that). No one can do this like Gaiman does. This may be the most nostalgic of his works, and possibly one of the most personal. It feels like a short story (and it started life as a short story that outgrew its own pages), but I can't imagine it being any shorter than it is. Gaiman's own stories contain the magic he talks about, magic of universal myth, the power of words, and the ultimate mysterious but good structure of the universe. (No wonder he keeps returning to Lewis and Chesterton!) That's why I'll read anything he puts out and remember enjoying it even after I've forgotten the details of the plot. Those details are not what matters with Gaiman, and what does matter, matters a lot.

Wednesday, September 25, 2013

Book Review: Brief Interviews with Hideous Men by David Foster Wallace

I tried to read Infinite Jest but got bogged down about 2% in (which is still longer than some books). Still, I enjoyed David Foster Wallace's digressive, honest, and compassionate voice. Then his famous commencement address blew me away, and George Sanders' Tenth of December kept getting compared to Wallace, so I gave Brief Interviews with Hideous Men a try. It's full of short -- some very short -- stories and most of them are, as advertised, brief and in the voice of hideous males, although usually that adjective only becomes obvious gradually. If anything, the feel is that of a horror story, and although Wallace is about as good as King in creating warmth in the face of very dark subjects, the warmth here is always ambivalent and contradictory. The men are hideous but they hide it well. It depressed me a little to be a man and I'm glad it wasn't longer because I don't think I could take much more of the darkness. I have to say that this book probably needs to be balanced by the notes in Infinite Jest, for example, and I don't recommend reading it on its own. But for a dark, disturbing book, it does have a few elements of light. Definitely at the very least incomplete on its own. But Wallace's voice is a literary treasure and it adds up to be worth reading, if a lot more difficult than I thought it would be.

Sunday, September 22, 2013

Book Review: My Bright Abyss by Christian Wiman

The book My Bright Abyss is subtitled Meditation of a Modern Believer, but the believer of the subtitle (Christian Wiman) is a poet who deconstructs and inverts the very word belief. It's not for nothing that someone else called Wiman the "atheist Christian." He's fond of apophatic language (describing God, not by what God is like, but by what God is not like), paradox, and the search for meaning in silence despite a loud, modern world set against anything quiet. But this is not Chesteron's sometimes-too-triumphant paradox, it is a true puzzle that no one knows. What shapes Wiman's whole perspective is a seven-year struggle with a rare cancer and the intense intimacy with pain and struggle that comes with that. Wiman also believes that Christ is God and that God was crucified (he also quotes Jurgen Moltmann on this) -- that God was somehow calling out to Godself when he cried "Why have you forsaken me?"

Overall, this book is billed as modern, and Wiman is thoroughly modern, but his perspective on suffering and the cross feels old, like a medieval saint's reflections, with shades of Kierkegaard. This book is hard going at times, just like life is, but it is dense and rewarding. There are a few head-scratching moments, like when Wiman mistakes Isaiah for Elijah, and I would like to know more about what Wiman thinks about scripture's poetry, the stories we share as Christians, although there are frequent enough allusions to it. I'd like to know more. Hopefully there will be a next book, the Gilead to this book's Housekeeping (to continue the Robinson references). I think sometimes Wiman tilts too far toward the question when there is a partial, through-a-glass-darkly answer to ponder. I occasionally found this book frustrating and slow but in a good way, like a hard poem. Wiman's voice is a unique creation and well worth hearing in the harmony of the believers.

Monday, September 16, 2013

See-Thru Dirt

In Star Trek IV, Scotty famously gives away the chemical formula for transparent aluminum to a 20th-century engineer. The formula for transparent soil is not quite as sexy but it is better because it exists (at least, that engineer's company should be making the transparent aluminum by now, don't you think?). Information here.

Transparent soil can be considered to be even more interesting than a fictional super-hard glass. A menagerie of microorganisms live both on and in roots. Microscopic armies attack roots and kill crops. Now with transparent soil we can watch as it happens, and who knows what we'll see?

Thrifty Idea of the Week

How's this for a thrifty idea? Build big greenhouses next to power plants. Take the carbon dioxide exhaust from a power plant and use it to grow plants you can eat. The natural carbon-fixing biochemistry of the plants turns waste gas into tomatoes. Oh, and someone's already doing it.

Even if you doubt the warming influence of CO2, that doesn't really matter here -- it's about making tomatoes from what would be thrown away even more than what the thrown away stuff would do once it's thrown away.

I don't know how much of a dent this actually makes in rising CO2 levels (probably not much really), and I'm not sure how the workers in the greenhouse are impacted by higher CO2 (it's probably low enough that they are unaffected). But it seems like a good idea overall. Let's close the carbon loop.

Friday, September 13, 2013

When the Scriptures of Science Fail

Sometimes the best part of the book comes out after it's published. Rebecca Skloot's book on Henrietta Lacks led to many fascinating developments after it came out, including a remarkable agreement on her genome publication with Lacks's family, something that would never have been possible without the book. Into the Wild by John Krakauer is now another example. Why did Chris McCandless starve in a bus walking distance from a highway? Krakauer originally had a biochemical explanation for this, but recent evidence has come out that refocuses and implicates a different biochemical cause. Read about it here.

What strikes me about the story now is that McCandless trusted his field guide. He had to. He was right to. It represented centuries of experience. But that field guide did not include the fact that, in a weakened state, eating this one plant would have enough of a neurotoxin to take out the nerves, moving your legs in a slow, weakening erosion of your ability to keep yourself alive. The field guide was flawed. (I'm even leaving out the part about how he could have crossed the river to safety if he had a good enough map ... )

McCandless trusted his book, and his book let him down. This can happen with any book -- all knowledge is incomplete. Scientific summaries of experience may be more reliable but they are still incomplete.

This is true with the Hebrew Scriptures, too. When Israel trusted their rituals and the presence of the temple in Jerusalem, trusting that this would protect the nation from invaders, they were shown to be wrong. (Well, right with Assyria, wrong with Babylon, it's complicated.) Both stories show that books can let you down.

But the story with Israel is more complicated. Israel was ignoring the book as it trusted in the building. Particularly brushed under the rug were passages in the Torah against idolatry and worship with the heart. Prophets pointed this out; false prophets reassured that it was OK ("The temple of the Lord, the temple of the Lord, the temple of the Lord"). Then judgement came, and the unique place on earth where the Lord of the cosmos was worshipped was leveled. Even now, that feels wrong, unfair, disproportionate. The sheer cry of lament in Lamentations shows just how horrible it was. My heart takes Israel's side in this, probably as a defensive maneuver for my own coverups.

Yet, in the face of a cataclysm, embers survived, waiting for breath to glow again. The Jewish faith survived the destruction of the temple, rising from the ashes. And then the second temple was destroyed -- and Israel survived, and Christianity rose as well. The second destruction led to two religions where before there had been one. Who could predict that?

Faith is not faith that nothing bad will ever happen. Faith is faith that when the bad things happen that God remains faithful. Even when death happens, times thousands.

I don't know how it all adds up. There are always false prophets and idols in every person's own mind. There are times of adundance and times of abundance. A time to be born and a time to die.

When you're going out by yourself, a science field guide is the only community you have. It, like any community, can let you down, and may be more likely to let you down than a living, breathing community, as messed up as that community may be.

In the middle of all this "letting down" -- books letting us down, friends letting us down, ourselves letting us down every hour -- faith says, despite what it looks like right now, I know God holds us in his hand. It's a simple point, but it's a point I hear in the story of McCandless as it's now told. Rest in peace, Chris.

Thursday, September 12, 2013

A Summer Making Proteins

This summer I supervised a student project in which a student made four new versions of the protein we study, and then we tested them for binding to learn about the molecular basis of transplantation immunology. The data is coming in now and it looks good. This is just one of a dozen projects that went on over the summer in the chemistry/biology area, and they all got together for presentations and an end-of-summer BBQ.

Here's pictures and titles to give you an idea of the scope of what went on. Water bears! Next-generation sequencing! Metal-organic frameworks for hydrogen storage! Our students will have a lot to say when people ask what they did over summer vacation. Nice job, everyone.

Hearing New Puns by Using an Old Accent

By reconstructing ancient accents, professors have found that Shakespeare is a lot punnier than we knew. The old accent sounds like Scottish or Welsh to me, and my favorite result is what happens when "proved" and "loved" actually rhyme (about 2/3 through I think):

The Tardis in the Van Gogh

A great episode of Doctor Who involved time traveling to solve the mystery of a rampaging alien with none other than Vincent Van Gogh. But what made it truly great was that all that stuff was wrapped up 3/4 of the way through the episode. The last act involved the Doctor and Amy taking Vincent .... well, I won't ruin it, but it was low-key and absolutely beautiful (and it even involved Bill Nighy). At the end of the episode you can see how Vincent worked the Doctor and Amy into one of his paintings, at the beginning there was a sighting of the alien in another Van Gogh, and then later in the series, Van Gogh paints an exploding Tardis. Three Van Goghs and three involvements of the Doctor. In fiction. Right?

That's all very nice, but it (sort of) happened in real life. Recently an old Van Gogh landscape was found that was previously deemed a fake, but it looks like it's truly a Van Gogh. And in the back left of this newly discovered Van Gogh is ... a blue box?!

You know that newfound Van Gogh painting has the TARDIS in it, right?

Close enough for impressionism. Strange but true. Source of info here.

Wednesday, September 11, 2013

Everything You Need to Know about Radiation

When I was in tenth-grade US history, the teacher allowed us to take one sheet of paper along for the test as a crib sheet. Anything could be hand-written on that sheet of paper. I was the sort who'd cram in basically all possible text onto every inch of space so that from a distance it looked like one big blue ink-spot covering both sides of the paper. (I didn't notice at the time that in the process of creating the crib sheet I learned everything twice, so I rarely used it on the test!) If I had those same parameters for physics tests on radiation, it would have looked something like the picture below, but it wouldn't have been half as nice. Also, the fundamental physics is the same so all the information is as relevant today as it used to be when the chart was made. Enjoy! (Here is where I found it and a link to a bigger version.)

Tuesday, September 10, 2013

The LEGO Laboratory

Who needs 3D printing in the lab? Just use LEGOs. See these two instruments from the Brothers Brick website:

1.) The working LEGO compound microscope
LEGO Microscope MkII - Hero

2.) The working LEGO balance
Scientific Scales

What's next? The working LEGO GC-MS? (It could work at low temps, right?)

Sunday, September 8, 2013

Living from the Diaphragm

In church, I love it when the translation is wrong.

In a sense, the translation is always wrong. When reading the New Testament, we're always fitting English words over the Greek, and sometimes they fit snugly, while other times they don't fit at all, hanging off in one place, pinching in another, truncating and even obscuring the best parts.

Just today this showed up in Romans 12:3. Romans 12:1-2 is one of the most well-read verses, and justly so. Romans 12:3 is different because it's practical and straightforward, and it can also be deflected and moved past a little too easily if you're not careful.

Romans 12:3 reads "Don't be uperphronein but rather be sōphronein," which is translated something like "Don't be high-minded but be sober-minded." That works, but it sounds a little bumper-stickery, maybe too moralistic. Don't drink and drive, you know. If you didn't come to church drunk then you can pat yourself on the back and move on. You'd be missing the heart of the verse.

If words were garments, then one of these fits well while the other doesn't. Uperphronein as "high-minded" fits pretty well -- you can even see the "Uper" that relates to our "hyper" or "uber-" prefix. But the "so" in sophronein is not really about sobering up, it's more about being sane and being safe. It's about being balanced and connected with reality rather than disconnected. The person who has unplugged from the lying distant voices online, the one connected to local reality, seasons, rhythms, and relationships is the one who is "sophronein." "Safe" is also a nice angle on this word. I want my students to be "safe-minded" in lab, so we take care and work deliberately.

Also, the "phronein" has multiple layers of meaning. It's about how you see yourself, so "-minded" works, but it's also about much more. It's about the center of things, where your heart is, and how you have trained yourself to see, how you self-control ot regulate yourself. It comes from the root "phren", which means the regulator of all other things. We get the word "diaphragm" from it, and this is where it really makes sense for me.

Soon after I joined choir (and married the accompanist), I learned that I wasn't singing right. I may have had emotion and volume but it was not regulated. I wasn't singing from the diaphragm. I had to learn to stand stright, shoulders back, breathe deep, and most of all, keep the right things tense and the right things loose.

The diaphragm supports all the other things going on -- it is the core and the discipline regulating all other singing. Every time we sing the first thing we do is take 5-10 minutes to sing warm-ups, nonsensical sounds that are designed to get the diaphragm toned up and regulating the way it should. It is boring, it is work, it is hard, and some days are better than others, but it comes from a true place, which is the constant need to hold the diaphragm right as you're singing. Your heart may in the right place, but if your diaphragm isn't, you won't sound right.

Paul is saying here that we need to live warmed-up, and need to maintain self-control in all things, including especially our self-assessment of "how am I doing today." We'll mess up, sometimes even when we warmed up right, sometimes in a place where everyone can see, sometimes where only God can see. The danger is not in the messing up but in thinking too highly of ourselves so that we don't give ourselves the chance to mess up.

Live loud and balanced, from the diaphragm.

All that is contained in a contrast between two Greek words, and it's well-nigh impossible to capture in English so succinctly. So there are tools online to help you unpack (I like the Biblos Interlinear Greek Bible, as someone who doesn't really know Greek at all!). These tools help me hear more layers of what there is to hear and help bridge the gap between the 21st-century English and the 1st-century Greek. Inbetween are textures of meaning. It adds another dimension to reading, and it allows the ancient words to speak more clearly.

Thursday, August 29, 2013

Calvin and Hobbes Apocrypha

I found this at Paste magazine. Words by Bill Watterson, creator of Calvin and Hobbes, art so closely inspired by his style that it might as well be by him. A good end to a busy day (click to embiggen):

Thursday, August 22, 2013

Congratulations, We're Getting Nowhere

The New York Times published a letter by a scientist about science literacy today. It is a prime example of how to waste words in a public forum. The author talks about how we've gone backwards (with a 2% change in a statistic, which has got to be within the error bars), says God and science don't conflict and then implies that God and science do conflict, insults creationists without making any distinction between the many varieties, and throws in climate change just in case any minds were still open to slam them shut.

It's preaching to the choir, and the comments bear this out. 90% are empty "you go girl" affirmations of scientism echoing the author's statements and 10% are empty, defiant "I'm a creationist" negations of everything the author says. (At least stubborn denial is interesting.) The "needle" gauging belief of NYT readers did not budge. This just gave them a chance to yell at each other.

It's kind of funny to be saying popularization is what science needs when your very writing style is 1.) boring and 2.) polarizing at once. At least Sagan was never boring. But, honestly, what is interesting or even new in this essay? It gets us nowhere.

When a scientist praises the Manhattan Project without any of the self-reflection of the destruction that project resulted in, then that scientist is indulging in nostalgia and idolizing science. Oppenheimer realized the double-edged nature of science right away with his "I am become Shiva, destroyer of worlds" remark. Every scientist after him has to acknowledge the same.

This essay is venting without nuance, and it only makes things worse. I say that as a scientist lucky enough to work with the beauty and strangeness of the natural world every day. This is a noble and fascinating calling, so when you write to a public audience, make sure you get that across. Instead, we have a political screed, dressed up in a lab coat, arguing against political screeds. Oy.

Wednesday, August 21, 2013

Book Review: Pilgrim at Tinker Creek by Annie Dillard

How a few decades changes a person. When assigned to read this book in high school, my friends made fun of its intense, detailed, natural focus, and, conforming to the non-conformity, I joined right in. Even so, there were images I never forgot: a cat's bloody footprints and a frog sucked hollow by a waterbug. And that was just in the first few chapters.

Now I've returned to finish it for good and find that Annie Dillard has produced a readable, vivid book of what can only be called natural theology. Her willingness to look at the harsh parts of nature unflinchingly, even with an appropriate understated fascination, is the bitter streak that balances the talk of balance and harmony. The book hasn't changed in twenty years, so it must be me.

I wonder how Dillard's occasional God-talk sounds to someone who doesn't come from the Christian viewpoint. I would like to see a new Atheist response to someone who would take the time to read this book. (Alas, they don't seem to have time to turn from the science to something like this.) Also, I'd like to see a secular science writer who can describe nature with the force and power of Dillard. Haven't seen it yet. Maybe Loren Eiseley comes close, and he's even quoted in this, but his work is much more placid than the energy that pulses through Dillard's prose.

It's too early to review this book -- I just finished it and my head's still reeling -- but it was worth reading slowly, as summer changed from early to late, only a few pages at a time. It's that rich and multi-layered. I'd like to know what others think of it, so comment below if you have ...

Friday, August 16, 2013

Book Review: Charles Darwin's On the Origin of Species (A Graphic Adaptation)

If you want to "see the movie" instead of reading the book, this graphic novel edition of The Origin of Species will do the trick (Michael Keller wrote, Nicolle Roger Fuller drew). Darwin's arguments are appropriately distilled and discussed, and the high points of his prose are pulled out. As an example of the art of comics I can't recommend it. Technical issues such as layout, movement between boxes, and the quality of drawing aren't up to average for the field. I also would have liked more recent science supporting Darwin's thoughts. There's a few examples but there could be many more. Still, if Darwin's words are what you're interested in (and you should be), then this is probably the most efficient way to examine them.

Monday, August 12, 2013

Making Copper Pennies Glow Bright Red

Chemistry comes closest to Harry-Potter style magic when it dramatically reveals the hidden. For example, let's say you have two pennies, one made before 1982 and one made after. If you heat the first one in a flame and dip it in nail polish remover, it will glow bright red, like an iron poker. But the second one won't do it at all.

The difference is in the minting of the coins. Copper has become so valuable (and pennies so, well, not valuable) that it ceased to make financial sense to put a lot of copper in pennies after 1982. They could make them out of zinc and they'd still look the same to most everyone. But anyone trying to use the special properties of copper would notice.

Copper is better than zinc at binding oxygen, and that's how the whole thing works. Oxygen plus hot acetone burns red-hot, and the penny is catalyzing the approach of the gas to the liquid. Zinc just doesn't stick to oxygen as much as iron, and it does not burn the nail polish remover.

Of course, this requires a bunsen burner and a flask rather than a magic wand and a cauldron, but it works for me all the same. Plus, I can actually do it. Do I have a volunteer from the audience?

Color Wheel of Cartoons

This is a bit old, and I can't get it to work on the blog, but when something comes along that organizes the world in a new way I just have to share it: It's a color wheel of cartoon characters. The interactive wheel will zoom in on the character you mouse over. I was most excited to see Totoro included.

Here's the link.

Branches of Bacteria

"I think that I shall never see // A poem as lovely as a tree" -- but check out these bacterial plates!

Each has the same grace and flowing beauty of a tree. They grow out instead of up, and the colors are artifically added, but the structures are fascinating. Enjoy more at this link. Don't miss the interesting quote at the end about how these are like musical compositions.

Wednesday, August 7, 2013

Book Review: Chemistry, Quantum Mechanics, and Reductionism by Hans Primas

Well, with a title like that, how can you go wrong? In this book, Hans Primas walks the line between physics-chemistry-mathematics and philosophy. Sections involving advanced mechanics algebra are outside of my field and it's not my field to critique those, but I found this fascinating. Two quotes by Goethe in a physical chemistry text is two more than what I've seen before, and there are other parallels I could make to Owen Barfield's arguments at times. Also, frequently Polanyi comes to mind. This book is as much philosophy as it is physical chemistry. Natural philosophy, of course.

Primas argues that it is not a trivial thing to cross from the quantum physical world to the classical physical world, and that some of the ways we "bridge the gap" mathematically don't work. To do it right, he starts from the ground up with a non-Boolean quantum logic that allows for superposition of states and also for the influence of the environment/measurement on the experiment. The biggest experimental indication that we need to do this seems to be the EPR correlations, which Primas argues shows that experiments are not as separable as we assume. I think I agree but am not enitrely convinced that EPR correlations affect classical outcomes.

Primas argues that we cannot so easily separate the experiment from the experimenter, and that we cannot build a classical physics from quantum mechanics alone. The extra ingredient we need to do so is context or observation on a classical level. Classical properties like chirality and molecular structure constrain the quantum mechanics. The world cannot be added up from quantum mechanics alone with a big enough computer, in other words.

What impressed me was the depth of philosophical thought. Primas is searching for a quantum ontology (if that's the right way to say it), and is not content with the standard "it's just what we measure, let's not think about what it means" Copenhagen interpretation. He digs back to Greek philosophy and makes the connections between his ideas and history as well as experiment and theory. He put his thoughts in the proper context, just like he argues we should do with our experiments.

It's strange to be reading a typed set of lectures from the 80's, but it worked for me, just like reading Polanyi's seminal article on similar topics still works. I found Primas by talking to Robert Bishop (philosophy of science, Wheaton) and reading his article "Whence Chemistry?" published in 2010, so people are still thinking about it, and it's not clear that Primas's objections have been adequately answered in the two decades since publication.

I'd like to list here for reference the six limits Robert mentioned to me that Primas lists, which must be crossed when moving from quantum to classical physics (p. 332ff). These are where the rubber meets the road for Primas's ideas, so they are particularly important:
1.) Shadow edges
2.) The van Hove limit
3.) The Boltzmann-Grad limit
4.) The Brownian-motion limit
5.) The Hartree limit
6.) Molecular structure (e.g., chirality)

I did not expect to get as involved in this book as I did, but it was a fascinating if somewhat vertiginous trip. Still processing and probably will be for quite some time.

PS: One useful tidbit: I did not know, or I knew but then forgot, that the Uncertainty Principle is not only found in Quantum Mechanics, but instead originated in the classical world. It's a consequence of limits on data transmittal, and in fact Heisenberg may have gotten the idea from a classical origin! So one of the prime examples of quantum weirdness actually doesn't require quanta.

PPS: As I was reading this a philosopher of science ran a pair of articles on the NYT philsophy blog about how he's frustrated at people who abuse quantum mechanics to make weird philosophical statements. I agree with him on many points but find his argument ultimately a lot less convincing on what really matters than the arguments of Primas. In fact, Primas argues forcefully against some of the statements made on that blog. Mostly, I'm frustrated with the attitude that if some people do the philosophy wrong, then EVERYONE must be doing the philosophy wrong and we all should just bite the bullet of the Copenhagen interpretation (or worse yet the Everett Many-Worlds interpretation). This is not a subject that can be resolved on a blog. Therefore ... I will shut up now!

Friday, July 26, 2013

Book Review: Mr. Penumbra's 24-Hour Bookstore

Ah, that was nice. Mr. Penumbra's 24-Hour Bookstore is a tidy literary thriller with a secret society and encoded messages but with complete avoidance of the worst inclinations of Dan Brown and reasonable inclusion of new technology, and even some touching character moments, and an underlying love of books (and even the oft-maligned genre of fantasy) running as a thread through it all ... this is what summer reading is about. Actually, summer listening to the audiobook, and I recommend it for a scene involving an audiobook near the end, but this is an entertaining tale however you cut it. Perhaps a little light and underwhelming, but after some of the previous books I read, I needed something light yet brain-tickling. Better in terms of length, story, characters, and innovation than REAMDE, but in many ways the stories are similar, and I did enjoy both. Just this one more. Recommended.

Monday, July 15, 2013

To Succeed, Keep Your Eye in FRONT of the Ball

I always heard that the way karate fighters break through all those boards is that they focus on a point below/past all the boards. (Not sure if that's true, but at least it correlates with this post!) This recent study in PLoSONE fits with that for baseball. The best baseball hitters don't keep their eye on the ball, but in front of it. Their gaze automatically anticipates the location of the ball where it will hit the bat. This may be too fast for them to even know what they are doing, but they are not so much reacting as predicting. They are literally seeing -- or at least anticipating -- the future.

This is what learning can do, make prediction automatic. I propose that if learning anticipation is the trick to baseball and to karate, then it's also the trick to science and biochemistry and all sorts of other things.

And no number of Google searches will compensate for this trick when it comes to abstract knowledge. This is what I will try to teach -- keep your mind in front of the ball.

Scientists Redesigned

Here's a nifty little set of logos designed (by Kapil Bhagat for Science Day in India) to explain what scientists are best known for. Looks like a good teaching tool, especially for a science and history course:

Saturday, July 13, 2013

An Illuminated Manuscript of Tolkien's Silmarillion

This just plain fits: someone has made an illuminated manuscript of the Silmarillion. I can think of no modern book that better meshes with this physical presentation. (Although it feels wrong to use the modifier modern for a book like the Silmarillion ... )

This is amazing, and it also points out to me how the Saint John's Bible is even more amazing (made by a group of people with more time and resources). What could a group like that do with this as a starting point?

Nice interview with the creator and more pictures here.

Friday, July 12, 2013

Book Review: Weird Life by David Toomey

Books are fascinating windows into people. Take Weird Life, for example. The author is interested in the biology and physics, and in presenting a bunch of ideas, not tearing them down. On the Myers-Briggs J vs. P metric this book is clearly a Perceiving "P" not a Judging "J."  This has an important place in the ecosystem of scientific information, and it was a very entertaining book in its sheer diversity of ideas.

In this book, David Toomey describes all forms of life in the weirdest settings possible. He essentially starts with the tube worms at hydrothermal vents, which seem as weird as it gets, but wait, it gets weirder from there. At the same time, the book ventures out away from biology and toward physics, when usually you start with the physics. It becomes more and more speculative and (to this biochemist) less and less relevant as it goes on. Toomey deserves a lot of credit for describing some weird physics very well, like certain aspects of multiverse theory, better than any other book I've read. The biochemistry, on the other hand, is something I'd want much more of, but is not part of this book, reasonably so. Pretty much, this book starts with fascinating biological observations and then jumps to multiverse physics without much of the chemistry inbetween, at least at the level I would like. So I am happy to provide the chemist's perspective on this some day, I'm sure!

Weird Life does a nice job of cataloguing the biology and physics. I think I could be a lot more critical of some of the weird ideas here, and I found a few inaccuracies, but that's not really the point of a book like this. This book is a list of possibilities, and who knows, maybe some of them work. I hold out more hope for the first half of the book "working" than the second half, which gets into infinity paradoxes that, as a chemist, I think are closer to sophistry than to convincing arguments. But that's just one chapter at the end. This book is worth a read just for the discussion of Titan, that too is done better than any other treatment I've seen. Makes me want to go there, right now, where's the bus?

This was a fun book and enjoyable. Let's hope there's more material for another Weird Life book in a decade or two.

The Stained-Glass Planet

"Captain's Log, Stardate 071213. We have now ventured close to the planet HD 189733b and can see it with our own eyes for the first time. It is a deep blue, not an ocean-blue, but brilliant sapphire against the backdrop of space. The away team is preparing their protective gear to withstand the raining glass shards and 9000 mile-per-hour winds... "

If we can't go to this planet, at least we can see the light. For the first time the light from a distant planet has been analyzed and, at the risk of mixing genres, it is the blue of the TARDIS. See the graph above to see how different this is from our system's planets. Two words: silicate rain.

This planet is so inhospitable to conceivable life that it makes our Jupiter seem downright cozy. But it's not about the possibility of life for this planet. It's about the color, and what a glorious color it is.

More information and a link to the paper preprint here.

Wednesday, July 3, 2013

Book Review: The Accursed by Joyce Carol Oates

This was not the book I was hoping for.

Going in, I knew that this was a historical novel by the historian Joyce Carol Oates that involved a supernatural curse on members of the Princeton community shortly after the turn of the (20th) century. Woodrow Wilson, president -- of Princeton! -- was a main character. Upton Sinclair, Jack London, Mark Twain, and others also make appearances, along with demons, vampires, and Sherlock Holmes. I was hoping for a darker, scarier version of the fantasy-history novel of which Jonathan Strange and Mr. Norrell is the epitome (and The Night Circus was quite good, too). A glowing review of The Accursed by Stephen King sold me on the prospect despite the length.

There's some good detail here, historically, and Oates's device of telling the story through the pen of an 80's amateur historian is amusing. But this novel is far less than the sum of its parts. I was frustrated by the "one damn thing after another" sense in the middle, and although it's tied together a bit at the end, the tying-up depends on a view of the universe that I simply can't accept as having any truth in it. Anything good at the end, and there's some surprising deus ex machina stuff, makes no sense whatsoever in any moral sense. I find this interesting because Stephen King's universe is something I rarely have trouble accepting, but Joyce Carol Oates's universe, for all its historical detail, does not seem to have real people in it. On the surface the two universes may seem similar but on an experiential level I have totally different reactions to them. Oates holds an unconvincing view of faith and theology, for example.

The best examples of this genre seem real and also teach about the history of the era. This one teaches little and seems fake. Your story may be intricately researched and told, but if there's no point to it ... there's no point to my reading it.

Monday, July 1, 2013

Coffee Charts

Here's two coffee graphs. Consider them figures for a great unpublished coffee-drinking paper. The first would be from the results section (tasting) and the second is methods (brewing). Click to enlarge:


Friday, June 28, 2013

Book Review: The Fall of Arthur by J.R.R. Tolkien

Tolkien fans are currently reduced to purchasing books by Tolkien that probably should be labeled “25% pure Tolkien”. At least, that’s about the percentage of words directly written by Tolkien in this book. Many other words are written by Christopher Tolkien, who represents about half of his father’s genes, and the rest are examples of the English and French poems of Arthurian legend, so depending on how you count we may consider a near majority.


Yet even 25% pure Tolkien is still very much worthwhile. Tolkien’s unfinished poem itself opens the book and it is so dense with meaning that it warrants most of the rest of the book to explain it. Only near the end does the analysis begin to bog down in reconstructing edits that seem to mean less and less as you near the end. But then the very end is a lecture by Tolkien on Anglo-Saxon poetry, which would fit earlier as well but at least ends the book on a high note.


So for the Tolkien fan but non-expert in Arthurian legend and poetry, this book is pretty much exactly what it should be. Did you know that Tolkien toyed with the idea of identifying the isle of Avalon with Tol Eressea, the Lonely Isle off Valinor? Placing Arthur and Lancelot in Middle-Earth with the legends of the Silmarillion is tentative but intriguing. Can you imagine Frodo arriving in his gray boat and seeing on the shore Arthur in a golden crown? (Don’t tell Peter Jackson, he might try to make a nine-hour set of movies about it … )


This book is for anyone who read the Silmarillion and liked it. You know who you are. Not necessarily as bad as Stephen Colbert-level interest, perhaps James Franco-level or even less. Itn other words, it worked for me.

Sunday, June 23, 2013

Book Review: The Periodic Table by Primo Levi

The Periodic Table is a renowned example of chemistry literature, and what Primo Levi has done in this book is unique. Each chapter is an element, but this is not a science book. Each chapter is primarily a story from Levi's life, arranged roughly chronologically, but this is not an autobiography. It skips over whole crucial episodes in Levi's life that are described in other books -- most of his time at Auschwitz, for example -- but rather does indeed focus each story on a particular element, usually literally, as in Levi in his job as a chemist was working with that element in some way, shape or form. Not sure what the word for this is: biochemgraphy, perhaps? At any rate, Levi is as much a writer as he is a chemist, which is to say, he's a very, very good writer.

Levi's crystalline prose is something that I simply hope will absorb in some ways into my own work, but there is something left unsaid. As good as this is, it was written several decades ago, and usually concerns work done in the 40's, 50's and 60's. At the end, in his discussion of the journey of an atom of carbon, Levi mentions that there are many steps that are not known here as he passes them by. But now, they are known! That's what it most exciting about this book, that it is episodic, and therefore it is necessarily incomplete. Others can now complete it. Let's hope there's a future for chem lit ... The Periodic Table clearly shows there was a glorious past for it.

Friday, June 21, 2013

Colbert's Mom

This has already made the rounds on social media by this point, but just in case someone is out there who hasn't seen it, Stephen Colbert paid tribute to his mother in this clip from his show, one of the best written three minutes of TV I've seen this year:

The fact that he's "in character" 99% of the time makes the moments when he steps out of character that much more powerful.

Another brick in the wall of evidence that (IMHO) the sequel has outdone the original Daily Show, which I didn't think would be possible.

Thursday, June 20, 2013

DIY Molecular Gastronomy

This article describes itself as Molecular Gastronomy but it's really just cooking with possibly-hard-to-find ingredients. Most of the chemistry is biochemistry, especially the transparent ravioli with an explanation that involves phospholipids. I am going to have to look into that one a little more because I'm not sure the explanation explains. But the point of this is first to do something cool with chemistry and only second to explain it: the proof is in the pudding, or the parfait, or whatever the end result is. This article will be bookmarked for possible inclusion in next year's biochemistry lectures ... or could it form the basis for at-home labs? Something to consider.

The Periodic Table of the Muppets

To the periodic tables of M&M's, TV shows, and the Empire Strikes Back previously posted on this blog, now add one more: The Periodic Table of the Muppets by Mike Boon of Mike BaBoon Design. I appreciate that this one is truly organized by its own internal logic and not forced into the chemical periodic table structure. More info (and links to order posters) found here:

Friday, June 14, 2013

The Wooden Cow Digestive System

Cows eat grass, which is made of cellulose, so it makes perfect sense biochemically to make a model of a cow out of wood, which is made of cellulose. For those who would like to know more about bovine digestion and have a learning style that works best with intricate, life-sized mechanical contraptions (and after all who doesn't fall in that category), I give you the Wooden Cow Which Eats Orange Spheres:

Cow from Nova Jiang on Vimeo.

I'm not sure where this falls on the science/education/art continuum, but all I know is I'm digging the style.

Making Water Act Like Mercury

I don't like to put too many commercials on my blog, but this is science! All the science papers/news stories I've been collecting about hydrophobic surfaces have resulted in an actual Rust-o-Leum product you can buy at Home Depot. This really repels water. Caveats apply: it's a 3-step treatment to put on and it will wear off. But look at what it did to that boot! Ideas for biochemistry demos on the hydrophobic effect? I wonder if this is powerful enough to make a large-scale model of a protein fold up ... I'll have to think about it ...

More about the technical details on the Popular Science blog.

Thursday, June 13, 2013

Why Does Slate Think Basic Biology is Esoteric?

The news for today is not that the Supreme Count unanimously ruled against patenting naturally occurring genes in the Myriad case. At least, I saw that as such an obvious no-brainer that my fingers will not type a sentence that unequivocally states that such an item is actual news. No, the surprising part was in the Slate article I read on it, ostensibly about Justice Scalia's ignorance of the science, a key paragraph clearly condemns us all:

To Scalia’s credit, the science in Myriad is convoluted, especially for someone who hasn’t taken biology in decades. Justice Clarence Thomas, who wrote the majority opinion, takes an admirable stab at elucidating it at the outset, explaining the basics of genes, chromosomes, and “the familiar ‘double helix.’ ” He even expounds upon nucleotides for a time, penning what must be the most esoteric sentence in the court’s modern history: “[T]he nucleotide cross-bars are chemically connected to a sugar-phosphate backbone.” (One suspects Thomas was less than enthused to be assigned this case.)

I'm left spluttering at the idea that a high-school biology sentence (which I italicized in the quote above) can be classified as "most esoteric" in any way. That is about as straightforward a description of DNA structure as you can get. It's probably at about the level of the letter Francis Crick wrote to his 5th-grade son describing the Watson-Crick DNA structure.

I don't want to name the particular author because it's not about that one author -- there's an editor, there's a readership, there's a whole culture implicated here, including me, because it's my job to let everyone know how this stuff works. It's about a whole culture that depends upon, even worships, science, and yet considers the word "nucleotide" to be excruciatingly esoteric, even boring. And that's the worst word in that sentence, folks. All of the other words are numbingly common. In fact, to me, those other words are the boring ones.

Power to the people through general biology and chemistry courses required for all college grads! Those courses are crucial. We need to understand how genes work, and I need to teach my students to the utmost end of my ability to prepare them for a world in which they will need to know DNA structure to understand Supreme Court rulings. Their language needs to include the word "nucleotide."

Also, the polticial angle in the wording of the headline: in my view Scalia is not being ignorant here -- he's being honest about his own limits in the face of complicated science. The article is clear on this, but the headline is not, and I have the feeling that an anonymous editor is more responsible for that tone than the byline author.

On the other hand, come on, the science is really not all that complicated, not compared to thousands of daily tasks. It's just that it seems complicated because it is not a daily task to you. That's fine, but we've got to try and address that, perhaps by making it closer to a daily task to use the word "nucleotide." You have a citizen's responsibility to learn biochemistry, just as I do to learn law. I promise not to be bored by law if you promise the same for my topic!

Friday, June 7, 2013

Genomes for Africa

This link tells the story of how the Mars company (yes, that Mars-bar company) has decided to fund the sequencing of several plant genomes and post the information online. That's cool enough, but look at the list of included genomes: yam, finger millet, tef, groundnut, cassava and sweet potato, among others. These are staple crops in the developing world, and therefore they have eluded sequencing money, until now.

How this could really help is probably not in detailed gene manipulations, but in more mundane areas: grafting/cross-overs to make stronger crops and investigations into the plants' defenses against fungi. It's already helped with the cacao genome, funded and implemented in the same way a few years back.

Wouldn't this make a great project for undergraduates to investigate, using biochemistry in a way to help farmers across the world? I for one can't wait for these to come out. Biochemistry students of the future, you may have a lab exercise in this area. 

Wednesday, June 5, 2013

Should We All Just Give Cash Directly to the Poor?

Should We All Just Give Cash Directly to the Poor?

[In case anyone's wondering, I'm trying to use the share button more to see how it works, because I have at least 20 stories in my backlog that haven't seen the light of day on the blog yet. Consider this an experiment.]

Now this story gets the left and right halves of my brain yelling at each other. It's about a charity that just transfers money to poor people. Talk about minimal administration. No buildings, no campaigns, no nothing except giving the poor money.

It cuts out corruption and intrusive bureaucratic structures, so the libertarian in me rejoices.

But it has no regulation or constraint for how it's too be used, so the teacher in me (who watches out for student cheating) is concerned.

But it is simple and uses the freely available technology (cell phones) well, so the tech-efficiency side of me rejoices.

But there are so many poor people that I have to wonder about unfair distribution or spreading it out so much that it's too small to do any good, like that $8 class action settlement check I got a week ago, so the financial side of me is concerned. How does this work without relationship?

Bottom line, however, is when I turn to what Jesus and the prophets say about giving, they don't seem to be worried about how, they just say do it, give. This is the most straight-forward fulfillment of that command that I've seen short of a hand-to-hand transfer.

And that's the question: is this good enough or not good, because there is no relationship whatsoever? How much of a relationship is there when one of the disciples would give to one of the beggars at the gate of the temple, after all?

Barns Are Painted Red Because of the Physics of Dying Stars

Barns Are Painted Red Because of the Physics of Dying Stars | Smart News

The upshot of this link? Because of nuclear physics, iron has the most stable nucleus of all the elements. It just does. All else follows from this: Because iron is the most stable nucleus available, when stars smash atoms together, they will make more and make stable atoms till they get to iron, and then they will stop. Therefore there's a lot of iron, therefore iron is cheap. It's red when it combines with oxygen, so it's the most cost-effective paint pigment around, and it was used on all the barns.

I'd turn it around and say that barns and Mars are red for the same reason. Mars is pigmented like a barn.

It's interesting to think about this ... even more interesting to think about what it leaves out from the equation. But it works for a nice little blog post.

Thursday, May 30, 2013

Book Review: Housekeeping

It's not every day you get to read the acclaimed first novel by one of your favorite authors. Marilynne Robinson published Housekeeping in 1980, and apparently it by itself was enough to establish her reputation as a writer of writers for two decades plus, till in the 2000's she published both Gilead and Home [reviewed here]. I got on the bandwagon at that point, and have also enjoyed her nonfiction, written with the same precise, elegant style, dividing bone from marrow. Her pattern of more frequent recent output seems to me to be another parallel between her and Terrence Malick. That and the indelible, unique impression they each make.

This book is remarkable, showing the same focus on families -- this one broken deeply -- with the same surprising sunbreaks of upward-eddying transendence, meditations on what are really theological subjects but with non-theological language. Whereas Robinson's other novels are warm, even cozy, this one is cold and sharp, transient where the others are rooted, lake-blue where the others are sun-yellow. Like a train it may start slow but it picks up speed and the last chapter is in my opinion truly breathtaking. Robinson is simply worth reading, and this book is the proper entry point for those on the English-lit side of the spectrum, where the chill edge of loneliness is described in painfully clear prose. Other readers may do well to start with Gilead, in which the narrator is a pastor, or with her non-fiction Absence of Mind, in which Robinson takes on Freud and Dawkins. All are remarkable, for some very similar reasons and for some that could not be more different. Housekeeping was nothing like what I expected and yet it is undeniably Robinson's book and it reminds me all over again why she is one of my favorites.

Before and After at the Nanoscale

On this picture (a sideways triptych?), the bottom panel is how we draw the atomic model for a covalent-bond-forming reaction in organic chemistry class. The triple bonds, shown as extra lines on the left, can react with each other and share electrons to form the multicycle molecule on the right. The top two panels are actual pictures of the molecules, shown before and after heating it up. Looks like our models are pretty good representations of reality, no? Read more here.

Before I took chemistry classes I thought that pictures like this would be easy to take. After all, those models are easy to draw. But it's very hard to see on the atomic scale -- atoms are so small that (in a sense) light waves shine right around them. It's nice to see that technology is catching up to my "when I was a child I thought as a child" perceptions. It's kind of pretty too.

Saturday, May 25, 2013

Indiana Jones Biochemistry: The Prevenge of the Black Death

The Black Plague had a prequel.

It's clear that Yersinia pestis was the microbe behind the Black Plague in the 14th century, and there was a worldwide sequel pandemic in the 19th/20th century. But in the 6th-8th centuries a plague swept the Byzantine empire, called Justinian's plague. Now a DNA analysis of the remains of plague victims shows that this plague was caused by Yersinia pestis as well -- and it originated in Asia like the other two pandemics.

This biochemical archaelogy isn't exactly like the Indiana Jones movies, but I find it pretty exciting to see the recurrence of this insidious enemy throughout human history. (Maybe it's more like Doctor Who?) Read the paper here.

Friday, May 24, 2013

Book Review: Tenth of December

Authors like George Saunders are making me rethink my longtime aversion to short stories. In Tenth of December, Saunders crafts several stories that are excellent in two ways: the voices of the characters and the subtle role of science/technology in the stories. The first I expected but the second surprised me. Fully half of these stories say something deep (but not necessarily obvious) about science or technology, and some even have what I would call science fiction elements, if calling them that didn't painfully highlight how much the the typical "science fiction" style of writing pales in comparison to Saunders's writing. I'm not sure I've ever encountered a writer who was able to convincingly voice a teenage girl (in "Victory Lap," the first story) and a middle-lower-class working father (in "The Semplica Girl Diaries," almost certainly my personal favorite) and a terminal cancer patient (in the title story). Saunders clearly understands what it's like to be poor in a way that many other writers simply do not (or at least do not communicate). His characters are painfully tangible and tragicomic, sometimes causing cringe like a good episode of The Office, sometimes evoking heroism in unexpected ways. Only one story, "Home", comes off to me as less than perfectly shaped. Themes of salvation and true humanity and family recur again and again.  This is just what good writing can do. Even better, I got to hear the author himself read it on the audiobook from the library. That is just what a good audiobook can do.

Thursday, May 16, 2013

The Town Built Under a Rock

This is a picture from Setenil de las Bodegas in Spain, a small town built in -- and into -- a gorge. This results in streets that have natural rock awnings. And rocks in the roof. And rock as a back wall. The village grows out of the rock like an organic development. Which, in a sense, it is.

The house built upon a rock will stand when the flood comes. What about the town built under one?

Take a virtual tour at this page, or visit the Flickr photo network here.

Tuesday, May 14, 2013

Movie Review: Star Trek Into Darkness

A spoiler-free review in three run-on sentences (Not quite a haiku, but perhaps an extended one):

What it gets right: The technical realism of the engine room and the entire world, a few things going on the fritz leading to exciting sequences I've always wanted to see (and related to a particular favorite Calvin and Hobbes comic strip), the armor of a certain important adversarial race, Benedict Cumberbatch once he finally really gets going, and enough little jokes and plot twists to keep things going along (one of the hardest things for a Trek movie is to juggle the whole crew, and it's possible this one did a better job than the last of giving everyone something important to do).

What it gets wrong:  too little true cleverness, too little about the characters truly interacting (some scenes depend on an audience connection to the characters that just isn't there yet for me), too obvious at points (at least for this obsessive trailer-watcher and Trek fan), just this side of too much action (and I like the action), and that transwarp device is WAY too powerful.

In short: A smidgen too Star Wars-ish for a Star Trek movie, but I still loved the ride; in terms of the ride analogy, it's more Big Thunder Mountain Railroad than The Hulk Rollercoaster (no inversions, but nicely themed).

Book Review: The Dog Stars

On the scale of post-apocalyptic novels, this one is very high on scientific realism (no zombies, just flu and disease, and very good estimates of what would and wouldn't work after a decade of neglect), very high on the depravity of man (one must be absolutely ruthless again and again), and very high on poetry. Oh, and it may be the best written example of the genre I've read in terms of both description and psychology. Makes you really think through what that "if you were the last person on earth" phrase would imply, and the long impact of devastation, even for the survivors. I don't want to give away too much other than that it's intense and well-written, but I didn't quite connect the way I did with Age of Miracles: maybe someone who's more into dogs, flying, and the outdoors would connect better. It's also not half as gentle as Age of Miracles, this is Walking Dead-style intensity. I understand why it was a staff pick at my local library, but it doesn't make the cut for me, just for personal reasons I don't really control. Yet there's three or four moments/phrases that are just crystalline perfect (one involving the Book of Lamentations), and ultimately I genuinely like what Peter Heller does with the story compared to all the other examples out there of the genre. High quality writing and you may like it even more than I did. If you have a dog maybe.

Monday, May 13, 2013

iPhone + Case = Portable ECG

Alivecor is a company that makes an iPhone case. There's two big bumps on the back of it, but those aren't a design flaw. They are contacts that allow you to complete a circuit with your fingertips and measure your heartbeat, so accurately that an electrocardiogram can be recorded. So a doctor can carry an ECG recorder in her pocket, on an airplane, and/or to Africa ...

When this was presented at a recent meeting, it was mentioned that one of the early-adopter docs who carries this around has been able to take ECG readings on not one but two plane flights so far and diagnose the problem accurately at 30,000 feet.

Here is the website for this fascinating invention. I wonder, what's next? How will cheap, portable computing change health?

Wednesday, May 8, 2013

Best Commencement Speech Ever?: The Film

In 2007 (is it possible I've been blogging that long?) I commented on the full text of David Foster Wallace's commencement speech at Kenyon College, so you should check that out again. A different part of the speech has been made into a film, with visuals that don't interfere with but rather amplify DFW's words. Well worth checking out the film at this link.

(In a side note, I tried to tell the fish joke at the beginning in my biochemistry class about water, in 2008 or 2009. I initially thought it didn't "work" because it didn't get a laugh, but I don't think it's intended to be a haha funny joke, come to think of it. Still, it turns out that Sam and Aidan were "visiting" the class that day and I named the fish Sam and Aidan, and Sam still remembers that. So it had a different level of value than intended. There's something appropriate about that.)

Tuesday, May 7, 2013

New Star Trek I-VI Posters Redesign the Past Future

Now that we can look back at the entire series of Star Trek from I-VI, some fans have redesigned the entire series of posters, and I really think they are not only a cohesive whole but also much improved from the originals. Only Star Trek III seems to contain a major spoiler (which doesn't really matter now of course), and in Star Trek V they actually managed to make a good poster for an awful movie. I don't know how they did it. Here's the link to all 6 posters, and here's my favorite, for Star Trek IV: