Monday, December 31, 2012

C.S. Lewis and the Courage to be a Craftsman

Taking stock of the last year and planning for the next, it's easy to keep the same old evaluation system when deciding what worked and what didn't. But sometimes the evaluation system itself needs fixing. I had never read the essay titled "The Inner Ring" by C.S. Lewis before, but it hit me at just the right time, because it speaks to this question of what are you doing and why. Here is the essay/speech itself, it's a fast read with a high value-to-word ratio:

The idea of constantly striving for the next inner ring reminds me of the answer to the question "How much money does a person need?": "Just one more dollar." Just one more inner ring, and then I'll be set. One more step into the onion. Here Lewis turns the onion to transparent glass (all John Lennon references aside).

This especially echoes with the state of Lewis's life in 1944. It was a good time for his "output," roughly contemporaneous with the Mere Christianity lectures and The Great Divorce, 5 years before the publication of the Chronicles of Narnia and 10 years before he would move to Cambridge after repeatedly failing to enter the academic inner ring in his department at Oxford. Lewis never reached that inner ring, probably because he was true to his own words here and realized that it wasn't worth what it seemed to be worth. Instead, he focused on his craft, finished the Space Trilogy and after it didn't go as well as he hoped -- read Planet Narnia for more on this -- he turned to Narnia, which would be his true hallmark work. (Is this an act of literary kenosis?)

If C.S. Lewis had focused on the inner ring rather than his craft, he may have stayed at Oxford, but would we have Narnia today? Academics is political and those politics have probably prevented some great works from being written as academics work more to impress their fellow academics than to create something lasting. Today I don't know who was in that Oxfordian inner ring, but I do know Lewis's words. That's lasting.

Thanks to this essay, I resolve to begin the new year wary of reaching for the inner ring when instead I should be looking to the work I've been given. It will take time and care to carve out the right words for the right time and the right student. Inner rings can wait -- I resolve this year to create value, carefully, the best I can, with focus and labor.

(PS: Looking back on this I can see how my thoughts are also colored by all this talk of the politics of the fiscal cliff, too!)

Saturday, December 29, 2012

Jupiter Rising Over the Moon on Christmas Day

In Brazil on Christmas Day, there was an occultation. Lest you think this is the beginning to a sub-par Edgar Allan Poe story, let me note that Jupiter was occulted -- covered -- by the moon. An astronomer named Rafael Defavari caught the following video with a 20-cm telescope. It's a beautifully inverted echo of a sunset and sunrise. Consider this another belated Christmas gift.

(found on the Bad Astronomy blog)

Friday, December 28, 2012

Book Review: Faith Seeking Understanding (Essays in Memory of Paul Brand and Ralph Winter)

I can only review 16/17 of this book in good conscience, because, after all, I wrote 1/17 of it (Chapter 16, "Trees of Life", to be precise). It was edited and assembled by David Marshall. And you probably won't believe anything I say about it after all. I'm not sure if you should, it's like reviewing your own book on Amazon. If this book was on Amazon. But I digress! If you can get past my own selfish-gene-like involvement here, I'd say this is a good collection of essays. Of course, I personally don't agree with everything here, but I agree with a lot of it, and the combination of viewpoints is synergistic. Like the Church itself. Overall it works.

These other 16 chapters are written by names I recognize: Philip Yancey, Earl Palmer, Rodney Stark, Alvin Plantinga, and Don Richardson. The names I didn't recognize are just as interesting. For example, I found the essay by Yuan Zhiming about faith in China to be fascinating. Historians, missionaries, scientists, and a philosopher, all sharing the perspective of faith and honoring the memory of Brand, Winter, and Anselm.

I would have liked there to be some more conversation among the authors, but I don't know how you do that in book form. I would like to press some of the comments others made about Islam that I think are too harsh, for example. And some more back and forth on the topic of evolution would have been interesting -- it's clear there's some disagreement there but I hope it's obvious that I consider there to be substantial agreement as well.

Because the focus of the conversation could be Anselm, Paul Brand, or Ralph Winter, there's a wide diversity of topics, but David Marshall's arrangement into four sections is helpful. Just realize that this is an anthology album, not a concept album (or a rock opera).

And my favorite part is that Philip Jenkins and Nicholas Wolterstorff -- two scholars whom I admire -- provided complementary blurbs for the back of the book. So I'll let their quotes be the review, and provide the obligatory link to buy the book straight from the publisher for the curious.

“What makes the collection especially fascinating tha valuable is the individuality and particularity of the stories–a concrete testimony to the fact that the Christian intellectual life takes many forms.” — Nicholas Wolterstorff, Noah Porter Professor Emeritus of Philosophical Theology, Yale University and senior research fellow, Institute for Advanced Studies in Culture, University of Virginia
“David Marshall has gathered a really distinguished array of contributors, who have all thought deeply about faith in its global context, and the different essays work wonderfully together. The book makes a splendid memorial to two truly great individuals Paul Brand and Ralph Winter.” — Philip Jenkins, Emeritus Edwin Erle Sparks Professor of Humanities, Pennsylvania State University

Wednesday, December 26, 2012

The Last "Real" Chemistry Kit?

The New York Times had a nice set of articles yesterday about a chemistry sets: that is, Chemistry Kits for kids. What's nice about this is that the set of articles covers all the bases: one recognizes the Harry-Potter-ish origin of the sets, another shows how the old experiments inspired today's scientists, a third explains why they can't explode so much anymore (and yet also describes the current sets' advantages), and at last there's a slideshow of old sets so you can see what's changed.

I agree that there's a bit of a sepia-tinged nostalgia about how dangerous the old sets used to be, but I agree even more that most of the sets sold today are not worth buying because they can be recreated with stuff you already have on hand. Why spend ten bucks when you can spend two? (For example: the typical red-blue acid-base indicator can be easily extracted from red cabbage for pennies on the dollar.) But recently I did find a set worth buying: the Thames and Kosmos CHEM C1000 and related sets.

The Thames and Kosmos sets have real chemicals, some of which are actually slightly dangerous, and real equipment like what I'd use in the lab. Although the reactions aren't too exothermic (i.e., no explosions) they do teach chemistry and safety with colorful, quick experiments. And if you really need explosions there's some gas-expanding experiments that come close. There's some little points of ingenuity, such as the way the chemical vials are opened, which is simple yet child-safe enough that it took this Ph.D. chemist an embarrassingly long time to figure out how to do it. So it's ingenious, real, and safe. If you're going to spend money on a chemistry set, I'd recommend this one. And Merry Christmas everyone!

Friday, December 21, 2012

Book Review: Exploring J.R.R. Tolkien's The Hobbit

There should be more books like this one. I used to listen to The Tolkien Professor's podcasts on iTunesU -- in fact, it's where I got the idea for the Day of Common Learning Lecture that turned into the "Trees of Life" book chapter on J.R.R. Tolkien and Paul Brand. In Exploring J.R.R. Tolkien's The Hobbit, Corey Olsen (AKA The Tolkien Professor) recapitulates his Hobbit podcasts in book form.

Olsen's focus is on the character of Bilbo Baggins, on the nature of luck in Tolkien's writing, and on what we can get from the frequent songs and poems. It gave me a new appreciation for the quiet faith of Tolkien: in his writing, luck is never just luck and the wind is also spirit, just like in the ancient Greek. Also, Olsen points out the teasing of the elves and the natural beauty of the Arkenstone. Tolkien's pure joy in the natural world is something we all share, and one of the reasons everyone can relate to these books. Although the elves are too somber in Jackson's movies, the natural beauty of New Zealand does provide this element. In Olsen's book, I would have liked more connections to Old English literature and to The Silmarillion (there's a really nice one comparing Gollum's riddle to Sauron's old speeches that left me wanting more). That can be the next book.

This book's unique strength is that it is written for the ordinary person interested in The Hobbit, and as such, it's a very nice gateway drug into the land of scholarship. In fact, I was able to give this book to my 10-year-old son Sam and he finished it before I did. That is as valuable as the Arkenstone to me. So while the writing at times felt a bit baggy and redundant to me, I've got to say there's enough scholarly articles out there for me as it is. Fellow profs, let's write more things like this for my boy ... and who knows what he'll be some day?

The Book-O-Matic

I remember that it seemed like every time I walked into Waldenbooks during middle school that Piers Anthony would have a new novel out, whether Xanth or sci-fi or whatever else he wrote. My friend Adam theorized that Piers Anthony was actually a computer that would churn out these things on a monthly basis by combining words, adjectives, and made-up geographies Mad-Libs style.

Looks like Adam was ahead of his time. Here's a story about a professor who has written a computer program that compiles books for niche markets, sold on Amazon, working kind of like Adam's theory. The process is designed to mimic a writer's process of determining the best things to write about and how they should go together. And it's patented. (Say Piers Anthony really was a computer: Can two computers sue each other for patent infringement?)

So what exactly is a book anymore? If you buy one of these it comes in book form, but it's essentially a well-crafted search engine result. This will probably work well as a super-Google but I suppose it can only enhance, not replace, true thought.

But now I'm worried ... will I some day find out that Stephen King has been a robot all along? Or, in a twist ending, M. Night Shyamalan is actually an old iMac? In the words of Keanu Reeves, whoa.

Thursday, December 20, 2012

Looking Back at Saturn

This beautiful picture was pieced together from many images taken by Cassini as it went "behind" Saturn, with the sun serving as the flashbulb. That's for your eyes. For your ears, Holst has a soundtrack. Actually, I know that my Dad worked on Cassini before it was launched and it's nice to know that in a way he helped take this picture.

PS: Try clicking on the "art and science" label link to see more incredible astronomy pics -- many are showing up on year-end best-of lists even now ...

Wednesday, December 12, 2012

Book Review: Evolution's Destiny

Yesterday, Stephen King. Today, RJP Williams. What other blog gives you this?

I have written (and spoken) about the idea of Williams before and as for his ideas, I summarize many of them in my Survey of Physical Chemistry course (last I checked, the only Survey of Physical Chemistry course on iTunesU). If Owen Barfield's right and all authors write the same book repeatedly, then Williams definitely stays true to that statement and to his own character in this one. Evolution's Destiny: Co-evolving Chemistry of the Environment and Life is another facet of the same ideas, and the ideas are fascinating enough that it's worth reading them again.

Perhaps it's because I'm reading Return of the King aloud to the boys as I went through this book, but the essential Britishness of Williams's and Tolkien's writing really stands out to me. Even the sentence construction and the drawing of the graphs (or maps) is understated. Reading Williams is not like reading science writing, it's reading real science -- after all, it's a scientist emeritus putting together inorganic chemistry with evolution. Those are kind of big subjects, and this is kind of a big-idea book of the sort that we need more of.

This new book of Williams's finds him with a new co-author, R.E.M. Rickaby (those with a mere two initials need not apply), who is a geologist. As a result, in the first third of the book, geochemistry takes precedence over geobiochemistry, and there's some interesting passages about the chemistry of rocks and the like. If there's something I wanted to change about Williams's writing before, it's that I wanted more references and evidence along the way rather than sweeping (yet still scientific) generalizations. Rickaby's geological chops make it clear that this book is more substantial in that regard from the beginning.

The really nice thing is that the second two-thirds of the book, when Williams recapitulates his to-me-familiar scheme of biogeochemistry driven by oxidation, the references and evidences (mostly) keep up. I was already familiar with the work of Dupont, Alm, and others published since 2006, and how it supported Williams's earlier hypothesis with genetic analysis, but it's awful fun to see Williams incorporate their findings into his work. Bottom line: Williams was right. And for those who don't have the patience to read a chemist for a whole book, I'll work on translating Williams for the masses. Stay tuned.

Another thing about Williams is that after several books he has come out with the most evidence to go along with his most provocative title. Evolution's Destiny is determined by chemistry. I'm enjoying this meta-story and I enjoyed this latest installment. May there be more ...

Tuesday, December 11, 2012

Book Review: Full Dark, No Stars

Full Dark, No Stars is another collection of short stories by Stephen King. You may be wondering why I'm spending time on America's best-known horror writer. Not much science here, but I continue to find that elements of faith are there for those with ears to hear. Nothing organized but something universal. Has horror become the place to write about sin? Because this is Stephen King, the stories are not truly short (at least one is longer than the last novel I reviewed here ...) , and they come with moments of shock and grossness that are nearly unbearable, but that is the point. King's universe is not devoid of love or even justice, although they can be hard to find. They are that much better when found.

Two of the stories are really "ghost" stories but not in the campfire sense, more in the G.K. Chesterton sense. The first, "1922," is far and away the best. If you have time for one ghost-ish story, read this one. King's attention to detail in historical fiction and his ability to put it together into a suspenseful sequence that rings true is remarkable. This story is good like his recent novel about the Kennedy assassination was good.

He's writing several female characters in this, and I don't find them entirely convincing, but it's nothing that gets in the way of the story by any means.

I continue to find a substrate of goodness, or at least yearning for goodness, in all of King's stories (even in the shorter, "quick" one). With all the repellant detail they remind me of Old Testament stories in parts. In "A Good Marriage" I believe he acknowledges this. In the Afterword, King says (I listened to the audiobook after all): "If you're going into a very dark place ... then you should take a bright light and shine it on everything." I think C.S. Lewis even said something kind of like that. As King has matured as a writer, he's focused more and more not on the obviously supernatural -- the vampires, the mists of monsters, the telekinesis -- and more on the not-so-obviously supernatural, that is, the dark recesses of the human mind. I really can't take more than one or two of these a year, but in that kind of dose his writing is bracing, and I would argue worthwhile.

(One more word: listening to the audiobook adds an element of suspense to the mix because you don't know when the story ends. I may prefer King this way.)

Friday, December 7, 2012

Is It Networks All the Way Down?

Quick: What do the brain, the Internet, and the universe have in common?

The chemist in me wants to say that electrons are very important to each, just at different scales, but that's not really a unique relationship. Rather, there may be a deep commonality among them, in that they can all be described with the same laws of network structure. This is the conclusion of a paper titled "Network Cosmology" out of the Cooperative Association for Internet Data Analysis (CAIDA), based at the San Diego Supercomputer Center (SDSC) at the University of California, San Diego.

It's almost funny to see how much science bloggers have to bend over backwards to point out that THIS DOES NOT MEAN THAT THE UNIVERSE IS A BRAIN. Please, please don't think that. It's not, nor is it a computer -- at least, if it is, I doubt we would be able to understand that it is anyway.

What it does mean is that when you graph out how these three complex networks are organized, that there are structural similarities at a surprisingly deep level. The physical forces organize the universe; the demands of life organize the brain; the demands of information flow organize the Internet. There must be structures and laws that work well for network organization, and it's very possible we haven't found the deepest, best formulations of those laws yet.

I'm fascinated by a quick observation near the end of the paper that this may have something to do with dark energy, which structures the universe. Does that mean that dark energy is a manifestion of this organization in some way? But I'm way over my head here so I'll leave that to the physicists.

One of the most beautiful things in science is the ability to see the same ordered patterns (fractals?) at multiple levels, such that the patterns fit together simply and satisfyingly. This "Network Cosmology" fits the brain, the Internet, and the universe together just so, like a major chord of three notes, and this paper feels like a major chord to me at first glance.

Now let's let wide peer review continue to do its job and see if it lasts the test of time, or if it's just a one-hit wonder.

The Thinking Brain's Music

This is what a brain sounds like. With a little help from math and science, that is. In a recent issue of PLoS ONE, researchers used math to turn brain waves into music. The result sounds to me a bit like some of the music James Horner put into the most recent Spider-Man movie when Gwen was hiding from the lizard in the tower -- in other words, it actually almost sounds like music! (That was one of my favorite moments of the movie, by the way.) For those of us who can't read that music above in our heads ... um, for all of us ... the music itself is can be heard from where it's embedded on the left side of this Wired article.

The upshot of all this is that if brain waves can be turned into sound waves this easily, perhaps there's something to the idea that music is fundamental to consciousness. Your neurons are all singing together in concert as the waves of chemotransmitters and sodium/potassium fluxes rock to and fro inside your head.

Or, in fewer words, life is music.

Considering that tomorrow is the Christmas concert that my whole family* has been preparing for, for months now, it gives me hope that all those hours of prep for an hour or so of sounds might be worthwhile and real.

* Baby Ben and Brendan have been helping out by keeping us in shape running after them so that our stamina is up for the concert. Sam and Aidan will be in it!

Thursday, December 6, 2012

The Largest Work of Art is Under Your Feet

Speaking of the value of nuance, here are some incredibly nuanced NASA satellite photos of the Earth, which are particularly beautiful and diverse. A lot more complexity here than simply dirt, ice, and water. The whole gallery is found here at Popular Science. Enjoy! (In order, the landscapes I chose are from Iran, Iceland, Mongolia and the Mississippi.)

News Flash: Both Science and Faith Require Nuance, Reason, and Logic

A week ago Nicholas Wade, New York Times science writer, published an op-ed on science and religion, and a week ago the blogosphere lit up. There's a lot to write about in just that, because the atheist reaction to Wade's "accommodationism" surprised me. I merely found Wade's op-ed boring, occasionally wrong, and historically inaccurate, but ultimately inoffensive: on some fronts at least he was trying. Kind of like E.O. Wilson at times. I just didn't see it as something for people to get worked up about. But worked up people did get, leading to a long letters to the editor section in yesterday's Times, reproduced on the Why Evolution is True blog as "A bunch of us go after Nicholas Wade" (what do you call a witch hunt for people who don't believe in witches?).

Jerry Coyne was the first to "go after Nicholas Wade" by pointing out BioLogos:

"Organizations like BioLogos, founded by National Institutes of Health director Francis Collins, have spent many years and much money trying to turn Christian creationists toward evolution by “respecting their faith”. It hasn’t worked."

Never mind that BioLogos has only existed for half a decade or so now. People haven't changed their minds on a complex issue that rarely directly impacts them after five years of an organization's existence (BioLogos is just running their first big RFE now, in fact!). Time to throw in the towel on dialogue, then.

But it was really this sentence of Coyne's that caught my eye, pithily put but problematic:

"Teaching that the book of Genesis is a metaphor, as Wade suggests, is anathema to fundamentalists since it implies that Jesus died for a metaphor—the original sin of a nonexistent Adam and Eve."

Coyne is certainly right in that some unreflective fundamentalists say this. But repeating it (unreflectively) as applicable to all Christians, even all fundamentalists, is the strawiest of straw men. It's the "Lowest Common Denominator" argument: scrub away all nuance from the argument and then attack the others for believing something without nuance. It's the mirror image of the fundamentalist attacking the evolutionist because single nucleotide changes can't add up to make a flagellum. The evolutionist might even agree with that way of putting it, but it's the other ways of changing DNA that might be true. (In this case, changes larger than single nucleotide changes, for example.)

If Coyne wants fundamentalists to adopt nuance beyond the arguments of intelligent design then he himself needs to adopt nuance toward theology. But I don't blame him for this lack of nuance, because the church itself has slipped into a materialist interpretation of original sin, a medieval-style thought in which something must physically soil the atoms passed down from father to son. Then Jesus' redemption would be some kind of physical actions that scrubbed the soul-atom clean, some kind of cleansing enzyme (in his blood?). If you think about it enough it doesn't totally make sense, whether you're fundamentalist or atheist.

There's also the matter of history. There's no evidence that Jesus would have thought of original sin this way. Paul has some verses that were interpreted by Augustine a certain too-material way, perhaps, which blossomed into the medieval-substance way of looking at sin. The church needs to do a lot of thinking about what this means, and has done too much "coasting" on what Augustine thought, with subtle tweaks that have degenerated the doctrine of original sin through the years into the medieval-substance way of looking at it that Coyne thinks is our only option.

It comes down to what Jesus died for. If we reduce it to some sort of heavenly transaction that reverses Adam and Eve's bad choice, only, then maybe Coyne has a point. But nothing in Christianity is heavenly only. Jesus died to show us how to make choices now that will affect the future, not just to reverse some event in the distant past. If Jesus' death means anything, it means that change and redemption can come now. If Jesus can change people now and put together a community that is different from the world in a qualitative way, we must start from that, and then we can worry about exactly what Adam and Eve were and what the nature of Original Sin is.

Of course, that paragraph itself is without nuance. We're never going to perfect the present, and it's fine to think about the past. But this one-track-mind-focus on Adam and Eve is clearly missing the point of what Jesus did and continues to do. I'm just frustrated with the lack of nuance. The intricacies of theology are just as fascinating (and as dependent on logic) as the intricacies of science, and I'm tired of people selling one or the other short. I'm as fascinated by the question of "What is original sin?" as I am by the question of "How was life formed?". We need nuance all around. (Isn't that what the Beatles sang -- "all you need is nuance"? No?)

Coyne closes with "Reconciliation doesn’t change minds; reason and logic do." For the record, I disagree that reconciliation is useless -- in fact, reconciliation is one of those Things That Jesus Died For, possible more than original sin, if you read all of Paul. But beyond that, I'm agreeing with the second half of the statement and am asking for reason and logic. I'm just asking that the reason and logic be applied theologically to the doctrine of original sin as well, by the church first and then by its critics.

Whatever the answers are, I can tell you that they'll be complex enough that it will take more than five years for an originization like BioLogos to even raise them, much less answer them. Let's leave Nicholas Wade alone for daring to propose something, even wrong-headed as it may be, because talking this out is the only way we're going to get anywhere.

Tuesday, November 27, 2012

Book Review: The Alchemist by Paulo Coehlo

I had a feeling going into this book that it's a little too well-loved to be orthodox. That feeling was right. But overall I'm still glad I read it/listened to it, and not just because it was read by Jeremy Irons on the audiobook. That's because I was able to distill some gold from the dross, but believe me, it is all mixed together in this book. You have to be an alchemist of your own to separate good from bad here.

Myself, I'd take the frequently interesting Biblical allusions (from Melchizidek to Joseph to Abraham to Jesus and the woman caught in adultery) and find what's worthwhile in them, and I'd leave the pseudo-gnostic drivel behind. But there's hints of what to toss, such as the words "personal legend", as in "find your personal legend" (there's GOT to be a better translation of that term), or the "all is one, so everything should be content as it is" stuff.

At least sin is present but it's not really dangerous or warping. Inaction is a far greater sin than action. The great god Plato rises over this book, with a bit of Spinoza, and some other philosophy that drove by too fast to pin down.

It's a fast read, and provocative, just it's only half right, so if you have time to read something half right then this is for you. This is one of those books that I'd be fascinated to analyze in detail why it's so popular, what is true and what is not, because it frequently has flashes of insight, but it also has flashes of the opposite of insight, too. (Would that be out-blind? See what deep questions this raises for me?) I'd say read it skeptically. But that's true for everything, right?

Wednesday, November 21, 2012

A New Game: Find the Point of Vaccination

I've just come up with a new game. The following is a graph of diarrhea-caused deaths of children in Mexico month by month for eight years. At one point on the graph, a vaccine was introduced that was designed to stop diarrhea-caused deaths of children. The game is, can you pinpoint when the vaccine was introduced?

(If I could do Encyclopedia-Brown-style upside down type I'd do it here!)

ANSWER: May 2007. Any point from April to September in 2007, after the seasonal spikes of death stop, will be counted correct for the purposes of your grade.

Just for reference, most of my test questions are not this easy.

For more details, you can find the original paper here. And thanks to Matthew Herper from Forbes magazine for writing the article that brought my attention to this graph.

Tuesday, November 20, 2012

Don't You Go Breakin' My (Glass) Heart

The company that built this glass vasculature may not have intended to build a work of art, but it did. What was intended was an accurate model of all the major blood vessels in proper proportion so that flow tests could be carried out. What resulted is a beautiful, tree-like structure that walks the line between life and mechanism. More info found here.

I can't imagine how carefully you must move when you're carrying one of these.  I await the inevitable artist who will make videos of worn-out glass models smashing on the sidewalk or something like that.

Monday, November 19, 2012

Quick Thought of the Day

It's true that extraordinary claims require extraordinary evidence.

I'd extend that: The ability to make an extraordinary claim is itself a piece of extraordinary evidence. Evidence that you are alive and wondering in a vast and marvelous universe. How under heaven did that happen?

(In memory of Carl Sagan.)

Ambiance and Archaeology

If the nicer restaurants are all dark, then maybe the nicer ancient Roman villas were too. In this archaeological study, scientists created a simulation of an ancient Roman villa and turned down the lights -- more specifically, they put in lights that would flicker with warmth like candles rather than reflect cold blue like electric lights. Check out the result above. Wouldn't you rather live in the house on the left? Everything looks nicer by candlelight, including the tilework and mosaics.

This reminds me of a nighttime tour of the abbey on Mt. St. Michel I took about a decade ago. In the dark it was lit with brightly colored floodlights but the shadows definitely left more to the imagination and made the experience unforgettable. The type of light is important. Looks like the Romans designed for candlelight and didn't anticipate fluorescent bulbs!

Also, this reminds me of what I read about what it must have been like to enter the Jewish tabernacle in the time of the Judges. It would be dark and mysterious and very impressive. Much more like the picture on the left than the one on the right.

And, at home, why clean up after the kids when you can just turn down the lights?

Sunday, November 18, 2012

A Glass Pyramid of Books

If the Egyptians built stone pyramids for Pharoahs, we're building glass pyramids for books. This is a library in Rotterdam, but it reminds me of the new Central Library here in Seattle. I've been to our library several times but have never checked out a book from it -- I just like to walk around such a unique, free, and open building. It's more like a park than a bookstore, and that's OK with me. I've also walked around the library in Back Bay/Copland Square in Boston with a similar sense that just walking around can be part of the library experience. Maybe someday I'll get the chance to walk around this library in Rotterdam too. For now we've got the pictures at this link.

Friday, November 16, 2012

Book Review: The Age of Miracles

Finishing a book in the genre of "apocalyptic science fiction" does not usually inspire the emotion of gratitude or wistfulness. But for this book it does. Most sci-fi books I've read don't celebrate faithfulness, or sensations, or growing up (2001's version of the human race growing up definitely does not count, I mean truly growing up like all of us have to).

Part of the sign that The Age of Miracles is a different kind of sci-fi book (if it really can be shelved there, it's arguable that it can't) is that it's told unflinchingly from the perspective of a 12-year-old girl. The apocalypse in this case is a quiet one, in which the Earth's rotation slows down from its precise 24-hour tick and then stuff starts to go wrong accordingly. The genius of Karen Thompson Walker is that she couples this kind of not-a-bang-but-a-whimper setting with the gradual and sudden changes of adolescence, and does it with a perfect tone, not sentimental but elegaic, never overstepping her narrator's voice. The subtle realism of this book insinuates itself into the listener to the point that I caught myself occasionally thinking of the book as real. A truly bittersweet, simple joy of a book.

DNA Polymerase, Stereograms, and Faith

Last year I was asked if I'd let a few videographers tape my class for a learning-and-faith project from different disciplines sponsored by the CCCU, a collection of Christian universities including SPU. So here's the final product, about 10 minutes of class about DNA, stereograms of protein structure, and how that reflects the "Two Books" philosophy of science and faith (thank you Sir Francis Bacon, which reminds me to check out my colleague Rod Stiling's talk on Newton on the same "channel"!).

Here's a link to the video (can't find an embed code yet!):

From this "experiment" I found out that having a videocamera trained on me causes my voice to rise in pitch by a certain interval. Interesting result ...

Monday, November 12, 2012

Two Concrete Ideas: Glow-in-the-Dark Roads and Self-Healing Bacterial Concrete

What's better than a good idea? Two good ideas in one blog post! Both have to do with concrete or asphalt, so I thought they'd go together.

1.) Even when I mentioned the long-lasting glow-in-the-dark pebbles for driveways earlier, I didn't think of this use for them: embed them in roads for glowing directional signals, even without streetlights. They can even be made temperature sensitive, so when the road gets icy, big glowing snowflakes could appear on it. This is a great idea (although implementing it could run into some problems in Seattle given our infamous lack of sun in the winter months).

2.) Instead of glowing pebbles, mix in something much smaller into concrete: bacteria. Bacterial spores can survive a long time without water or nutrients. When the concrete is cracked, the water will wake them up (like Sea Monkeys) and they'll start making carbonate. Deposits of calcium will react with this to make calcium carbonate (calcite) which is a little bit of mortar that will fill in the crack. The result is self-healing concrete.

The problem is keeping the bacteria alive in the concrete for a long enough time, but they're working on that. Given how long some spores can survive, this might just work.

Realize that this shows that you can use bacterial spores as dormant little chemists waiting to control their environment through chemistry: in this case, ejecting carbonate and making concrete in a newly formed crack. Life is a powerful thing, if you can keep it alive in the place where you want it to work.

Sunday, November 11, 2012

Dante + Scientific Fraud = Peer-Reviewed Amusement

Midway upon the journey of our life // I found myself in a forest dark // Oh, and I was a scientist too ...

Science blogger Neuroskeptic has come up with a spot-on version of Dante's inferno translated into the realm of scientific fraud. The picture give you a general feel for the shenanigans but to really enjoy it you should read the short, pithy, and peer-reviewed article found here.

My favorite thing about it may be the way Neuroskeptic makes the punishment fit the crime in exactly the same way Dante did. Each level just fits the universal sense of justice that we all share. And it makes me wonder if Dante intended us to take his tale only semi-literally, like Neuroskeptic does. There's value in this kind of semi-literalism to be sure.

Saturday, November 10, 2012

Are We in a Goldilocks Zone in Time as Well as Space?

A recent finding has just blown my mind and I'm not sure if anyone else has put it together with other results yet. To me at least, putting it together, it makes the universe look much different than I thought at the beginning of the day, so I'd like to share it with you and see what you think. It also suggests that Earth is that much more special. Let me explain.

The Kepler space telescope is exciting stuff, because it's looking for planets around distant stars and finding them all over the place. Here's an orrery of the planets found by Kepler (and even this is more than 18 months old now!):

The real key is to find a planet in the habitable zone (the "Goldilocks zone"), which is the right distance away from a sun so that ice melts and steam condenses, giving liquid water. Note that even this is only one element in the recipe for life, but it's got to be one of the most important ones. Here's one planet recently discovered to be "in the zone."

But, like I mentioned, you need more than liquid water for life. For instance, you need metals far down on the periodic table like iron, molybdenum, etc., to build a rocky planet out of, and to provide important catalysts for life. Basically, you need a decent portion of the periodic table built in order to do complex chemistry. After the Big Bang you start with the simple stuff, hydrogen and helium, and have to build up to iron and company. That's takes a while, past the first generation of stars, at least, according to this article, "a few billion years."

I've been aware of that for a while, and that some people say you need more than "a few" billion years, you need something more like 7 or 8 billion years. (You need at least three because the oldest stars of this type are about 10 billion years old, and our sun's right in the middle of that.) The universe is 13.7 billion years old and the earth is 4.5 billion years old, so by that logic, there's a "few billion"-year window in which an earth-like planet could have been built and produce complex life. Kind of like a "Goldilocks zone" in time rather than space. I've always wondered if the reason why we're not hearing much through SETI or seeing many aliens coming down from the sky (well, I haven't seen them, have you?) is if we're kind of the first kids on the block, because it's taken this long for the periodic table to form and then a planet to form and gestate life. I've assumed there's plenty of time for more planets and stars to form in the universe. I may have assumed wrong.

So, you need water and you need metals. But don't forget, you also need a star to have formed at the same time as the planet. The "photo" part of the whole photosynthesis thing is kind of important. That's why I was shocked to hear that a recent comprehensive study of star formation has suggested that the universe is almost done making new stars. By looking at star formation rates, the astronomers concluded that the golden age for star formation was 11 billion years ago and has been declining ever since, and recently it's just dropped off the table. Check out this graph:

It's not that the universe's biological clock is ticking ... it's more like it's wheezing its last. The universe is not just out of childbearing age, it's close to collecting retirement. [Insert bad "my universe is so old/how old is it?" joke here.] This -- if it holds up, and it looks solid to me -- is one of the most mind-boggling things I've read. It also means that complex life is that much more likely to be rare and precious. If it ain't happened yet, it ain't happening.

Maybe complex life can form in 3 billion years rather than 4 (maybe the "boring billion" didn't have to happen ... but my impression is that it did). Maybe a star has formed 2 billion years ago that will have complex life in 2 billion years. But it looks like the constantly-expanding universe combined with limited energy and matter would suggest that if something hasn't happened yet it will not have much more of a chance to happen. That's a "few billion"-year window that may have already closed. The numbers are adding up to be surprisingly restrictive in time, even in a universe that is huge in space beyond comprehension.

As my physics colleague likes to quote, "There are two possibilities: either we are alone in the universe or there are others like us out there. Either way it blows your mind." For me, the likelihood of the former just got raised, and my mind is suitably blown.

Wednesday, November 7, 2012

Play Without Ceasing

Great article (with a great title) written by my friend Jeffrey Overstreet about the overlap of play and work in the recently released issue of Response (the SPU magazine). Oh, and they took a picture of me playing with LEGOs in my lab too, but I'm too self-conscious to put that on my blog. Maybe it's time to change my Facebook profile pic?

Wednesday, October 31, 2012

Book Review: This is How You Lose Her

You must be a good writer if a book that's a bit of a let-down is still a finalist for the 2012 National Book Award. At least that's my take on This is How You Lose Her by Junot Diaz: a bit of a let-down. The Brief Wondrous Life of Oscar Wao is an incredible book (reviewed previously!) and elements of what I loved about that show through in this collection of short stories occasionally, but there's just not enough history or nerd-lit in this to make it as surprising and, well, wondrous as the novel. There's some powerful moments in it but there's also some moments that aren't quite as powerful as they should be, and sometimes I felt buried under an avalanche of trivialities and superficial events. Also, the characters just aren't as likable, and I know, they aren't supposed to be likeable but it sure helps to move things along if they are. On the level of literature Diaz is still the excellent writer he always was -- but I have to admit if this was the first book by him I read, that I probably wouldn't read another. Still, Oscar Wao was such a revelation I will definitely read the next novel by Diaz, and I'm sure that'll be worth it.

Saturday, October 27, 2012

Singing Sand: The Rocks Cry Out

Several dunes around the world "sing" when the sand is disturbed, and no one knows quite why. But now we seem to be closing in on what it is: not the shape of the dune but the type of sand in it. In other words, not so much the topography as the geochemistry and the geophysics.

The two different-sounding dunes in the video above still sound different when the sand is put in a shallow pan in the lab, and sifting the sand will change the sound. I find this all very cool. What kind of musical instruments could result from this? Something like the theremin at the very least.

More on the data, and another video, can be found here.

Wednesday, October 24, 2012

Elevensies (AM or PM) Soon Available at Your Local Franchise

J.R.R. Tolkien and Denny's. We have truly amused ourselves to death:

Tuesday, October 23, 2012

Beautiful, Breaking Bat

(Here I go making a pun reference to a  TV show I haven't seen but really want to start, some day ...)

I didn't see this happen but heard about it second-hand: the hit that broke open Game 7 of the NLCS last night shattered the hitter's bat and actually hit the bat two or three times. Just look at this:

Something about that is just beautiful, the way the bat bends and the ball just rolls along the line of the wavering wood of the bat, more scooped than struck. It's like one of those slo-mo water droplet pictures, and it basically meant the Giants return to the World Series and the Cardinals don't. So, more Angel Pagan!

Nice analysis of whether this was a legal hit or not, and why it faked out the shortstop, here at Fangraphs.

Monday, October 22, 2012

How to Advertise Science: Gold, Cat Pee, and Einstein's Happy Thoughts

Yes, that's really 2 oz. of gold.

This series of billboards (and other outdoor advertisements) put around Vancouver by the Vancouver Science Center shows that a clever marketing campaign is a lot like good teaching.

My favorite's either the Cat Pee one or the Gold one. I guess the gold one's classier but the cat pee one cracks me up. It's also the biochemistry one and a reason to carry around a UV light on your keychain (well, I do, in fact, why do you ask?).

Hopefully in my biochem lectures I can capture this spirit sometimes. This is what science teaching is about.

Oh, and thanks to my fellow physics prof that I co-teach a science seminar with, I now know that this particular advertisement ...

... has a unique place in science history, because it is this thought in 1907 led Einstein to the theory of relativity (his "happiest thought" of his life). It's an amazing world if a scale in an elevator can lead, through the right train of thoughts, to predictions of black holes and gravity warping space itself.


Sunday, October 21, 2012

Book Review: Life Ascending

This is the first book I've read by Nick Lane and I already know I'm going to read more. Lane approaches scientific controversy with a light hand, but he talks about the real issues and the real science going on. Lane is a practicing biochemist who writes popular science, and it shows. This book is framed around 10 "innovations" evolved by life: all the way from the origin of life to mitochondria to consciousness and death. A lot of the general issues I've become familiar with from the scientific literature (Lane himself writes on these topics for Nature and refers to those articles throughout the book), but this book is at the Goldilocks level of enough but not too much detail. Sometimes I feel like the book gets a little too scientific for a general audience, and once in a while I wonder if the study Lane is highlighting is really "all that"; for example, I'd like to see the findings replicated that he reports as a tiny change in mitochondria causing a huge change in human lifespan, but it appears to rest on one paper from Japan. I do give Lane props for addressing consciousness with fairness, arguing for his interpretation rather than disparaging the Pope as he quotes him, little things like that. As interesting as the content of this book is, it's the tone that really impresses me and is something I'd like to emulate from my viewpoint.

Saturday, October 20, 2012

And Now For the Trolls' Point of View

This is a very well made and very short take-off on the Mines of Moria. Now I'm feeling bad for those poor trolls.

Friday, October 19, 2012

Another Reason to Like Gummi Bears

Gummi bears are already my favorite candy, but the fact that they do THIS when you add one (just one!) to heated potassium perchlorate piles on the reasons to love 'em:

Oxygen is a powerful element, no? It's what turns a gummi bear into a firework (and CO2).

Tuesday, October 16, 2012

What's Inbetween a Single Bond and a Double Bond?

Anyone who's made it through the gauntlet of organic chemistry may remember that there's not only single bonds and double bonds, but there's "mixture" sort of bonds half way between the two. You can tell how much of a mixture by measuring the bond length accurately; the shorter the bond, the more "double bond" character it has. Measuring these bond lengths can lead to some very pretty pictures, with more pretty pictures here:

I got this one from this blog but it's all over the web in other places as well. It was made by atomic force microscopy looking at a "nanographene" molecule that's basically a collection of fused benzene rings. Each ring is a hexagon with six single-bond sides and three double bonds on top of that. The question is, where exactly do the double bonds spend their time most?

In a single hexagon/benzene ring, the three extra bonds are distributed evenly and each bond is more like a 1.5-bond than a single or double bond. Nanographene is more complex structurally and has more complex patterns of electron-sharing. The IBM researchers found that if you look at the hexagon in the exact center, that those bonds are shorter than the ones radiating out from the center, meaning the electron-sharing is a bit better in the ring in the center, like they're spinning around on the innermost wheel. Like a record player, if anyone remembers those. The "spokes" are a little stretched and are slightly worse bonds.

And I just realized ... this looks like a Settlers of Catan board! The smallest game of Settlers ever may now be possible.

Sunday, October 14, 2012

The Sociology of Middle Earth

It was bound to happen. Someone was bound to take the detailed years and dates of Tolkien's appendices from Lord of the Rings, etc., and make them into graphs and charts. Here's the link; go at it!

Two quick comments:

1.) Yes, the first chart proves a point, but I think it doesn't do much good to rail against the lack of women in Tolkien. He's kind of done writing, after all, not like you'll get him to write more for Arwen. He was kind of stubborn about that stuff. It's much more interesting to discuss Tolkien's roles for women in the context of the "saga" he was trying to write. In other words, the number of women in Lord of the Rings should be discussed in the context of the number of women in Beowulf or the Elder Edda. In that case I think you'll see Tolkien doing some very interesting things with the role of women, such as Eowyn (post-ring). But, yeah, overall it's a boy's story. (I'd like to see a chart like this for Jane Austen, although "weighted by lines given" would be even more interesting!)

2.) The distance graph is my favorite. For instance, it shows that about as much time was spent in the Hobbit as in the Lord of the Rings in total, for all events. In fact, more time was spent lounging around Rivendell in the latter! This gives me hope that maybe, just maybe, the source material for the Hobbit is rich enough to support three movies by Peter Jackson. We'll see.

Friday, October 12, 2012

Set the Controls for the Heart of the Nebula

(This makes two old Pink Floyd references today -- the first was when I was talking about separation science in biochem lecture and showed the cover of Dark Side of the Moon as an example.)

Here is a very detailed 3-D reconstruction of what a nearby nebula located in the constellation of Cepheus looks like (probably). It's quite beautiful, and reminds me of the Doomsday Machine from the original Star Trek:

There's a whole site of these out there located here. And thanks to this post for alerting me to this work of art. Or is it science? Hard to tell.

Tuesday, October 9, 2012

No Tenure for Indiana Jones

McSweeney's published a great piece that is an academic review document for Dr. Henry "Indiana" Jones, explaining why his tenure has been denied. Read it here.

I just prepared one of these files myself. In fact, I think this would be a little funnier if it wasn't quite so negative -- academic documents are not as negative as this one, but the application of experience to standards does ring quite true.

I have an idea for one of these that is a "student evaluation form" of Jesus as teacher/rabbi. Maybe some day I'll have time.

Any other ideas for academic reviews of prominent figures?

Wednesday, October 3, 2012

LEGO to Teach Color Inversion?

So there's a use for all those pink pieces after all! If you build something like this:

And then invert the colors of the picture, it suddenly looks like this:
Something tells me someone could make a pretty cool color physics learning exercise out of something like this ... let the students build structures and invert the colors to see what happens.


Sunday, September 30, 2012

LOST as a 1987 Computer Game

What if LOST had been a point-and-click computer game like what LucasArts used to do? Admit it, it fits like hand in glove. Go to this link to see more screens from your possible pasts.

The only other option would be an Infocom text adventure. Especially with entering the numbers into the Dharma Initiative terminal. Unless that actually already exists ...

Thursday, September 27, 2012

Liquid Nitrogen + a Trashcan Full of Ping-Pong Balls

Oh, I so want to do this. And the beauty of it is, maybe some day I will! Just need to pick up the ping-pong ball jumbo-pack at Costco.

Subtitled: The power of PV=nRT.

Monday, September 24, 2012

Which MacFarlane's Lantern is Better?

It's fun having a last name that comes from a clan in Scotland. Sure, the MacFarlanes are a small clan, but that's only because they stole cows from the Calhouns and all their men kept getting killed off (or so I'd been told). I found plenty of women's names on gravestones in my trip to Scotland with MacFarlane as their middle name ... not so many men. But I'd always thought that MacFarlane's Lantern referred to the full moon when the MacFarlanes would go cattle raidin'.

Today I found this post on Strange Maps about Scottish tartans and history, of interest to anyone with one of those 16 last names, and I saw immediately that it had a different version of history:
(15) Clan MacFarlane
In past, more violent times, the Moon in Scotland was known as MacFarlane’s Lantern, for the clan was famous for its daring night-time raids on the English during Scotland’s Wars of Independence. The last chieftain of this once much-feared clan died in 1886, since which time its chiefship is dormant, although the clan remains armigerous.

So I'm torn -- do I want my ancestors to be brave or rascals? What would you choose? I'll reconcile the two by imagining them raiding British cattle.

When I visited the old clan grounds in my Scotland trip, I was aware of the chiefship vacancy, but I couldn't find out how to apply ... probably involves something horrible like animal sacrifices or caber tosses or, worst of all, eating haggis.

Music as Medicine

As a pre-med advisor who's married to a musician (and as someone who sort of collects inspirational academic speeches as a hobby), I thought this Welcome Address to The Boston Conservatory really nailed a lot of why we do what we do. Read the whole thing by clicking on that link ... or if you really need to cut to the chase, this is the conclusion and heart of it:

"If we were a medical school, and you were here as a med student practicing appendectomies, you'd take your work very seriously because you would imagine that some night at two AM someone is going to waltz into your emergency room and you're going to have to save their life. Well, my friends, someday at 8 PM someone is going to walk into your concert hall and bring you a mind that is confused, a heart that is overwhelmed, a soul that is weary. Whether they go out whole again will depend partly on how well you do your craft. 

You're not here to become an entertainer, and you don't have to sell yourself. The truth is you don't have anything to sell; being a musician isn't about dispensing a product, like selling used cars. I'm not an entertainer; I'm a lot closer to a paramedic, a firefighter, a rescue worker. You're here to become a sort of therapist for the human soul, a spiritual version of a chiropractor, physical therapist, someone who works with our insides to see if they get things to line up, to see if we can come into harmony with ourselves and be healthy and happy and well.

Frankly, ladies and gentlemen, I expect you not only to master music; I expect you to save the planet. If there is a future wave of wellness on this planet, of harmony, of peace, of an end to war, of mutual understanding, of equality, of fairness, I don't expect it will come from a government, a military force or a corporation. I no longer even expect it to come from the religions of the world, which together seem to have brought us as much war as they have peace. If there is a future of peace for humankind, if there is to be an understanding of how these invisible, internal things should fit together, I expect it will come from the artists, because that's what we do. As in the concentration camp and the evening of 9/11, the artists are the ones who might be able to help us with our internal, invisible lives."

I have one problem with the last paragraph (just a little idolatry going on as Barfield might say, nothing too unusual): religion that doesn't do this is not religion, because this healing is precisely the point of God's saving action. See Micah 6:8 + James 1:27 + the whole book of Isaiah (which translated means "God saves" and is one of the more incredible word symphonies ever assembled). 

Sunday, September 23, 2012

What If We're All Wrong About Genesis 1?

I spend a lot of my time arguing (with myself as well as with others) about what Genesis 1 means. After all, it's the first words you read in the Bible, and it literally covers all of creation in its scope. Whatever the conclusion, I start from the conviction that Genesis contains multiple layers of truth, and learning to read those words is more complicated than the child's process of learning to read: they're translations from another language, they're thousands of years old, they're more poetic than prosaic, and the ancient texts don't even bother to include the vowels. So it's a problem more complicated than the most complicated Doctor Who episode. Still, both Doctor Who and Genesis are fascinating because they're complicated; it's their puzzle-like nature that makes the best parts the best parts.

But for all the debates about what Genesis says about the events of creation (that happened, at any rate, before any human was around to observe them); for all the sturm und drang about the ancient terms like "firmament" (which, needless to say, implies something "firm" up where we know there is empty space); and for all the people leaving and coming to different faiths from the results of interpreations of these texts, I just heard a talk that made me wonder, what if we're all wrong? Not wrong in content, necessarily, but wrong in emphasis? What if what really matters about Genesis is another point entirely, one that does not negate arguments about creation but rather goes in another direction entirely?

The talk that sums this up best is a half-hour lecture (less if played at 2X) by Paul H. Seely at the recent ASA national meeting in San Diego, titled "Why the Framework Hypothesis Does Not Work and What Does." You can listen to it here.

In this pithy little talk, Paul Seely* argues against the framework hypothesis, which basically says the six days in Genesis are a poetic device to organize nature into heavens, sea/sky, and earth, and then to fill each of those domains with, respectively, stars, fish/birds, and plants/animals. Now, when most people argue against the framework hypothesis, they say that instead, we should read Genesis 1 as a literal sequence of events, organized chronologically (then there's the question of how long the timescale is, what each word means, how X could come before Y when X depends on Y ... ). Interpretations that run the gamut from the framework hypothesis to literal six-times-24-hours creation basically assume that this text is focused on creation itself. Seely changes the focus when he says, what if Genesis 1 is as much about the Creator, and as much about us, as it is about creation? And if Genesis 1 is for us, maybe it's as much about how we should work as it is about how God worked.

It should be clear when we look at the ancient Hebrew terms that we're scratching our head for exactly what they mean. One of the biggest headscratchers is how could light be made, and morning and evening, before the sun and stars were made? Seely's answer is, because when you're working you need light. That's what everyone understood back then. So for God to work, first he made light so he could work. He was showing us how to work, and he put it in terms we (back then) could understand -- just like Jesus came to us using terms we could understand. It's a basic fact about God that he pursues us and meets us where we are, speaking Hebrew to the Hebrews.

If this is so, the most important thing about Genesis 1 is not what these weird Hebrew vocabulary words mean so we can sequence what kind of creatures were here first, although that may be an interesting puzzle. Did the placement of dinosaurs in the sequence of creation really matter to the ancient Israelite? Is the sequence of Genesis 1 supposed to be some kind of hidden Bible code (like a DVD's easter egg), so that only after 5000 years we could finally look back and see, hey, they didn't know what it was about but we do! Or is what science can see (at last) not the most important thing at all? After all, the text gives us five verbs at the end of the sequence in a massive repetition: "God ended his work," "he rested," "God blessed the seventh day, and sanctified it," "he had rested." Last I checked, none of us can create a universe -- but we all work and we all rest. We all choose how to rest, and we can all choose to rest once every seven days.

What good news! It's a holy thing to rest! This is something to shout from the housetops. And I'm not kidding.

There's good puzzles, and real truth, in knowing that God worked to create creation. Thinking about how the Genesis 1 days are ordered can complement our scientific observation that creation too is organized and ordered. I think this insight is so important that I'm thinking of writing a whole book about how the world was ordered by chemistry, in fact. I believe Genesis 1 contains truth on that level. But the usefulness of that insight is more limited than an insight about how you should organize your work, day in and day out. For those of us not actively writing a book about creation or investigating the science of origins, what we really need to know is that God himself rested after six days of work, so we should too. The other stuff is secondary, or at least more infrequent.

Resting is deceptively hard. Both me and my first-born boy have trouble going to sleep with all the thoughts, memories, even regrets of the day whizzing around through our heads like a little hamster on a wheel. To bring the good Doctor back into it, one of the best parts of yesterday's Doctor Who episode ("The Power of Three") was when the Doctor had to wait -- and ended up driving himself and everyone around him crazy, like a five-year-old with a sugar high. He couldn't wait. Neither can we. But God says we need to when he says we need to rest.

Every time we sleep we die a little death and become completely dependent on what is beyond our control. Maybe that's why the stories of those who die in their sleep are so unsettling. It could happen anytime. We are most vulnerable when we sleep, and we are that way one-third of our lives. Actually, we're that way our whole lives; we just don't always know it.

One of my basic rules is, if we want to understand Genesis, we need to look at Psalms, and Psalms backs me up on this. In Psalm 127 I find that this attitude is at least part of what we should take away from Genesis 1 -- and if we aren't maybe we're reading it wrong. I'll close with these thoughts on dependency and rest:

Unless the Lord builds the house, they labor in vain who build it;
Unless the Lord guards the city, the watchman stays awake in vain.
It is vain for you to rise up early, to sit up late, to eat the bread of sorrows;
For so He gives His beloved sleep.

[More thoughts on rest and Genesis, but from the standpoint of Hebrews, found here.]

* = I realize that many others have indeed made this argument, but I'm speaking from my own experience, which has heard those other voices but not really heard them till listening to Seely's argument all at once.

Saturday, September 22, 2012

My Favorite Astronomy Photo of the Year

Since this link has the Royal Society's best astronomy photos of the year, and this photo below is my favorite of the Royal Society's album, then it must therefore be the best astronomy photo of the year. I see no problem with that logic. Enjoy the photo. (The green is oxygen, which may mean oxygen is my favorite element?)

Friday, September 21, 2012

Simplifying the Cell

This is a wonderful video that teaches students about a different way to look at the contents of a cell. Looking at something differently is the first step of education, after all. Perfect for the first Biochem lecture of the year (coming up on Monday). There's a multiple choice question ... can you get it right?:

Wednesday, September 19, 2012

A Galaxy for a Driveway

No, this isn't about Rainbow Road in Mario Kart. It's about glow-in-the-dark pebbles you can scatter on a gravel driveway so at night it looks like this:

I'm thinking this could be useful for dark paths at a campground, too. The possibilities are endless. An "easter egg"-like hunt after the sun goes down? Cosmic-Bowling-style fish tanks? Kitchen countertops for midnight snacks? Feel free to develop your own...

[via Discovery News]

Written With the Heavens

The site at this link can turn any message into a collection of galaxies that appears to spell out that message. Even, for example, a certain blog title:

My first reaction was to spell out Sam's name since he was the birthday boy yesterday. A nice (and free) gift.

For some reason, about 2% of the messages arrange the galaxies to spell out swear words ...

[via Popsci]

Sunday, September 16, 2012

Book Review: Reading Isaiah: Poetry and Vision

Reading Isaiah: Poetry and Vision by Peter D. Quinn-Miscall is my "textbook" in a way. My university is reading Isaiah together during the Fall Quarter and I took a day-long class in Isaiah (given by my theology department colleague) about a week ago. I've always been fascinated by this sprawling, vivid and even contradictory book, and Quinn-Miscall's "textbook" is a good introduction.

Quinn-Miscall translates big bunches of text himself anew and resists the temptation to split up Isaiah into parts, instead looking at how different images are used throughout the book. This ties the book together rather than forcing it apart, and it's how I choose to look at it, too. The juxtaposition of the different images and parts of Isaiah is one of the powerful things about the book. I have the meta-image of a large stained glass window, with jagged chunks of glass, some blood-red, some sky blue, and some the green of a new tree; some faces from history painted in there; and the sun blazing behind it turning them to jewels and painting the reader with colored light. The fractal pattern of judgement-desolation-return is a useful pattern to see at all levels of Isaiah.

Quinn-Miscall's insistence on focusing on the poetry and only the poetry leads him to not even speculate about the speaker or referent at some points when I think he could go more out on a limb, so I think he could have loosened his own rules a bit for the benefit of people who want to know, "but what do you think?". But perhaps the whole point is that Quinn-Miscall himself fades away and when all's said and done, you're left with the vision of Isaiah itself. That's a good thing. This book helps you see it.

Friday, September 14, 2012

When is a Mistake Not a Mistake?

Writing science journalism is hard, and is bound to include mistakes, but even the mistakes are illuminating. The act of condensing and translating complicated science invariably lets in half-truths and downright errors that spell out hidden assumptions. I undoubtedly made a few in this article. So mistakes are not always simply mistakes, if they still let the truth in through the cracks.

One such mistake I'd like to point out involves the term mistake. (Hopefully I can write this without creating an infinite regression of self-referentiality a la Douglas Hofstadter.) The headline reads 
"500-Million-Year-Old 'Mistake' Led to Humans." The article describes an organism without a backbone that is ancestor to all organisms with backbones. Right before the backbone appeared, the genome doubled, not once, but twice. Now there were four copies of every protein, so that one copy could keep doing its protein thing but the other three could gradually start doing something else and the organism would survive. In the sense of now having four genes instead of one, there is more "space" for the proteins to try to do new things and pick up new attributes. This expanded genomic space allowed new signaling networks of dozens of proteins to evolve. Ultimately, a backbone resulted because of the duplicated proteins.

This is a great example of how creation-by-evolution doesn't have to take small steps. It can take big steps -- a whole genome duplicated, twice! -- and then can move forward from there. Whole systems can duplicate, and that redundancy is like having a computer backup of files. The old files are still there, and then the new files can change. If the system crashes, bring out the old files. If the system works better, keep the new files and charge on ahead.

Unfortunately it's also a great example of how assumptions can color headlines. The doubling is repeatedly referred to as a "mistake" in the news story, and by the original scientists. Kind of funny that a mistake could happen twice in quick succession like that. It starts to look like a pattern, as in "Fool me once, shame on you; fool me twice, shame on me." Sure, the doubling could have been brought on by a random event, if that's what they mean by mistake. But in a community of organisms even unlikely random events are bound to happen. Someone's going to win the lottery, somewhere, eventually, and someone's going to get a backbone.

More than that, the "mistake" terminology neglects the possibility that genome doubling events may actually be intentionally regulated by the organism. Maybe it meant to do that! This is the main thrust of Shapiro's Evolution: A View From the 21st Century (my review here), that regulation plays a role in evolution. Shapiro documents cases where environmental stress causes genome remodeling, specifically mentioning that organisms can undergo genome duplications deliberately (more precisely, as a response to conditions). The increased "space" for genes to change and morph that results in changes in the organism is an amazing thing, and a lot of words could be used to describe it, but the best word for it is clearly not the word "mistake."

Ultimately, the real damage is done to the people who may have otherwise read that article who turned away as soon as they saw the word "mistake." I used to be one of those people, and it was science journalism like this that actually got in the way of my understanding the science, because it jumped to the conclusion that something is a mistake simply because we don't entirely understand it. That's a philosophical conclusion, not a scientific one. And, yes, it's a mistake.

Tuesday, September 11, 2012

Return, Rabbit, Return

I never thought I'd see the return of Oswald the Lucky Rabbit as he is right now. For those who don't know this Trivial-Pursuit-level tidbit, Oswald was the first significant cartoon character Walt Disney came up with, but was essentially taken from him by a studio contract or something like that. Oswald shows up in the early days section of the Walt Disney Museum in the Presidio (trust me, the whole museum is very much worth it). Then Walt came up with Mickey. Cue the rest of the museum.

But now Oswald is returning to Disney with expanding roles in the Epic Mickey video game series, and he can be spotted on Buena Vista Street, California Adventure's new entry land, which recreates the California that Walt stepped into, suitcase in hand.

Which leads to the thing I really thought I'd never see, shown below. Who's the leader of the club not made for you or me? O-S-W-A-L-D:

More things to buy (or better yet, look at and enjoy but not buy) here.

Sunday, September 9, 2012

Video Games, for Science!

If my childhood was any example then I spent many hours developing the dexterity of my thumbs and the ability to plan any number of jumps across moving platforms floating in mid-air while collecting golden coins. But for some reason none of that got on my resume. Is there any way to make video games actually educational?

Today's New York Times has a profile of Valve, makers of the video games Half-Life and Portal. Portal I can vouch for as a video game good enough that it's worth playing even with my first-person-perspective motion sickness. ("Portal: Worth the Headache").  Portal has such a detailed physics engine behind it, and such simple controls, that you can use it to teach physics. This article links to lots more articles about how that can be done, for instance, turning Portal's cube into a harmonic oscillator. Maybe someday one of the required texts for physics will be a copy of Portal?

Video games can be used to teach immunology, too, although the case of Immune Attack is different because gameplay follows education, and it's clear that results in a different kind of game.

I didn't know just how unusual (that is, absent) Valve's corporate structure is. It's fascinating that they can get that to work to make these great games.