Wednesday, December 23, 2015

Book Review: The 13 Clocks by James Thurber

Picked this one up on the strength of Neil Gaiman's introduction, and reading it after Gaiman is like reading George MacDonald after C.S. Lewis, or perhaps Beowulf after Tolkien. It seems like a Gaiman story written out of time. It's all there: the archetypical fairy-tale plot-shape, the cast of characters in which the evil is just a little more creatively evil than usual and the good is just a little more ambiguous and odd than usual (but, if anything, warmer), the magic in which the ordinary is cut and pasted with unexpected but fitting rules for its use, the strange but wonderful idea of 13 frozen clocks... the only elements of Thurber that don't show up in Gaiman is that the women don't have enough to do here (they're still above average for the time, but people who want to complain about the women in Tolkien should take this as context) and Thurber makes up new words at a higher rate than Gaiman. Recommended for Gaiman fans.

Saturday, December 19, 2015

Book Review: Sandman Overture by Neil Gaiman

Gaiman's first issue of Sandman opens with many unresolved questions that, honestly, always bugged me. Throughout the 10 "books" of Sandman, you learn much more about Dream and his universe, but you never find out why the first issue opens with him so weak and diminished. Here Gaiman explains, and the story fits perfectly into both the style and substance of the Sandman mythos. This is the most beautiful comic book I have ever read, hands down. It's been a decade since I read Sandman, but I was able (with a little help from the DC wikia) to even make the small connections back to later/earlier events.

My only question is whether it would be best to start reading Sandman with this overture instead of issue one. I'm usually a purist when it comes to reading things in publication order, but this seems like it would be a very good introduction to the whole world, and it would resolve those nagging questions before they occur. I would say start here.

My only quibble is that the nature of the plot's resolution feels surprisingly similar to one of my favorite Doctor Who episodes, but it works better here than in Who, so I can only say that there's an echo there. Anyway, Gaiman's stories are never really about originality, they are about setting and character and beauty and terror and fitting cleverness, so I can say that this exceeded my expectations in all those.

Thursday, December 17, 2015

My Year in Books

Well, the year's not yet done, but that's not stopping anyone ... I just think the extremes of shortest to longest book must be maximal.

Book Review: The Givenness of Things by Marilynne Robinson

I will (and have) read anything by Marilynne Robinson. This latest book is a collection of loosely connected and building essays. There's some real gems in here, especially when Robinson analyzes Shakespeare at the beginning, and the Gospels at the end. In the middle, there's some writing about science that I find very convincing and welcome when it focuses on wonder and the limits of knowledge, but a little less so when it critiques science in terms that the scientists will never respond to. There's also some politics that falls even farther short of the earlier nuanced and provocative literary analysis. In the end, this rambles more than other works and I will probably always prefer Absence of Mind to this one -- but when it's good, it's good in a way only Robinson can evoke.

Monday, December 7, 2015

Book Review: The Innovators by Walter Isaacson

The subtitle of this book is "How a Group of Hackers, Geniuses, and Geeks Created the Digital Revolution." That about sums it up: this is a long story that reads more like a collection of short stories on a string, which occasionally falls into listing names rather than interpreting them, but which fills its particular niche admirably by focusing on the unique new ideas that built computers and then put them into everyone's pockets.

The timeline runs from Babbage's Difference Engine to Google. Steve Jobs is mentioned but there's not time to do more than allude to his ouster, comeback, and passing. Rather, Jobs is mostly explored in terms of his relationship with Bill Gates (even a bit more than with Steve Wozniak). There are filters placed on this history, as there must be: everything is simplified and every person reduced not so much to an individual as to various dyads. That filter coincides with Joshua Wolf Shenk's Powers of Two, reviewed a year ago here, and it would be interesting to compare and contrast the two books, which provide a corrective to the "lone genius" theme that seems to be the current default.

Here the glass is half-full, and the negative effects of technology are mostly left on the cutting room floor. You don't really learn something new and different like I did in, say, Godel, Escher, Bach. Innovation remains somewhat elusive. But really, that's what this kind of book The Innovators has to be, and it gives an overview that demystifies those ubiquitous data processors, and in doing so, performs a public service. If you can see how THEY did it, then maybe you can see how YOU might do it too. Once you read a lot more books in your area, of course, so you can figure out how this stuff really works.

Friday, December 4, 2015

A World from Dust (Plus): What are the Microbes a Mile Deep Missing?

Scientists drilled down through more than a mile of underwater sediment and, very carefully, isolated the microbes that live in the coal seams down there. Just finding these microbes (while avoiding contamination) was impressive, so we don't know everything about them yet. But we do find them much more abundant in the coal layers, where they can eat the carbon-rich rocks.

Most of the characteristics of these extremely deep microbes are what we expected. For reasons discussed in Chapter 6 of A World from Dust, these microbes use nickel and heme to process their food, and they emit tiny clouds of methane. They seem slightly out of place, because a limited genetic analysis finds they look more like surface soil bacteria than shallow sediment bacteria, but they made have been carried there from when the sediments were first laid down.

The only real surprise so far is how few of these microbes live down there. There's plentiful food, including hydrogen that, for some reason, they eschew, leaving it on their plate like uneaten broccoli. Something else is holding life back down there. The authors note that proteins and DNA fall apart more readily at high temperature and suggest that the hot, high-pressure environment makes the constant repair too costly. If this is so, then a deep underwater coal seam would be like a planned community in Las Vegas after the housing bust of 2008: plenty of rooms but no one willing to move out there because of the heat.

What this says to me is that the limits on life look a little more stringent than we thought. Whether it's the cost of repair, or something else related to high pressure, or something else entirely, what we have here is a reasonably good environment for methanogens that they don't fully exploit. With more investigation, maybe we can find out what's missing, and that will help us figure out just how prevalent life may be in extreme environments, both on this planet and on others. If life can't live well in this environment, then the same thing may be wrong with other environments that right now look OK to us. This one clue makes the universe seem a bit more lonely.

Reference: Science, July 24, 2015, "Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor." DOI: 10.1126/science.aaa6882

Wednesday, November 25, 2015

Book Review: Trigger Warning by Neil Gaiman

This collection of short stories by Neil Gaiman is a lot of fun but also uneven. As he says in the introduction, the poems are thrown in for free. There's a Doctor Who story and an American Gods story and an reinvented Sleeping Beauty fairy tale (which is the best of the three). But all the stories, with the exception of that fairy tale and the masterful "The Truth is a Cave in the Black Mountains," seem to be missing something that would take them to the next level. Also, some of the ideas are recycled, which normally is fine with me but in this instance makes them seem a little repetitive. This is more like a good anthology TV show than a must-read blockbuster. But it's still very good for all that and well worth the read.

The Natural Chain of Command

One of the take-home messages of A World from Dust is that concepts like causation and function can look different at different "levels" of the world. I was listening to Walter Isaacson's The Innovators: How a Group of Inventors, Hackers, Geniuses and Geeks Created the Digital Revolution this morning when a historical analogy occurred to me.

You may have heard that the Internet was created as a radically decentralized system so that it could withstand a nuclear attack. You have also have heard the scientists who invented the Internet loudly proclaiming that it had no such purpose. Which purpose was it? Both are true, and Isaacson does a good job of showing how.

The engineers and academics working on the nascent Internet technology were building a new way to pass around information. They had no reason to anticipate its military use or purpose. Yet the higher up the chain of command you go, the more you find the military purpose layered on top of the basic communications purpose. The people getting the money from Congress justified its expense with the military purpose that it could withstand a major, disruptive attack. The scientists didn't need that purpose at their "layer" of knowledge; the politicians required it at theirs.

In the same way, a process that is for one purpose locally may serve an additional purpose globally. A chemical process may serve and shape a biological function. Random gene flow and change may interact with a chemically ordered environment to produce a predictable change and even increase in complexity. In fact, a random process can gain a function at a higher level. The genes and elements may not "know" that the network they're building has a biological purpose, but that in no way negates the biological purpose.  (For more on how this might happen, read Terrence Deacon's Incomplete Nature.)

In A World from Dust I focus on the "politicians" of the process, the legislative branch of chemical law-makers that we call the periodic table. These chemical rules result in predictable patterns emerging from random flow. You can stand close to the waterfall to see the random flow, or step back to see that it inexorably flows down and looks similar from moment to moment. It's all a matter of the width of your scope and your point of focus on the chain of command.

Sunday, November 22, 2015

Book Review: The Many Faces of Christ by Philip Jenkins

This is book on a fascinating topic, but it doesn't go quite far enough. As in his previous books, Jenkins explores the reality of Christianity in places and times that you didn't know enough about before. This time, he focuses on the apocryphal writings that were treated as Scripture in some contexts. This means he takes on Dan Brown and shows that, yes, there was a time when texts were suppressed, but it was only by a part of the church, and it was in the 16th century, not the 4th. Before the Reformation, non-canonical scriptures fluorished, and though they were certainly discouraged and persecuted, the fact of the matter is that the pre-modern state didn't have the ability to truly repress gospels it didn't like. Only with the advent of the printing press did such suppression become possible (which is a historical irony if ever I've seen one). The suppressor is not Constantinian -- he is Protestant!

To find out more about what this surprising statement means, you'll have to read the book. Unfortunately (I say with irony), Jenkins is a careful scholar, and so at times the book reads more like a card catalog than a thriller. Only in the final chapter does he really expand on the central thesis that these alternate Christianities and heresies, however fuzzy the line between them may be, are emblematic of the eternal variation and struggle in Christianity itself, and in every Christian's heart. This conclusion means that the history of the previous centuries can apply to us, today -- but Jenkins is cautious in his application, so those connections are mostly left up to the reader. So much thinking to do, so little time. Here Jenkins brings new treasures out of old storehouses, and the result is fascinating and even, in an odd way, encouraging. Dan Brown is nothing new.

Book Review: The Laws of Medicine by Siddhartha Mukherjee

This short, pithy book could be the start of an admirable project, if other academics follow Mukherjee's lead. I don't see why experienced scientists can't assemble three laws specific to their disciplines. Sure, it tells you as much about the writer as about the discipline, but it's a provocative thought exercise. In a sense, my own in-press book is looking for biochemical laws. My only regret is that this book is $17 (unless you get it from the library like I did). I'm not sure it would be worth that much money, but it was worth the time to read. The laws themselves are useful, especially for those considering a career in medicine, and interesting for scientists to eavesdrop on. I won't spoil them in this review -- read it for yourself and then consider how you'd expand on it in your own "field," whatever that may be.

Tuesday, November 10, 2015

Book Review: Authority by Jeff VanderMeer

This book suffers from the middle-book blues in which the second book of a trilogy is neither here nor there. The first book in the trilogy, Annihilation, was told from the perspective of an expedition member, and the sense of exploring a new environment was exhilarating. This book shifts perspective to that of an agency director for the government's science facility that sent all those expeditions.

Narratively the sense of discovery is actually more natural in this second book, because there's less "hypnosis made me forget" artificial suspense enhancement, and some of the descriptions of the facility are creepy enough to evoke the Dharma Initiative from LOST in the best moments. But it ultimately doesn't pay off or answer enough questions to justify the time spent in telling it, and feels like a shaggy dog story. Some narrative jumps make the story harder to follow without building suspense, and the really weird reveals are mostly in the first half, while the second half seems more predictable. It might pay off in the third book, but reading it seems more like a duty than a pleasure at the moment. Don't get me wrong, I will read it, and the atmosphere itself almost makes this second book worthwhile -- I just think it'll be better if I keep my expectations low.

Thursday, November 5, 2015

Book Review: The Marvels by Brian Selznick

The Marvels fails to find the alchemy that made Selznick's Hugo Cabret work so well. It's more like the lower-key Wonderstruck, but even that made a deeper impact on me than this story. I can't quite put my finger on it, but I don't think the spirit of London is truly captured the way it needs to be for this story to work. Although the rich history of London seems like an ideal setting for Selznick's storytelling skills, the book doesn't seem to live into its setting or tap into London's mix of past, present, and future. Perhaps in the end, it's a story that sets up something like Mad King Ludwig's Neuschwanstein Castle and pretends that the fake castle is what's real. It's much better to me to recognize that the castle is fake but then to ask how was it made, and why do we still love it so much. So this story stops short of what it should be. I surprise myself a bit with my reaction, because the story is well-crafted and warm (with some quibbles about the way the pacing of Selznick's characteristic pictures holds back the story rather than promotes it), and there's a nice melancholy yet comforting vibe to the ending. For some reason it doesn't come together the way Cabret did.

Saturday, October 31, 2015

Book Review: How Dante Can Save Your Life by Rod Dreher

This is the book I was hoping someone would write about the effect of Dante on a person's life (or, most precisely, a person's mid-life) today. What's interesting is that Dreher's circumstances are very different from mine, and yet his main conclusion is the same. It's like this: At the end of Purgatorio, Dante sees a vision of history that prepares him for the ascent to Paradise. At the time, another poet, Statius, is there as well, but Dante only mentions him in passing, implying that Statius didn't see Beatrice in his vision, but that he saw something else, something personal that would only make sense to Statius. In the same way, I see different things from Dreher, but at the end, the different things I see serve the exact same function of healing and restoration. Near the end, I increasingly dogeared the book, thinking "this is me."

The biggest flaw in the book may be a result of its own success. Throughout the first half of the book it's not clear exactly why Dreher's crisis is such a big deal. In the second half, it becomes more clear what the precise conflict is, and yes, it is a big deal. Maybe the redemption Dreher experiences is so complete that he can't quite remember the cutting nature of the hurt in the first part?

Although How Dante Can Save Your Life is written to a reader who has not read Dante yet, reading it post-Commedia I still found it very useful to see which passages resonated with Dreher. My hope is that there would be a genre of "Dante books" in which people write about how Dante helped them. I'd read that.

Monday, October 26, 2015

Book Review: Lock In by John Scalzi

I read this one because it was recommended to be the closest thing to Crichton. It's not Crichton -- in many ways it's better.

The premise is what technothrillers rise and fall on, and this premise is a good one, pretty complicated to explain but it becomes clear soon enough. I wish other novelists would learn from Scalzi that you should just jump into your world and set the stage as quickly as you can rather than withholding information to build the suspense. Scalzi has surprises in store, but they are good surprises that come after his world is fully realized, and they take you to places you didn't think of that, after the surprise wears off, are logical enough that you kick yourself a bit for not thinking of it. In other words, good surprises.

The plot's not quite as well-paced as Crichton, because the urgency seems slow to unfold and a lot of action seems to happen all at once. Also, the scope feels smaller and isn't as audacious as Crichton, but the social and political implications are better thought out than anything Crichton's worlds ever concoct. It's deeper sci-fi (although I do doubt that some of the technology is actually possible), and if anything the book's too short. I feel like Scalzi can set another few stories in this world and still be far from plumbing its depths.

This book also isn't as funny or as touching as Scalzi's Redshirts, and it has a sort of oral history appended to the end, which I'm wondering if it would have been better up front or in chunks spread throughout (which is what I think Crichton would have done). But it's as snappy and solid as they come, and it does what it should, which is plenty.

Thursday, October 15, 2015

Book Review: Dante's Paradise Translated by Dorothy Sayers

How do you review a book that describes the indescribable? All I can say is that I reserve 5-star reviews for books that change my life. This gets a 5-star review.

To elaborate, Paradise not always easy, but it's actually easier than Inferno, that most famous member of the trilogy. There's less politics and what's there is more comprehensible. It also focuses on describing beauty rather than torment. Dante's theological questions and issues still resonate today. Maybe these books shouldn't be read till mid-life, as Dante implies in the very first lines of Inferno, and maybe they shouldn't be read unless you have theological interests. Well, I'm that old, and those describe my interests.

Sometimes there are convoluted or what I think are incorrect passages. Dante himself describes changing his mind on points both theological and scientific, so I can imagine him changing his mind again. This isn't a description of Heaven, but a description of Heaven as seen through Dante's eyes and interpreted by his words. Those are two different things, and if you put the author in the center, as both the medievals and postmodernists would, then you see there's little point in arguing with him about theology. The bigger importance is the human experience living in a fallen universe. Dante is reluctant to speak out against the people he speaks out against, but he is encouraged to write by what he sees. It's his vocation. In the end, Dante isn't a self-righteous prig. Dante struggles with himself in all the ways that any artist or author who's trying to represent reality struggles. But he found a way through, with Beatrice (and Virgil, Lucy, and Bernard) as his Beatrice, and the Divine Comedy as his path.

In the end, I was surprised by the cumulative effect of this journey. Even though the translation takes a step down after Canto XX (Sayers' last canto) and the commentary isn't quite up to her standards, the later cantos have the best images and scenes for me. The superposition of images is paramount, and it's important that you descend through Hell and climb Mount Purgatory before you get to the final cantos. But once I did, they had me in tears just like an indescribably beautiful and sad piece of music -- such as Craig Courtney's "Sanctus."

The last three major images, the point of light, the river of light, and the rose of saints, are striking. After climbing through spheres which turn ever faster until they reach the Primum Mobile, which is set in the unmoving Empyrean realm of God's pure light, Dante sees another image of the powers of the universe in which, rather than an infinitely large Empyrean, God is revealed as an infinitely small, still point of piercing light, surrounded by spheres of angelic powers. It seems so perfect to say that God is both at once.

Maybe this isn't the time for you to read all three books. It wouldn't have been a decade ago when I read Inferno. But if you work on creating things, and if you like the big questions, and if you love the good you see around you but struggle with the hate, and especially if you're halfway through life -- try making it through the Divine Comedy, with the assurance that, for me, the higher I climbed the deeper it got.

Monday, October 12, 2015

"Streams in the Martian Desert" Posted at the BioLogos Blog

I wrote a response to NASA's recent press conference about water on the surface of Mars, and the resulting public shrug from most commentators. It also has a paragraph about a recent scientific finding that highlights the unique nature of Earth's geology. Here is the article, enjoy!

Friday, October 9, 2015

Book Review: The Book of Strange New Things by Michel Faber

Now this is different. It's sci-fi, but it's more about faith than science, and "faith-fi" won't attract any readers, so I guess we have to call it sci-fi. The story concerns a Christian missionary sent to minister to a tribe of native creatures on a distant planet. The planet is different enough to be intriguing, but it doesn't really hold together on a scientific level. Yet it does hold together (mostly) on a faith level.

There's some unevenness to the pacing and the way the narrative is presented. Information is withheld in the beginning. which ended up annoying me rather than creating suspense. In one case we don't know crucial information because the narrator doesn't remember his introductory tour of the facilities, which is almost a textbook use of amnesia to keep the reader going. There's enough going on that those sections could be streamlined considerably. The first half of the book drags in places and the reveals of what makes the biology of this planet different are placed toward the end of the book (if they come at all). And yet on a scientific level there must be some fascinating convergences that the author isn't interested in. The main biological divergence that sets up the drama is interesting and its consequences are pretty well thought out, but I doubt it could actually happen to such an extreme.

Normally this would frustrate me to no end, but in exchange for the lack of science we get a deep psychological study of faith, isolation, marriage, and the stresses of a mission, even in success. As someone who traveled to a distant land myself recently, much of the feeling of being so far from home is captured expertly by Faber. A few moments of faith don't ring true, which lead me to conclude that the author is writing about faith from the outside. If anything, that makes me like the book more and tend to overlook its overlookings. The main characters should have deeper spiritual resources than they are shown to have when crisis hits, and they should also have more vacillation and variation in their faith in the good times. They should doubt more; the internal life of a Christian is never quite so even and shiny. They also should depend more on the person of Jesus rather than the Bible stories in general, especially if the narrator has memorized Matthew as the book implies. The internal lives of the characters are not quite nuanced enough, but they come close enough to make the characters live and to remind me of my own time in the field.

By the end of the book, a subtle but thought-provoking contrast emerges between science and faith that centers around issues of safety and God's providence with shades of color and angles that I don't normally see outside of the typical great Christian authors. The way the story is left unfinished in terms of faith feels right, while the ways it's left unfinished in terms of science feels more wrong to me. But it's not really about the science -- so I can't help but consider this book a success and hope that more authors explore these questions and these kinds of characters. I know how I've reacted given my own surprising parallels to this story, so I'd like to know how others who don't share that history or faith react as well. But as for me and my brain, this strange little book did contain some new things, and some solid old ones as well.

Friday, September 25, 2015

Book Review: Neverwhere by Neil Gaiman (Author's Preferred Text)

I had read this back in the late 90's when it came out, but I've always wanted to re-read it aloud for the boys, and when I saw that a Director's Cut (really "Author's Preferred Edition") came out, I leapt at the chance. I'm not sure what differences there were in the story itself. It may have taken a little longer to get going. But the boys didn't seem to mind. Both of them were as enthralled with the strange parallel world of London Below as I was, and now that I've been to London and, for example, know exactly what the scene that takes place on the fragment of the London Wall looks like, I enjoyed this book all the more. A weird, and wonderful, and at heart old-fashioned book about how this isn't all there is. I liked it even more the second time. The short story appended to the end is also wonderful and allows me to keep voicing the Marquis, who may be my favorite character to read -- although for some reason I kept thinking of the Gaiman Doctor Who episodes as I read it. As a read-aloud book, it was even better than I thought I would be for that, and I was able to easily edit it down from a PG13 rating to a PG for the kids (and to mitigate my own blushing). Love this book.

Tuesday, September 22, 2015

Book Review: Redshirts by John Scalzi

This may be the best Star Trek novel I've read, and it's not really a Star Trek novel. It's clearly derived from Star Trek (a debt made explicit as the plot unfolds), in that the plot follows a group of red-shirted ensigns on a starship who have figured out that something very bad always happens to their type on away missions. How they find out and then what they do about it is a hilarious and even touching journey. This is like Star Trek IV if that movie was funnier, more self-aware, and more deeply moving. The audio book is even read by Wil Wheaton of all people! It really shines in the few moments of melancholy, and it's just sweet enough to balance the satire. My only real complaint is that many things are never explained that I thought would be possible to explain/not-explain in yet another homage to Star Trek, so to me the book didn't feel tied together, but that's also part of its charm. File this one under "better than I thought it would be."

Sunday, September 20, 2015

Book Review: Dante's Purgatory translated by Dorothy Sayers

I don't feel it's my place to review this book in the normal way. But I can say, as someone mid-way through life, I found that Dante's mid-way through life story to be what I needed to hear. Dante's poetry as translated by Sayers is surprisingly vivid and affecting. After reading Charles Williams' The Figure of Beatrice, I could see how the poem works on four levels at once (which Sayers sometimes spells out in her commentary, because she was inspired by Williams too). I still find the history somewhat dry but there seems to be less of it in Purgatory than in Hell, while the philosophical discourses on free will and love are timeless. Dante makes abstract concepts concrete in a way that every teacher can learn from. The medieval science is not as disconcerting as I thought it would be -- really only one passage was different enough that it threw me out of the narrative with its inaccuracies. But on the whole, those tempted to stereotype the Middle Ages as anti-science and pro-blind faith need to read Dante. He assumes that the reader can keep track of complicated astronomy, for instance, which he reproduces accurately. He also castigates the Church for not fulfilling its role in terms that might give Richard Dawkins a few ideas for new invective. I heard Dante's voice across the centuries -- and I found out that I genuinely LIKE him. His path resonates with my path. I found this book fresh and lively, and worth plowing through the occasional thicket for the overall journey.

Saturday, September 19, 2015

Finding Burgess Shale Fossils with Kids, Part 3: The Science

We found a great family day hike in Kootenay National Park in Canada and found small but important fossils. It worked well for our kids, and also for me -- I dug up some of the scientific literature describing this find after the fact. I'll describe what we found in three parts: The Prep, The Hike, and The Science.

So after our hike we found fossils. Or at least what I could pass off to the kids as possibly fossils? We took pictures of our putative fossils and left them in the field.

This looks like a leaf-shaped form with fuzzy appendages flowing out from it (found by my wife):

This looks like a bean with legs:

And these might be trails of something wormy (found by my 12-year-old):

Notice how, at least, these are all in a similar type of rock. This is the shale that used to be sandy seafloor. I think they might actually be something.

Finally, I looked up a little on the science of the area and pieced together some interesting leads for further study in the academic literature. First off, this appears to be a newer site than the others. At least two major sites are located north a few dozen kilometers, close to the town of Field and Kicking Horse Pass, including the Wolcott Quarry and the area where the first specimens were found.

It wasn't until 2010 that a paper came out describing the Stanley Glacier site. This paper discusses how the previous sites were part of a "thick" formation but the Stanley Glacier rock is part of a "thin" part of the formation. Previously scientists had thought the thin part wouldn't preserve specimens, but from our own exploration we can confirm that it did.

I imagine that someone may have been hiking the trail to the glacier, noticed the black-stained layered cliffs on the west end of the valley, and crossed over to the waterfall to check for fossils. Maybe other sites can be found by similar cliffs. We caught a glimpse of some in the area of Kicking Horse Pass, for example, where the older sites are located. Seems to be a good excuse for more hiking in the area.

Here is the map from the paper showing the site and how it relates to the other sites near Field, which are part of the Cathedral Escarpment:

In 2014, word got out that yet another site was found north of the Stanley Glacier site, across the road near Marble Canyon. This was a major find with many diverse new shapes, showing that buried in those rocks there are many, many lifeforms waiting to be discovered. Connecting the dots (or the "F's" in the map above), perhaps there are other sites located along this line. How many unknown shapes are stacked up in those black-stained cliffs?

I believe the other sites are rightfully kept off-limits to the public, so the Stanley Glacier may be the easiest way to play paleontologist and see for yourself what this kind of discovery is like. As we showed, even a four-year-old, with some help, can do it. There's nothing like a treasure hunt to motivate small legs to keep moving, and the likelihood of finding fossils seems amazingly high.

Finding Burgess Shale Fossils with Kids, Part 2: The Hike

We found a great family day hike in Kootenay National Park in Canada and found small but important fossils. It worked well for our kids, and also for me -- I dug up some of the scientific literature describing this find after the fact. I'll describe what we found in three parts: The Prep, The Hike, and The Science.

The trailhead for the hike is only about fifteen minutes west of the main highway through Banff, along Highway 93, just across into Alberta, so it's central and easy to get to from either the towns of Lake Louise or Banff. (We came in from Calgary and spent a couple hours in Banff, including a stop at the rock store to show the boys what fossils look like, before grabbing lunch from the supermarket and driving to the trailhead while eating on the way.) We left Banff at 1:15, started the hike at 2pm and got back to the car at 6:30. From there it was a quick hour's drive to Golden, BC for our next hotel stay.

The trail runs south from the trailhead, up to a hanging valley between ridges that you can see from the beginning. You proceed through very different stages, which can be used as goals to motivate the little ones. First you climb up through a landscape recovering from a fire maybe a decade ago:

You're climbing up a hill, and the grade is taxing on little legs, but actually easier than the grade on the Lake Agnes Tea House trail in Lake Louise that we had done the previous day. There's little shade on the slope, so an early afternoon start meant that the sun was getting easier to take as we went.

Early on there's a stream running to the east as you switch back and forth:
The top of the stream is about where this first stage ends. At our pace it's about an hour, and you can tell the kids that the hardest part is first.

Once you get to the top of that slope, the trail flattens out and turns toward the valley. Soon you cross a stream that used to be spanned with just a two-log bridge but now has a wider bridge that you could cartwheel across if you like:

This is a view heading south into the valley. The glacier is ahead and up to the right. Closer on the right is a sheer wall of layers of tan and brown rock smeared with black. This contains the shale of the Burgess shale and forms the backdrop of most of our pictures. There's a waterfall running down it at the south end that had helped to pull down some rocks from the cliff for little fossil hunters.

The flat part lets you catch your breath until the trail starts to climb again. It's not nearly as steep as before but much more rocky. At some point you'll feel a wave of chilly air blowing in your face from the valley, definitely cooler than the air on the sunlit hill. We also crossed into shade and at this point, were more certain that we could actually do this thing.

When you see this rocky staircase, you know you're maybe half an hour from your goal (and if you have a four-year-old you're probably going to have to carry him):

The trail is rougher from this point on. As you get closer to the glacier, you will soon be able to make out the waterfall, tiny against the huge cliffs of rock. This is your goal.

The glacier is just beyond it. If you have the energy you can hike all the way up to it, but for us, turning off at the waterfall was certainly enough. Here you can see the glacier peeking out on the left.

Stay on the trail until you are almost directly across from the waterfall on your right. There's a place where it looks like the trail branches, and stay on the rightward, downward branch. This takes you right next to a rock field in the center of the valley that is your final challenge. Scramble across to the base of the waterfall and you're there. I think the littler ones had an easier time with scrambling than we did, but we all had to watch out for shifty rocks.

Once  across (and even before), look for tan or beige flat ones with multiple layers, about the size of a dessert plate or a dinner plate (I may have been getting hungry by this point). Flip these rocks over and examine them closely. Just from a few minutes of searching ,we were able to find several tiny fossils.

The nice part about mountain hikes is that down is faster than up. It took us an easy 90 minutes to get back to the car.

In the next post, I'll show what our "fossils" looked like and describe some of the scientific literature about this particular site.

Finding Burgess Shale Fossils with Kids, Part 1: The Prep

We found a great family day hike in Kootenay National Park in Canada and found small but important fossils. It worked well for our kids, and also for me -- I dug up some of the scientific literature describing this find after the fact. I'll describe what we found in three parts: The Prep, The Hike, and The Science.

Right after Labor Day, we wanted to take a quick vacation that would take advantage of the fact that under the quarter system, school doesn't start till the last week in September. So we drove from Seattle to the Canadian Rockies for a five-day vacation.

Since I've written about the Burgess Shale fossils, I wanted to take the family to hike up and see a place where those fossils were found. The Burgess Shale contains evidence of life's Cambrian explosion, where  diverse forms most wonderful suddenly appear in the rocks a little more than half a billion years ago. I wondered if there was anything special about the rocks up there and wanted to feel what it would have been like to find these fossils.

Before we went I found an official site for this hike and several trip reports indicating that it would work for older kids, such as this one. We also found the guided tours offered to the two other official Burgess Shale sites, but we were too late to sign up, had kids below the age cut-off, and wanted to be able to go at our own pace (and turn back if need be). The Stanley Glacier hike looked like the one we could do, and it's a public hike that we can try on our own.

We have four boys, age 12 (going on 30), 11, 6, and 4. I wasn't sure that we'd make it, but I promised them if we did, they might find their own fossils. And it worked -- here's the proof, with the fossil area in the background:

I'll describe the hike in detail in the next post, so you can decide if your kids will make it. Most kids ages 10 and up should have no problem with this hike. It was a challenge for our little ones, but it actually got a bit easier as we went along. I want to publish that it worked for us, so it might work for you.

We spent four and a half hours total on this hike: 2 hours up, maybe an hour looking for fossils, and 1.5 hours back. To get to the fossils, you don't go all the way to Stanley Glacier, but turn off after about three miles. The first mile or so is a medium-grade upward climb that went the slowest for us, then there was a flat, fast part before the trail roughened and climbed again for the last half mile (ish). Then you turn off toward a waterfall on your right, scramble over some rocks, and there are the fossils.

Next I'll describe the hike in detail and how to find the fossil site.

Friday, September 4, 2015

Book Review: What Coleridge Thought by Owen Barfield

This may be the best of Barfield's books, or at least the most grounded and therefore far-reaching, but I really think that unless you're a Coleridge scholar, you're better off reading up to it with Barfield's previous works. In particular, Saving the Appearances seems to be a pre-requisite, and I've always thought it was hard to jump into that book without reading Poetic Diction first. The other works by Barfield are OK but I'd say these three are the most worthwhile, in this order.

The other examples of "late Barfield" I've read were too much influenced by Steiner and anthroposophy, but this one manages to avoid those topics (except for a few mentions). Also, Barfield is not focusing on Barfield's ideas so much as Coleridge's, filtered through Barfield, to be sure. I got the sense that the two are enough on the same wavelength that Barfield's filter is more a good teacher teaching than it is a partisan lobbying. I feel like I "get" Coleridge more after this book and that strengthens my estimation of both Coleridge and Barfield. This also fits with the picture of Coleridge from the wonderful history Age of Wonder.

To be sure, Barfield can't get through a whole book without making some annoying absolute and contrarian statements about modern science. I do think that my reading of Barfield can accommodate most of his intellectual puckishness by interpreting Barfield's "matter before mind didn't exist" to become "matter before mind didn't MATTER" (not in the same way as it matters now). It all comes down to what you mean by "exist," see?

But in this book that move of "translation" doesn't have to be made that often. It makes sense that Coleridge and Barfield are sympatico given the influence of German philosophy on Coleridge, which goes right along with Barfield's love for Goethe (which I'm OK with) and Steiner (which I'm not).

In the end, I think Coleridge's "polar logic" as described by Barfield may offer a way to interpret Barfield's philosophy in a way that throws light on modern experience without throwing out all of modern natural history. In fact, polar logic may be incorporated into a narrative interpretation of natural history. Barfield's own statements about the natural fit between evolution and Christianity imply that this should be possible, even when his sweeping dismissal of science of the past seems to get in the way.

Overall, a fascinating and helpful book that I'm working on integrating, but not for the faint of heart. I'm not sure how that interprets into a star rating, but Barfield's against quantitation anyway, so I'm sure he won't mind my avoiding the five stars on this one, even though I think it may be stronger on the whole than previous works I've given five stars to. This is definitely worth working your way up to.

Book Review: Annihiliation by Jeff VanderMeer

LOST meets Lovecraft meets Crichton. That's what this book is, and if that doesn't draw you in, it's probably not for you. It certainly drew me in. Since this is the first of a trilogy, many more questions are raised than are answered, and if you don't like that, it's probably not for you. (Although I think the mysteries will be resolved in a way that satisfies those frustrated by LOST's ending.) The biologist mostly acts like a biologist -- I would have liked to see her hypothesize more. Also, the plot gives hypnosis too much power, but this may be explained later. Overall, it's incredibly brisk, and manages to be both creative and realistic. I have quibbles about how things are done but again, it's hard to judge on the first book, and the overall story is compelling and interesting. My only dilemma now is how long to wait before reading book 2.

Friday, August 28, 2015

Book Review: The Corrections by Jonathan Franzen

I recognize that this book is at times exquisitely written. Franzen has a knack for vivid, unexpected, and appropriate psychological metaphor. I also recognize that we're screwed-up people living in a screwed-up world. Franzen cuts through the hypocrisy and reveals the dysfunction like no one else.

My problem's not with the head but the heart. The characters are revealed in such a stark and unforgiving light that you're reluctant to identify with any of them (although you do sound the laugh of recognition all too often). They aren't monsters but they act monstrously, and I just don't want to immerse myself in their world for that long, regardless of the skill of the author describing their actions and addictions. That skill works against him at times, as when there's a long and disgusting description of a family dinner around the middle of the book. Why should the reader endure that?

There are a few glimmers of true light here and there -- especially one scene about forgiveness near the end -- and it can be entertaining to see the characters get skewered by their own foibles, the fools caught by their folly. I think Frazen's most recent book, Purity, might be better because his targets are juicier there. And The Corrections seems to fit its time like a hand in a glove. It's just ... we've moved past that time now, and I don't think this book has retained its value with age.

Tuesday, August 25, 2015

Book Review: A New History of Life by Peter Ward and Joe Kirschvink

A New History of Life is a  natural history that stands out because of its large timescale (4.567 billion years, to be precise) and broad intended audience. Overall, it delivers on the promise of its title adjective, describing new findings and hypotheses connecting paleontology and geology, and offering genuine but grounded scientific speculation for future work. For the general reader, it provides a wealth of new information, but because its overall scientific narrative lacks momentum and internal connection, it may be most appropriate for a scientifically literate audience.

It is impressive to watch the authors address the central challenge of this genre, which I have faced myself in my writing for a general audience:  How do you filter oceans of information and translate it into general terms? Authors Ward and Kirschvink set up their filter by emphasizing physical evidence, and rocks and bones in particular. Their geological and paleontological emphasis gives this story a different tone and tempo than other natural histories that start with the Big Bang (physics) or the characteristics of life (biology). My own discipline, chemistry, is not as deeply integrated as a result – here, chemistry plays a role in dating the rocks and bones, and in transforming the environment, but the authors focus most attention on the change and flow of continents (and other aspects of geology) and body plans (developmental biology).

The flip side of the authors’ emphasis is their deemphasis. Ward and Kirschvink deemphasize evidence from genetic clocks and other results from molecular biology, which leads them a chain of reasoning that is mostly geological in nature. For example, they favor a very late evolution of water photosynthesis. Personally, I trust the genetic clocks that show how many forms of photosynthesis, including water photosynthesis, evolved much earlier than Ward and Kirschvink allow. But this is a moot point -- a few hundred million years one way or the other doesn’t change the story much for the general reader.

A New History of Life reads at the level of an undergraduate science course. Ward and Kirschvink recount the back-and-forth narrative of scientific discovery and rebuttal as hypotheses are set forward and discarded.  If the reader already understands how science works, these sections depict the drama of science in enjoyable detail. Sometimes the details seem more superfluous, as when some sections list other scientists in the field but without enough detail to make them distinct characters. A surprising number of the images in the book depict scientists working in the field but would not convey much information to the non-specialist.

The scientific detail is both an advantage and disadvantage. For example, the first chapter is all about geological nomenclature, which is too dry for a general reader. Throughout the book, the authors provide precise biological and geological terms for organisms and places, but more description of these would make the story more relevant. A photo of a fossil skull is not clearly connected to the chapter around it, and lists of details on dinosaur names and the shapes of lagoon habitats provide detailed “dots” of data, but they do not seem connected.

At such points, the book becomes more like a required course assignment than the flowing story it could be. On page 80 the authors write “We apologize for the complex chemistry necessary in the preceding section. But to get this story right requires complexity.” If this was placed before the section it described, the general reader would read that section differently – as it is, it amounts to locking the barn door after the horse is gone.

These narrative nits having been picked, this book is indeed new and interesting, both substantial and helpful for the prepared reader. In the chapters on the origin of life, the authors focus on the “RNA world” hypothesis, and include new findings that support this hypothesis, such as the nucleotide synthesis discovered half a decade ago by Sutherland and colleagues, but fail to cover recent experiments that point to “metabolism-first” explanations. The “new” hypothesis in this section is that life started on Mars, which is interesting and possible, but given the difficulties and distances, more speculative than other new proposals in the book.

Another “new” hypothesis the authors develop in several places is that major events like the Cambrian explosion and particular extinctions were started by “true polar wander” events. One true polar wander event coincided with the Cambrian explosion, but my enthusiasm is tempered by the fact that there have been thirty or so of these events throughout history, which is number large enough that the timing may be more coincidence than cause. A graph of the thirty events would have addressed my own skepticism but was not included.

The hypothesis I’m most attracted to appears throughout the book, but may have been deemphasized by the authors because it is not all that “new.” Ward and Kirschvink frequently allude to the power of oxygen, both at and after the Cambrian explosion. They connect oxygen to animal diversification and extinction more intimately than any other general text, and oxygen’s influence is found in nearly every chapter. This is an exciting and intriguing thread to follow throughout the narrative, but could have been emphasized more.

Curiously, in a section on dinosaur morphology, they downplay the power of oxygen. On page 266, they begin a paragraph with the statement, “No evolutionary history can even be pinned on one factor.” The paragraph ends, “Nevertheless, oxygen levels must have played a part.” This apparent underselling of the organizing chemical power of oxygen brought to my mind the stories of how Einstein resisted the Big Bang because of its implication that the universe had a beginning. But, as is common for popular science, philosophical and theological implications are kept implicit.

Another major theme of this book that is powerful (but not really new) is the generative power of past extinction events. As Ward and Kirschvink put it, “Over and over, however, it really looks like a dominant theme in the history of life is that times of crisis promote new innovation.” Many scientists from many fields, including myself, have converged on this finding, and it deserves to be repeated many times. What does that tell us about what kind of universe we call home?

The authors close the book by extrapolating the billion-year trends of change in carbon dioxide and oxygen levels into the distant future. This is an obituary for the future earth in which CO2 runs slowly out of the atmosphere, like air running out of a balloon.

In a book that tends to avoid large metaphors, this section stands out: “The fate of the nautilus is a metaphor for all animal life. Sooner or later evolution, competition, and the natural changing of our Earth and sun as they age will make any body plan obsolete.” The authors describe a bleak future that gives the sense of the universe running down and flickering out, which is accurate as far as science goes, but philosophically and theologically truncated.

In summary, this book is an excellent example of recent evidence in the history of life, with special emphases on geology and paleontology. Anyone with an interest in those two sciences will find new ideas and directions in these pages. The most powerful conclusions --  the emerging consensus on the driving role of oxygen and the creative power of even the most devastating extinctions -- give a sense of the vitality of life and the orderliness of creation that is somewhat at odds with the deflating final chapter. Here, new evidence is presented well, and its ultimate implications are left for the reader to ponder.

Sunday, August 23, 2015

Book Review: The Silver Trumpet by Owen Barfield

This was a fine read-aloud with the kids, but like Owen Barfield's later philosophy, it's entirely quirkly. Oddly paced and with some anachronistic characterizations that remind you that it's almost a century old now, it nonetheless has a bit of charm, novel characters that are both stock and not at the same time, and enough timeless fairy-tale detail to draw you in. It's fun to note the frequent references to dancing if you know that Barfield was part of a dance troupe, of all things. The story hints at depth but I don't think there's that much there. There's also a few shocking deaths partway through the story, which might disturb some children, but I thought it added a bit of heft to the feeling, and some of it is made right in the end. I'm not sure what to think of this, but it surprised me and kept me interested in a unique way -- much like Barfield's philosophy. Hard to find but worth waiting for from library loan.

Thursday, August 20, 2015

A World From Dust (Plus): This is Water, Part 2: Water Swims Around Worms

Ever looked in the wrong place for something? It happens to scientists all the time.

It happened in a previous post, where it was noted that very different animals swim with the same motion through water, because they have evolved to converge on an identical, efficient movement through the fluid. The eye is drawn to the animal, but the common denominator and the explanation is found in the water surrounding the animal. The properties of the water shape the movement of the animal, and evolution is just the method of search for the movement of greatest efficiency.

This flips what you expect on its head. If you want to understand how an animal swims through water, you look at the animal, not the water, right? Wrong. It's more accurate to say the water is swimming around the animal, as it guides the animal and shapes its movements.

This is shown even more clearly in another paper, a recent PNAS study titled "Propensity of undulatory swimmers, such as worms, to go against the flow." Worms swimming near a surface turn against the flow, and the question is why and how they do this.

The eye is drawn to the worm. Maybe it has a sensor, "sees" the wall, and turns, right? Wrong. The flow field in the water turns the worm. In the sense, the worm is as passive as a leaf flowing in the river -- an undulating leaf, perhaps, but the water is the active agent and the cause here. Because the water causes the turning, this turning happens in widely different organisms. As the study puts it, there is no involvement of the worm's nervous system, and the turning of the worm "results from purely mechanical interactions."

As Adrian Bejan puts it when describing the similarities among flying animals, where the fluid that shapes the movements is the air, but the idea is the same:

"It is the inanimate fluid in the wake of the leading body that organizes itself. It does so using no brain power whatsoever, so that it may travel and spread itself the fastest through the stationary fluid." p. 240, Shape and Structure

This is air, and this is water. Each flows where it wills. Even when you don't see it, it shapes complex behavior into an efficient and predictable biology.

Thursday, August 13, 2015

Book Review: The Figure of Beatrice by Charles Williams

One story recounted in The Fellowship is that Dorothy Sayers was inspired to translate the Divine Comedy (into a really good translation) by the enthusiasm of Charles Williams, the weirdest Inkling. I was intrigued by this and looked up Williams's The Figure of Beatrice -- and I sensed the same inspiration.

Before, I was a typical Dante reader: I made it through the Inferno easily, then gave up on the first terrace of Purgatorio. I didn't get it, and I'd heard that Paradiso was even more obscure. In The Figure of Beatrice, Williams is able to lose himself so much in Dante that through him I saw the beauty and practicality of Dante's final two volumes. To get there, Williams takes you through Dante's works in order. I still don't get Convivio or De Monarchia the same way that I "get" Vita or the Divine Comedy, so a few parts of Williams' book were hard going (and a few passages are ethically knotty), but the reward is enormous. There is treasure laid up in heaven here.

The other thing that surprised me about this book is how personally practical is was to me. This was a healing book that I've needed for more than a year now. It allowed Dante to speak through the centuries, and what he has to say is intensely relevant, especially as translated by Williams. I actually found myself thinking when reading social media that Dante's perspective would help bring "peace and direction," in Williams' words.

The point of this book is not just to be able to read this book, but to be able to read all the books from one of the greatest writers in history. So you can see that in the next few months there will be posted reviews for Purgatorio and Paradiso!

A World From Dust talk highlighted on Emerging Scholars Blog

My recent talk in Grand Rapids got highlighted in IV's Emerging Scholars blog! I like the author's summary and the first adjective made my day:
"Ben McFarland of Seattle Pacific University gave a cool talk about how chemistry makes life possible, and perhaps even inevitable. In a sense, biology and life are contained in the period table in the way that a whole range of geometry theorems are contained in Euclid’s postulates, or the way that American society is encoded in the Constitution."

Hadn't even thought about the political analogy. I'll have to keep that metaphor.

The blog, including linked audio, can be found here.

Tuesday, August 11, 2015

"On Being Wrong in Science" posted at the BioLogos Blog

I just posted a guest blog at the BioLogos blog about my scientific and theological journeys titled "On Being Wrong in Science." Check it out, and also check out the post from John Walton that inspired it (referred to in the first sentence).

Monday, August 3, 2015

A World From Dust (Plus): The Higher the Level, the More Repeatable the Evolution

I'm not very good at using microscopes. Maybe that's one of the reasons I'm a chemist, not a biologist. The first problem is getting my eye to line up with that pesky small hole. The second problem is finding the right level of focus. If I'm focused in too much or out too much I don't see anything in the microscope at all. When I finally hit that magic level, everything comes crystal clear  and I feel like a veil has been removed.
The same thing happens when looking at how evolution works. There are different "levels" to the world, and what you see differs depending on which level you're focused on. If you're focused on the level of nucleotides and genes, not much appears repeatable. But if you move your focus up, to the level of organism and environment, repeatable parallels suddenly come into sharp focus.
A paper that just measured this is titled "The Effect of Selection Environment on the Probability of Parallel Evolution". Here's a quote:
"Briefly, we find that parallel evolution is very common at the highest level of biological organization we can study, fitness, and becomes less and less common as one descends down the hierarchy to phenotypes, genes, and nucleotides."
This paper repeated evolution of a bacterium through about 1000 generations 15 times, varying the type of sugar and the location of the sugar. The most interesting finding was that evolution was more parallel when three sugars were located in distinct places than when they were mixed throughout the environment. This suggests that evolution is more predictable if the environment is more varied (and therefore more "natural," like the real Earth is, with diverse nooks, crannies, and caves). As we learn more about the heterogeneity of the early Earth environment, it's worth keeping in mind that any such heterogeneity may have made evolution more predictable, not less.
Evolution does have a random component, especially at the lowest levels. But it becomes more ordered the higher you go, until when you look at all of Earth's history, in the context of the complex Earth environment, the result becomes more and more predictable. And always remember, if you can't see anything, try twisting that focus knob on the side of the microscope.

Sunday, August 2, 2015

Book Review: Incomplete Nature by Terrence Deacon

It's been half a decade since I read a science book that inspired me this much. (The previous one was The Chemistry of Evolution by Williams and da Silva, and I've just written a full book inspired by that one.)* Deacon has built a dynamical theory of how things happen. By itself, that sounds kind of abstract, but he applies it to two mysteries that preoccupy my time: the origin of life and the workings of consciousness, or in short, evolution and mind.

The theory does appear to offer a possible ways forward on the first front, although I'm not as sure about the second, but that's not my primary area and I'm fascinated by the chemical possibilities. Deacon's take on physical chemistry and the nature of energy is solid enough and unique enough that I'm considering how to teach it in my physical chemistry course. Much better than I could do on neuroscience (Deacon's primary area), that's for sure.

As Deacon admits, this book is only a sketch, albeit a 545-page sketch. I could have used more. Since dynamical processes have particular structures, I could have used more figures to clarify some of Deacon's terms and "levels" of dynamics. Although the evolution and mind subjects are interrelated, I think we could have gotten one book on evolution and a second book on mind, and that would have left room to explore more side roads and give more examples. But I'm intrigued enough to come up with examples on my own.

The biggest ally left unenlisted may be theology. Apophatic theology involves double negatives and absential qualities like Deacon's work. Again, this is an open door for others to walk through. I think there's fruitful progress to be made in taking Deacon's ideas seriously and then using those as a basis for natural theology (a la McGrath, not a la Paley, of course!).

In sum, this is a book that I've only begun to soak in. It already makes the short list of "10 most influential books" in my life.

* Deacon and RJP Williams do both emphasize constraints, so much so that I'm already seeing new things by juxtaposing the two. My first public reflection on Williams was a lecture titled "The Chemical Constraints on Creation" no less!

Wednesday, July 15, 2015

Book Review: The Fellowship: The Literary Lives of the Inklings by Philip and Carol Zaleski

The easy access of information through the Internet has made some books smaller. These are the popcorn books, with large fonts and big colorful pictures. On the other hand, the Internet has allowed some types of books to grow larger and better, taking in more with their more expansive view brought in by artful integration of all this easy information. The Fellowship must be one of the latter category, and it pulls off some tricks of intellectual breadth that I didn't think were possible.

 The Zalekskis weave a narrative from four strands that meet in mid-20th-century Oxford: J.R.R. Tolkien, C.S. Lewis, Owen Barfield, and Charles Williams. My book reviews include numerous examples of all of the above. Of these, Tolkien and Lewis are preeminent and the obvious draws. Barfield and Williams are the ones you discover because of their association with the better-known duo. Barfield's story is more active near the beginning and end (he lived until 1997!) and Williams only gathers the equivalent of a chapter or two in the middle, fitting with his firework-like entrance and exit.

It's a lot of ground to cover, but I read it in just a few days. This book succeeds because it takes the Inklings' orientation toward story to heart. The narrative is told as stories that make a single story, at times even with suspense-building tactics on the part of the Zaleskis. I stayed up late reading it even though I knew the ending.
Much must be edited out, but what is kept in is what most Lewis and Tolkien fans want to know. What did Lewis and Tolkien really believe? How did they sharpen each other? This provides the deep connective tissue of the narrative.

Only real flaw I can put my finger on at present is that of proportion: there's too much bio that can be gleaned elsewhere, and too little of the interaction between the Inklings. So little is recorded about the actual meetings that this is completely understandable, but I focused on anything about who influenced whom and what came from where -- the chemistry. I think that some factual detail could have been sacrificed for more conjecture about the connections between, for example, Middle Earth and Narnia, or Williams and That Hideous Strength.
For example, the Zaleskis mention tentatively that Tolkien may have been influenced by Barfield. and quote Vernon Flieger. In my mind this is such a proven, sensible, and foundational connection that it underlines the importance of Barfield to the group -- but here, it is mentioned as peripheral. I don't mind such speculation; it's what makes a book like this sing! This book is about the connections, not the nodes, and a shifted focus more toward the connections would have allowed more integration of the minor Inklings as well. As it is, many works are mentioned with little speculation on possible cross-influences. However, I have already read several books on and by each of the authors here, so a more general approach may fit the audience this is really for.
On the whole, the juxtaposition of the authors allowed me to glean some of the connections that I crave, and to relate it to my own work and writing, so I must highly recommend this unique and highly readable book to anyone with any interest in how creativity works, or how faith works, or how Oxford worked in the mid-20th century.

A World From Dust (Plus): Why Pepto-Bismol Kills Bacteria but not Humans

Chapter 2 of A World From Dust explains how Pepto-Bismol works. That pink stuff kills ulcer bacteria because of its chemistry -- the bismuth in it is so sticky that it sticks to and jams up proteins in bacteria.

The sharp-eyed reader will notice that a key part of this story is left out. Human and bacteria proteins have the same basic chemistry, being made of the same CHON atoms. If bismuth is sticky to bacterial proteins, it must be just about as sticky to human proteins. So if bismuth kills bacteria, it should kill human cells as well. So why is it that we can drink the stuff? Why is there a novel titled Arsenic and Old Lace but Bismuth and Old Lace doesn't scare anyone?

Human cells can survive a dose of Pepto because they have an extra layer of chemical protection. Our internal chemical shield is built from sulfur, in the form of the molecule glutathione, mentioned in another part of Chapter 2. How this shield works is shown in a 2015 PNAS paper titled "Glutathione and multidrug resistance protein transporter mediate a self-propelled disposal of bismuth in human cells" (which, incidentally, is so well done that other scientists would do well to pattern their metal-life investigations on it).

As shown in the diagram above, purple bismuth (Bi) approaches from the left. It crosses the cell membrane and sticks to yellow glutathione's (GSH's) sulfur atoms. Bismuth is so sticky it collects multiple glutathiones, then the cell takes the assembly and tucks the dangerous metal away into a small sulfurous bubble (or vacuole) shown in gray on the right. This is what glutathione is for -- to preemptively stick to the sticky things before they can stick to something else.

The really nifty part of this is that as this process depletes glutathione, the cell senses that and turns on the machinery for making more glutathione. The more bismuth abounds, the more glutathione super-abounds to fix it. Excess glutathione is then available for sticking to other toxic metals as well, so that Pepto may incite a more general protection.

The bacteria killed by Pepto-Bismol don't have a complex glutathione system like this, so its stickiness turns their insides to solids, and they die. Human cells can resist internal petrification because of the chemistry of sulfur as corralled by glutathione's structure. Our cells sweep the sticky bismuth into a side chamber and our proteins remain nice and fluid.

This has implications for cancer therapy. Some forms of chemotherapy kill cancer cells with sticky, toxic metals like platinum. Cancer cells resist the chemo by turning up their glutathione production. Understanding how that system works should allow us to find a way to turn it off, which would make metal-based chemo much more effective. More details can be found in this summary article related to the research article above.

This is also why understanding the chemistry is so helpful. Bismuth-sulfur chemistry may lead to more effective chemo. So support your neighborhood chemist -- you never know what she'll find next.

Friday, July 10, 2015

A World From Dust (Plus): As Predictable as a Warm-Blooded Fish

This is a body-temperature scan of a fish. It should be dark blue because most fish are cold-blooded. Some have evolved biological spaceheaters next to strategic tissues that would show up as orange dots above. But the opah (Lampris guttatus)spreads its warm blood around, even keeping its heart warm, resulting in warm blood throughout its body, shown as yellow and light blue. This allows it to eat at depths other similar fish can't reach.

This expands on the narrative of A World From Dust in two important ways:

1.) The problem with being warm-blooded is not just making the heat, but keeping it. To insulate its precious heat from the cold waters around it, the opah pumps its blood through intricate and efficient blood vessels in twisted hairpin shapes. This structure is called a rete mirabile and can be built using Adrian Bejan's engineering theories for how heat flows. This hairpin structure is optimal for insulating a circulating fluid, so it is found repeatedly in warm-blooded animals. Bejan's Constructal Law could have been used to predict that a warm-blooded fish would have a complex rete mirabile structure before that structure was found in the fish -- it is a consequence of how heat moves. The opah is generating more heat, so I believe it would have a higher Energy Rate Density and Chaisson's ideas may apply, too. It has a more complex internal structure to match its higher energy throughput.

2.) Other fish that look like the opah and have genes like the opah are not warm-blooded, but a few very different fish (for example, tunas and lamnid sharks) have the biological spaceheaters that are halfway there. These fish obviously have different shapes and different genes, but they have independently developed similar systems for heat generation and insulation. In very different species, evolution has converged to produce similar and predictable warm-blooded temperatures and structures. Which species get it may depend on random rolls of the dice at the gene level, but that some species will get it and fluorish, that is predictable, given enough time.

So, not only is a warm-blooded fish very cool (see what I did there?), it also shows that evolution solves similar problems with similar features (warm blood) and similar structures (rete mirabile), in tuna, lamnid sharks, and opah, repeatedly producing predictable complexity.

Book Review: Battle Lines: A Graphic History of the Civil War

I picked this up to see if I should recommend it to my early-teen kids and ended up engrossed for myself. The basic idea is of seeing the Civil War through the lens (in one case literally) of ordinary objects. The graphic novel medium is used incredibly well, with the only problems coming when more exposition is needed to connect the dots, or in the case of the second episode, when trying to cram 100 years of legal history into a dozen pages. You won't get a bird's-eye view of the war from this, you'll get snapshots -- but some of the snapshots are incredibly moving. A graphic panel is worth 1000 words. One episode in particular uses the triptych style to tell three stories in parallel and accomplishes what no other medium can. It's a slight mixed bag, and if you're familiar with Civil War documentaries and movies, some of the episodes essentially recapitulate those. But a large majority of the episodes are creative, insightful, and tragic. I can only hope that the makers of this can return to the era and fill in more episodes based around other objects in the future. This is a fantastic way to teach and learn.

Book Review: Finders Keepers by Stephen King

Even though it's essentially a self-contained story, Finders Keepers suffers from the mid-trilogy blues. It's still a cracking read and finely crafted, as King weaves together several stories with nice parallels just on the right side of coincidence and characters that seem just a touch more human than other writers' characters. The motivations in this case are literary, as a reclusive writer's Moleskin notebooks play the MacGuffin. But Mr. Mercedes was better: more happened, with more twists, the evil was scarier, and the setup more unusual (just read the blurbs and tell me which story you're more interested in reading). A few foreshadowings of the third book, End of Watch, interested me more than the present story did. When all three are out, the shortcomings of Finders Keepers will probably fade and the trilogy should be considered as one big book. For now, it feels a bit too much like running in place, but I have a feeling King will make it pay off in the end.

Note: The audiobook reader is really excellent, changing tones to indicate different characters artfully, and throwing himself into King's over-the-top dialogue with gusto. I recommend listening to this rather than reading it.

Tuesday, July 7, 2015

Book Review: Coming Out Christian in the Roman World

This is one of those rare books that convinced me of the opposite of the author's thesis. There's some interesting historical examples but they don't connect, possibly because the author explicitly rejects the idea of explaining history through a narrative. If you don't think history forms any kind of narrative, then the narrative you present in your book will probably not be very engaging or cohesive. One chapter takes Constantine to task for being confused in one of his pivotal speeches, but I don't think it's Constantine who's confused here. I also don't feel like there's much of a window on the ancient psyche here -- the author protests against Manichean dichotomies, then turns around and sets a dichotomy between the firebrands preaching Christian separation from the world and the average Christian trying to figure out a balance. This is an issue Christians have always dealt with but I don't see additional insight beyond a list of the various historical pressures. How are those put together in the process of "Coming Out Christian" as in the book's title? I still don't know. I very much wanted to learn from this book, but it just has too many problems.

Saturday, July 4, 2015

Book Review: Infinite Jest by David Foster Wallace

Infinite Jest is the Pacific Coast Trail of books. Incredible scenery, but still, it's so much to do that many have turned off the trail before it's done. Since I've been on sabbatical I figured it's now or never for this half-a-million-word book. I'm very glad I did, but I was surprised by which parts I liked best.

There's three basic plot lines: a tennis academy of high achievers (including a flawed but fascinating family at its center), a halfway house of addicts and ex-addicts, and political/sci-fi satire of where we're going as a society. Before reading, I would have thought I'd prefer the poli-sci-fi most and the halfway house least, but it was precisely the opposite. It's the halfway house through the story of Don Gately that was compellingly horrifying and hopeful in all the right ways. In the other storylines the satire occasionally stepped so far out of reality that I laughed but with a smirk rather than the laugh of recognition (and/or the shudder) that I got from Gately's desperate circumstances.

For this reason, I actually look forward to The Pale King. Given what I like most about Infinite Jest, DFW writing about boredom and the IRS is going to be amazing.

DFW is a generous writer. Perhaps too generous at times. But on every page there's a well-turned phrase or touching insight, and since there's more than 1000 pages, that adds up to a unique experience.

Some of the plot turns on a movie that is more compelling than it should be, somehow reaching into your soul and changing you, narrowing you and reducing you to a mindless addict. The book itself is also more compelling than it should be, but it changes you to broaden your perspective and take in more than you saw before.

In the halfway house especially, the story descends to the bottom and also goes the farthest, and though the resolution remains at a distance, from the top of the mountain the veil lifts, and it (the resolution) can be glimpsed even if, for now, it can't be touched.

Monday, June 22, 2015

Book Review: Flash Boys by Michael Lewis

Flash Boys explains some of the mysterious behavior of Wall Street: why some firms would build a special fiber-optic line from New Jersey to Chicago to shave a few milliseconds off the time it takes to make a trade; why the stock market has frightening blips of instability, like the "flash crash" when it lost a huge chunk of value and then regained it in a matter of seconds; and what firms do with the computer-programming geniuses they hire for big money (but not nearly as big as traders' salaries).

As a piece of extended technical journalism, it's fabulous at explaining complex subjects that most people in the field don't understand. As a piece of general writing, it's a little too quick to assign white hats and black hats, especially when one of the main "black hats" (Goldman Sachs) actually gains quite a bit of gray by the end. (Don't worry, they're still a vampire squid, but they're an old and sometimes self-contradictory vampire squid. Gödel's Vampire Squid.)

The most surprising value of this is that you understand more of how computer programmers work, so if you love someone who codes and want to understand more of what they do, by the end you've have a few glimpses into the universalities of coding life -- distorted by the financial greed of the markets, which is the book's main subject, but computer programmers seem to be much the same in whatever field.

The book jumps around a little too much, trying to make a narrative out of disparate stories that don't really go together. It would have worked better as a collection of essays with a short intro and extro, I think. But it's an education in modern economics and computer science, with a good dose of old-fashioned morality thrown in. I would welcome a theologian's reflection on the nature of evil after reading this book, in fact.

Understanding Brain Science with Inside Out

Inside Out is not just an entertaining movie, it's also a worthwhile movie. It had enough bright colors and pratfalls for my four-year-old and enough deep psychological subtext for me. I may never look at certain thought processes the same way again. The subtext is sturdy enough that it provides another dimension to the movie: it forms a framework for understanding brain science. As Exhibit A, I submit a recent Cell paper that Inside Out can illuminate.

(Before I continue, let me say that this contains MILD SPOILERS for a location visited relatively late in the movie. If you want to discover this location for yourself, go see it right now and come back!)

The paper I'm thinking of is titled "Sleep Facilitates Memory by Blocking Dopamine Neuron-Mediated Forgetting." Like any good title, it contains the key point of the paper, which can be illustrated using the imagery of Inside Out.

Researchers started from the knowledge that sleep helps build memories. In the Inside Out world, the sky turns black during sleep time and the memories roll out to Long-Term Memory storage, which fits precisely with this knowledge. Some memories don't fit in Long-Term and are rolled down to the Memory Dump. By studying memories of smell in fruit flies, the researchers dug into the tubes and found one gatekeeper who determines which memories roll where.

Imagine an Inside Out Forgetter (as pictured above) who sits at the entry to Long-Term Memory, kicking some memories out of the rolling chute and down into the black funnel that is the memory dump. This Forgetter is Dopamine -- the same molecule that gives you that euphoric dopamine rush so many people talk about. Maybe this particular Forgetter is moonlighting, constructing pleasant sensations by day and working as a Forgetter by night.

What the scientists did is they kidnapped the Dopamine forgetter, and more memories rolled into Long-Term storage. The science is a lot more detailed and complicated, mostly because dopamine has so many jobs, but the basic message is smaller than a Pixar short.

Speaking of which, can we enlist the Inside Out crew to make some educational videos for psychology courses? Something tells me profs teaching next year's courses will have a whole new set of references in them thanks to this movie. Which provides one more small reason to see it.

Friday, June 19, 2015

Book Review: Brand New Ancients by Kate Tempest

This is one long poem by Kate Tempest based on modern gods in general rather than what she did in Hold Your Own,  where many poems focused on one figure in specific, Tiresias. I followed her directions this time and read it aloud to myself, which brought out the colors of Tempest's internal rhymes and unexpected rhythms. Tempest's language is musical and even Homeric.

As for what she's really saying with her language, the closest thematic analogue I can think of is Neil Gaiman's American Gods, which is one of my favorites of Gaiman's. The reason why Tempest writes what she writes intrigues me in the same way as American Gods did. This seems to be like what Owen Barfield called "putting things back together" but from a standpoint of polytheism and ancient Empire rather than from a standpoint of monotheism and ancient community in rebellion against Empire. Although I come from the latter standpoint, I'm fascinated and want to see what Tempest will continue to build with her words, because her poems are as tangible and feel as lasting as bricks and mortar.

I would build differently -- but I can't wait to see where she goes with this bringing mythology into the heart of modern life. It feels like a grand beginning to a brilliant career.

Friday, June 12, 2015

A World From Dust (Plus): How Oxygen Stress Steers a Protein

This is part of a series of posts expanding and updating the book A World From Dust: How the Periodic Table Shaped Life. This post involves biochemical concepts such as protein structure.

Complex I of the respiratory chain is one of the crucial enzymes that ultimately helps you use the oxygen you breathe. It is the first funnel through which electrons are poured on their path to combining with oxygen. Part of this funnel is shaped by oxygen's unique chemical properties.

Enzymes like Complex I, called hydrogenases, first show up around Chapter 6 of A World From Dust, well before oxygen fills the atmosphere in Chapter 8.  Still, if any oxygen is around at all, they are shaped by it, because they must avoid oxygen's negative power. Oxygen reacts with stray electrons to form Reactive Oxygen Species (ROS) that shatter the insides of a cell.

If a hydrogenase drops too many electrons out of its "funnel", they are picked up by oxygen and make havoc-wreaking ROS inside the cell. Avoiding the negative consequences of oxygen shapes life as much as running toward the positive consequences of oxygen's energy.

This was shown in the recent study "Reactive Oxygen Species Production by Escherichia coli Respiratory Complex I" in Biochemistry. This study is built on a previous experiment in that increased the amount of electron-carrying "electron boxes" inside the cell called NADPH. Normally Complex I only gathers electrons from the NADH electron box through its funnel, but when there's high amounts of NADPH, it will evolve to accept NADPH as well. It does so precisely at the green sticks at the bottom of this figure:

(Figure provided in supplemental materials to the paper cited above)
The orange sticks are NADH, and the green sticks are placed exactly where the "P" is that makes NADPH different from NADH. If this enzyme is to bind NADPH, those green sticks must get out of the way. In the previous experiment, they did, evolving to alanine (A) and glycine (G).
The key to the new paper is where the green sticks didn't evolve to. Other green sticks still bind NADPH just as well as alanine and glycine. In particular, histidine (H) and glutamine (Q) were not observed, although they interact well with the P in NADPH and can even increase binding. So why were these perfectly capable mutations not observed?
The answer provided in this new paper is that, with histidine and glutamine, too many electrons fall off the NADPH, out of the funnel, and onto oxygen, making too many Reactive Oxygen Species (ROS). Because these are dangerous to the cell, the protein does not evolve in that direction, but rather evolves in the direction of alanine and glycine.
This can be summarized as the letters for these particular positions. In the "word" that is the enzyme, at this one position, we don't see "H" or "Q", but we do see "A" and "G", not because the enzyme works better with those two letters, but because the whole cell works better with those two letters.
Instead of four possibilities, evolution chooses two, and in this very small way, it is constrained by the need to avoid oxygen stress. This is a biochemical example of two important points of the book:
1.) Because of oxygen's chemical tendency to form ROS, the protein has fewer options at that position than it would otherwise. (It is constrained by oxygen's chemistry.)
2.) To understand why it's restricted, we must account for the oxygen stress on the whole cell, not just the efficiency of the one enzyme or the NADPH-binding properties of the one residue. (We must look at the higher level of the cell biology rather than the lower level of the biochemistry; the higher level constrains the lower.)
To cite the central metaphor motivating the book, if this tiny motif in the "tape of life" were replayed, we would still "hear" A and G, not H and Q. There is freedom for the system to select A or G, but not H or Q. The possibilities are constrained by the double-edged sword of oxygen stress, and the river flows in one direction, but not the other.