Monday, December 26, 2016

Book Review: Abaddon's Gate

Book #3 of the Expanse manages to elevate the story from a very high level to an all-time-great level. For a series so rich in plot and invention, I struggle with how to review it without spoiling it (even the first sentence of the summary of Book #4 spoiled the ultimate result of this book for me!). Suffice it to say that my minor complaints from the first two books are turned into strengths in this one: in this universe, faith is realistically important, complex enough to be both good and bad, and even crucial to what the book is saying (I actually teared up at the major character turning point of forgiveness and trust). My other minor complaint was the slow reveal of alien purposes and intelligence, but that is mostly because the characters move through so much plot (they really put you through the wringer) that the alien part of the plot seems slow by comparison. I have some hunches about how that will play out, but it's really being strung out masterfully. This whole series is a masterclass in story, and Abaddon's Gate both surprises you and ups the game at the same time while avoiding cliché yet keeping everything thoroughly grounded in the universe we know. This series is very much worth the time for the science-oriented sci-fi reader.

Book Review: The Slavery of Death by Richard Beck

This little book is poor in pages but rich in substance. Part of the reason my book-reviewing pace has been so slow over the past few months is that I read this slowly and deliberately. Beck combines the Eastern Orthodox theology of Christus Victor with the psychology of death neurosis and personal experience (both his own and that of Therese of Lisieux). The result is new and old things brought out from the starting point of the verse from Hebrews that Jesus released us from the slavery of the fear of death. The best book to pair with this volume of the Little Way is NT Wright's huge tome on The Resurrection of the Son of God. Even though on the surface they look very different, both are works through which the Spirit spoke into my life, and I can still hear the resonant echoes.

Monday, November 21, 2016

The $1 Microscope

The Prakash Lab is one of the real sources of creativity and ingenuity in the world today. They've debuted both the "Dancing Droplets" exercise and the Foldscope: a functional microscope made from paper for $1. I've been waiting for the Foldscope to be available publicly... and now it is! The Kickstarter just went live, and yes indeed, you can buy 20 microscopes for about $25. Can't wait to get these into students' hands in the lab! And I'll try to get them to Burundi too, for use in medical education there. Don't get me started on my ideas for outreach with this thing.

Book Review: Caliban's War

The Expanse continues to expand, although this time with a more focused story. Where Book 1 was a detective story, Book 2 is a search for a lost girl and a fight against super-soldiers (both in military and political arenas). I appreciate that the scientist character actually acts like a scientist, politically naïve but good for figuring new things out, and that the politician character solves problems like a politician should. There's even a minor chaplain character that makes more of a contribution than the religious characters in the previous book. My only complaint is that this plays like a "Monster of the Week" episode of the X-files, in that the underlying mythology of the alien technology is not much advanced, although there are some tantalizing hints. If you need a little realistic escapism each day, I highly recommend this series so far.

Monday, October 10, 2016

Book Review: How I Changed My Mind About Evolution

This won't be an ordinary book review, because I personally know or am acquainted with at least half of the people involved in this book and both of its editors, as a result of my involvement with this question for the past decade-plus, and of my participation in the BioLogos Voices team. So this was less "let's find out what other people think" than "let's find out WHY these particular people agree on this thing." As such, I can't really assess its persuasiveness, being already persuaded! However, I did pick up on some interesting parallels as I read through the books, taking each as a letter written in a human heart.

If I had to pick a favorite chapter, it's probably NT Wright's, even though it's the least personal of them all. Wright looks on this phenomenon from the outside and ties it to American history. As a country, we're trying to talk about race and the past, and I personally am finding more ways in which the past lives on today. It actually never occurred to me that both the Scopes Trial and the Creation Museum are in the South, and that evolution is connected to the great American sin, chattel slavery -- and also to the red-state--blue-state cynicism and mutual antagonism. Wright puts all that together in a mere page, much like he puts together ancient history with theology in his other work.

The other stories are much more personal, and each one is kept short enough that the ultimate cumulative effect is all the stronger for it. Most (but not all) start as Christians and then come to evolution. Most (but not all) focus on the personal rather than the data, leaving the actual arguments to other books. What I think would be interesting at this point would be another book about "How I Changed My Mind About Science," in which Christians talk about the positive influence faith has on their scientific work. But this book is a necessary first step to remove the barriers, before we can talk about the synergistic boost that both faith and science can experience when they are put together.

Tuesday, October 4, 2016

A Letter to My Son About Creation

Dear Sam,

Today you are fourteen. I am so proud of how you’ve grown up from a little drooling turkey-sized thing to the young man you are today. I keep thinking about how we really only have four more years with you until you move out to college. I’m left with too many things to say in such a short time.

You inherited half of yourself from me. I see myself in your constant reading, in the way you are interested in so many things that it’s hard to pick a single thing, even in the way you file away the comics in your head. And it makes me remember what it felt like to be fourteen.

I had a lot of questions about how to put all that reading together, especially trying to reconcile the first few pages of my Bible with the first few pages of my science textbooks. After three decades of these thoughts, I’ve tried out just about every possibility to see how it works. When I was your age I read many people who insisted that the stories of the Bible and the stories of evolution don’t fit at all. These people said you have to trust one set of stories and throw away the others. Creationists said throw away the science, and Isaac Asimov (my favorite science writer) said throw away the Bible.

I remember a Saturday afternoon I spent sitting in church learning about how the six days that I read from the first chapter of Genesis were 24 hours long and each creation event was an abrupt creation from nothing. I started out believing them when they said that it gave God the glory to trust His Word over that of the scientists. But the more I learned and did experiments myself, the more I felt like there must be other ways to read all these books. So, I went through an “Intelligent Design” phase, and then a “God created everything else with evolution but Adam and Eve were separate” phase, and now?

I’d like to tell you where I am now in a story. I could tell you my biographical story, of how I changed my mind and why, but instead I’m reminded of the recent movie version of Noah. This movie took a lot of risks, and all of them didn’t work, but one of them worked very well. In the darkened ark, during the 40-day deluge, Noah sits down with his family and tells them the story of creation. In the movie, this is animated beautifully with images of nature, and I’m sure you remember how I’ve shown it to you on YouTube. (I even have a few issues with how the movie did this, but it’s better to tell your own story than correct someone else’s!)

Noah’s children walked out into a new world after 40 days. For you, it’ll be four short years. You need to know where you came from, and that God was here before you, me, anyone, or anything.

Here are a few words trying to capture a fraction of that story. Some of my words will be proved wrong, but the story remains true if it shows you who God is.


The story starts in the darkness. In the beginning, there was God. The Spirit of God fluttered over the empty chaos like a bird over the ocean. He spoke a word, and a pinpoint of something emerged, bright with light. Time and space flashed open, inflating like a balloon, obeying his command. Matter separated into pieces with positive charge and negative charge. These attracted each other like a swarm of magnets and joined into a multitude of indivisible bits that could snap together like so many LEGOs. God called these bits atoms. God set a limit for these atoms: they could not travel faster than light. God saw the atoms obey his limit, and he saw that it was good.

We watch as evenings and mornings pass. This ends the first part of the story.

God said, let many lights form. God made gravity, and the atoms gathered together. In some places, billions upon billions of atoms pressed down with enormous pressure. God called these places stars, and saw that they were good. Inside the stars, some atoms were squeezed into newer, bigger atoms, and the extra energy leaked out as light. One by one, the stars caught fire, blooming like flowers. They grew, and aged, and burst like seeds, spreading the new atoms across the universe.

We watch as evenings and mornings pass. This ends the second part of the story.

And God said, let a disc fly out from a new star and let it gather into new planets. After an intricate dance, eight planets obeyed his call. God saw that it was good, and he called that star the sun. Some say that the biggest planet moved in and out around the sun, clearing the space for the four planets inside. God set a limit: the planets settled into cycles, like dancers repeating the same steps again and again around the central star.

We watch as evenings and mornings pass. This ends the third part of the story.

One of the planets was not like the others. It was wet and open to the sun, warm but not too hot. God called this planet earth. God gave it a single moon that lit up its night sky and pulled the oceans over the dry land. God said, let the water form a cycle of weather, and, look, the water went up into clouds and came down as the rain. The water mixed with the dry land and, like an artist, drew shapes on its surface. And God said, let a cycle of life spring up from these atoms. And the earth brought forth tiny creatures, and they ate food that God gave them from the hot insides of the planet in chemical cycles. God blessed them, and the creatures built shelters and grew and changed. They filled the earth, and God saw that it was good.

We watch as evenings and mornings pass. This ends the fourth part of the story.

And God said, let the earth bring forth green things. And plants grew from the waters and the earth. These caught the light from the sun that God made, and turned it into sweet sugar and fresh oxygen. Oxygen’s power rusted and reacted with the planet and took away most of the food. There was a famine and life fell back. But, faithfully, the sun kept giving its light, and that light became more oxygen, and the oxygen became new life. Creatures learned to breathe the new air, and to use cycles of oxygen for energy and for building new things. These cells grew abundantly and joined together into animals big enough to see, but there was no one to see them yet.

We watch as evenings and mornings pass. This ends the fifth part of the story.

And God said, let the earth bring forth different kinds of animals, and the earth brought forth amphibians that crawled from the water, reptiles that basked in the sun, great sea creatures that lurked in the oceans, and birds that flew through the air. Some kinds ate plants and evolved strength and defense. Other kinds ate animals and evolved quickness and intelligence. Together the animals grew into cycles of biology that turned together to make ecosystems, like dancers repeating the same steps. Great extinctions pulled back on life, yet great expansions of new life followed.

Then God said to the earth, let us make humans in our image, after our likeness, male and female. God spoke, and his breath went out, and new cycles formed in the brains of humble primates. Out of those brains emerged minds that could see, understand, and even control the plants, the cattle, and the birds. And these humans became living souls reflecting the Creator into the creation. And God blessed them, and said unto them, Be fruitful, and multiply, and replenish the earth. I have given you all this – take care of it.

And God saw every thing that he had made, and, yes, it was very good.

We watch as evenings and mornings pass. This ends the sixth part of the story.

In the seventh part, God ended his work. The heavens and earth were complete. God set a limit: God blessed the seventh day of the week, and set it aside, so that we too can enter God’s rest.

We watch as evenings and mornings pass.

Then, something happened that was not good. The father and mother of us all were deceived because they did not believe that God was good. They followed evil whispers and stepped outside of God’s limits. We all followed in their footsteps, and death ruled in us. Brother killed brother in broken, decaying cycles of greed and fear, and we were lost.

Into this darkness, God again brought light. God called a man named Abraham to leave the limits of his father’s country. From this man God called the nation Israel. The name Israel means “struggle,” and they indeed struggled with God. They received stories and limits from God, but they forgot them and failed to trust God. So God gave them judges and kings, but they fell back. One day the light of God’s glory left them. They did not notice.

Then, as a humble carpenter, God’s glory returned. We did not notice. Life ruled through Jesus, a different kind of king. He was full of grace and truth -- yet he was cut off and killed by the people of Rome and Jerusalem together. It was another broken cycle of violence and fear.

But the broken cycle was fixed! On the third day, on the first Easter Sunday, God vindicated Jesus by giving him new life, through the same Spirit that formed the earth, recreating and raising him from the dead, with a new body that goes beyond our limits.

The Gospel of John hints that Easter Sunday was the eighth day of creation, recorded not in rocks or trees but in transformed minds, bodies, and words. Like the first seven days, it was a unique act of God that built on and emerged from the previous events in surprising and creative ways.

This Eighth Day is repeated when Jesus is born again in someone’s heart and mind. Together we look forward to that day when God will raise the bodies of all who believe as he did Jesus’ body, and will restore all of God’s creation, and will reveal God’s Kingdom here on earth.

If you look in the right places, with eyes of faith, you can already see God coming, as God is creating new life and filling the earth with good things through the community of believers. The best part is that you don’t have to just watch -- you can join in as God uses your life to bring more life to this beautiful, broken world. God made you with love, as he made this planet, to be part of the continuing, evolving act of new creation.


I hope this shows you how I have found peace in reading first the Bible and then the science books. God told us some of this story in each book, and part of life is putting it all together. Now, what questions do you have? This story isn’t complete without them.

Love, Dad

Wednesday, September 28, 2016

Book Review: Leviathan Wakes

This was recommended by an old friend, and between it and Stranger Things, I'm reliving my late 80's-early 90's teenage years. It feels like the good episodes of Star Trek: The Next Generation but with more detail, politics, realism, and grit. Einstein remains right in this universe -- no one can exceed the speed of light. Some advances in propulsion allow journeys among the planets and asteroids of our own system, but it's much more like sea voyages than "snap your fingers and you're there" warp drives (don't even get me started on Star Wars light speed). It's also fairly politically realistic, at least more so than the highly polished Star Trek universe or the highly myth-driven Star Wars universe. As a result, it feels like it could happen. And happen it does. The plot moves at breakneck speed through a multitude of genres. I don't care for zombie horror that much, but then it moves on to detective noir, and then a technical space battle that feels like a war movie. The characters are deftly drawn (for sci-fi, which does involve a handicap). I especially like how the idealistic leader figure is portrayed, neither rosily nor cynically. Overall, even though this was a long book, I was tempted to jump into Book 2 of the series right away, because it's that good. Enjoyed (almost) every minute of it.

Monday, September 26, 2016

Hall of Fame of Cheap Science

The first day of class is always fun. I try to review two things:

1.) Cell Biology: Zoom in and out through the cell. How big are different biomolecules?
2.) Instrumentation: How to separate and analyze the parts of the cell with everyday items that could be used globally -- e.g., in Burundi. In the past few years this has expanded exponentially thanks to portable phones and 3D printing.

If I had a theme park, the first point would make a really great dark ride and the second would make for some EPCOT-like interactive exhibits.

Here's so you can listen in if you like (sorry for the loud scratchy mic at the beginning when I have to quiet them all down!):

Saturday, September 24, 2016

Book Review: The Spirit of Creation by Amos Yong

I wish there was a shelf in the bookstore called "Interdisciplinary." It would have to be a curated shelf, because there's lots of books that claim to be interdisciplinary, but only a few that truly are -- in which it could stand on its own in more than one discipline, and which is accessible to practitioners of all. Come to think of it, such a shelf might not exist because there might not be enough good books to stock on it. At any rate, The Spirit of Creation would fit on that shelf, combining theology (and a specifically Pentecostal angle on that theology) with philosophy of science and becoming more than the sum of its parts. Since one of the themes of the book is emergence, that result is entirely appropriate.

Yong has a knack for describing historical developments in both science and theology with a few sentences more effectively than others in many paragraphs. His description of the historical development of the concept of "laws of nature" accomplishes in a few pages what takes whole chapters in other places. This means that I can put his ideas together with scientists' ideas (like those of Terrence Deacon, in particular) and I suspect that something genuinely novel will emerge.

[My only hesitation comes in a late section on parapsychology, which I found unconvincing and unnecessary at the first reading (to be clear, I'm still going back and forth with myself on the necessity of it to the overall argument), although Yong's disclaimers at the beginning do a good job of insulating it from the rest of the argument. My biggest concern comes with how antagonists could take that section out of context and try to discredit the rest of the very good arguments as a result.]

Most importantly, Yong's pentecostal faith provides a necessary and helpful perspective that informs and enhances my own faith perspective -- and my science perspective. The specific thoughts on emergence seem to point a way forward that I've been thinking about for the whole week since I finished this book, and so it has already stuck with me and will continue to do so. File this on the top shelf.

Thursday, September 22, 2016

Book Review: The Swerve by Stephen Greenblatt

This book is the closest thing we’ll get to the Gospel of Lucretius. It makes for an invigorating internal discussion in the vein of C.S. Lewis’s “second friend" (i.e., that friend who has read all the right things but gotten all the wrong ideas out from them). In Lewis’s case, he was referring to Owen Barfield’s fascinatingly flawed obsession with Rudolph Steiner and Theosophy, but the same sentiment applies to this book’s fascinatingly flawed obsession with Lucretius’s Epicurean philosophy.

It’s not that Greenblatt sees Lucretius’s influence in too many places – it’s that he sees them in too few. In this telling, Lucretius wrote On the Nature of Things, it had some influence but was all too soon eclipsed by Christianity, with the typical secular narrative example of "St. Hypatia" as told in the movie Agora.  Then, in this telling, Lucretius disappears until a chance discovery resurrects his ideas into glorious, enlightening victory.

But this ignores the central fact that Lucretius has always been around. Even in the "darkest" of Dark Ages, every Christian has an internal debate with doubt. It also ignores Stoicism’s constant presence in different guises throughout history. In my view, the writings of Augustine and Aquinas show the marks of struggle with Lucretian/Epicurean ideas and Stoic ideas. All writing that goes deep enough shows that each mind has a debate to settle between Lucretius and Christ, even if the ideas don't go by those names.

Exactly why Lucretius was eclipsed by Christianity in the first half of the first millennium is not convincingly explained; Greenblatt thinks the right ideas “lost” the intellectual battle but, to me, never explained why they lost (not convincingly at least). Greenblatt leans on explanations of a Christian emphasis on pain over pleasure, but if so I have no idea why anyone would take the Christian option ... yet that’s what happened historically. Something’s missing.

Then Greenblatt goes into great detail as to how a particular Italian rose to a certain clerical power and eventually found Lucretius through a string of luck. (Never mind that if I heard correctly, 50 copies of On the Nature of Things existed, and it seems that one would see the light of day eventually.) This story is told in so much detail that it takes up too much of the book. Rather than telling us exactly how convoluted (socially and morally) 15th-century Italy was, the story should have focused on why that situation existed and how the people thought. Instead of ideas we get a string of names.

But then, it does get interesting. The final chapters are the best, because once The Nature of Things emerges through the Renaissance, the influence of Lucretius can be traced all the way to Darwin (Erasmus, that is) and Jefferson. I'm not convinced that Lucretius is as central to these thinkers as Greenblatt seems to think he is, but at least we're talking about ideas here as ideas. This is where the history of ideas happens, and there should be more of it. (The chapter explaining the context of Lucretius and his early readers is also good and idea-rich.)

What stood out to me is how Lucretius’s ideas may have held back science in some cases. Atomism is right, but the Big Bang scenario is objectively closer to creation ex nihilo (at least on the surface) than it is to Lucretius’s endlessly cycling universe. Einstein resisted the Big Bang because he was too Lucretian, and reality turned out to look awfully medieval in this respect.

 I understand that you have to leave something out to write a book this short, but in that case, leave out the 15th-century Italian intrigue and talk about the ideas and the science more. I’d like something that could stand up to Thomas Pfau’s Minding the Modern, but instead, The Swerve is more on the level of The Purpose-Driven Life for people who don’t believe in purpose. Don't get me wrong -- it’s very worthwhile on that level, but it’s more about reaffirming the “faithful” than changing any minds. Obviously it didn't change mine!

Friday, September 16, 2016

A World from Dust (Plus): The Rapid Emergence of Life

For a scientist, opening up a new scientific journal is a bit like opening up a present on Christmas Day. I always get a slight thrill when I look through new journal articles and find one that further confirms something I'd suspected previously. I had that sensation a few weeks ago when I read "Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures" in Nature.

I admit that most people don't have their heart leap when reading those words, but compare that title to this quote that I wrote a year or two ago, now printed on p. 87 of A World from Dust:

"Before the clues, there is the question of timeline: When did life begin? This is a bit of a surprise in its own right. I would have thought that, given all the different molecules that have come together in any living thing, this assembly should have taken a long time. Instead, most evidence implies that life formed on this planet as quickly as possible, if not sooner."

"Living processes are even harder to pin down in rocks, but various lines of evidence (including unnatural imbalances of neutrons) can only be explained by life 3.5, 3.6, or even 3.8 billion years ago. A study of phosphorus in rocks 3.5 to 3.2 billion years old finds that life was mature enough to use phosphorus in a widespread, well- defined phosphorus cycle. Evidence for life immediately follows the evidence for oceans. An energy- diverting, growing, replicating chemistry followed the presence of liquid water in a geological blink of an eye."

This is why Chapter 5 (Clues to the Origins of Life) immediately follows Chapter 4 (the formation of the oceans). Many pieces of evidence point to the quick succession of these two chapters, including the "deep genealogy" studies that project what the oldest DNA sequences were like, resulting in an age of 3.8 billion years for the first proteins, as described on pages 87 and 88. Life springs up as soon as -- or even before -- the planet cools down enough to host it. This new Nature article is one more piece of evidence that fits into the quote above with an almost-audible snap.

Some have read the Nature article as a strike against "Darwinism" in some way, because this rapid emergence of complexity is inconsistent with slow, gradual change. But one of the main points of A World from Dust is that Darwinism isn't all about slow, gradual change. It's more like a symphony, a long, moving piece of music with different parts at different tempos, all reflecting the same theme of emerging life.

If the Nature article is a strike against Darwinism, then why was I, a scientist who admires Darwin and his ideas, so excited to read that sentence? Why did I write those two paragraphs as part of a whole book about evolution before this new finding was revealed? Yes, life emerged quickly, I've been saying that for a long time. I wrote those two paragraphs a year or two ago, and they are reinforced now. (Another point of my book is that it's possible to have disagreements about the nature and meaning of evolution without throwing out the idea of evolution, as shown by how often I contest Gould's "Tape of Life" metaphor yet remain convinced that evolution was the mechanism for generating life's diversity. For one thing, I think Gould's picture of evolution is at times too slow, and that it moved faster than he gave it credit.)

In the rest of my Chapter 5 I present seven chemical ideas, each one rooted in replicable laboratory experiments, for how the origin of life could have happened so quickly. I think that we might be able to understand how it happened by investigating chemistry -- in particular, the chemistry of oceans reacting with earth in oxygen-free water.

We live in a universe where we can see back 13 billion years with physics, all the way to the Big Bang, and we can understand how that worked. It stands to reason that we may be able to see back 4 billion years with biochemistry, all the way to this "Big Bang" of life, and to also understand how that worked.

I celebrate the fact that we have been given a universe we can understand, in which, periodically, life explodes with seeming joy. Understanding the chemical reasons that explain why the explosions happened doesn't take away that joy, but rather magnifies it. As I understand just how quickly life emerged, my heart leaps a little and I participate in that same old joy, as I receive that gift.

Thursday, August 18, 2016

A World from Dust (Plus): Yes, Air-Breathing Fishes Evolved Dozens of Times

I couldn't help myself. I was sitting there, with the proof of A World from Dust in hand, facing a deadline, and unable to change anything beyond the occasional sentence. Yet I had just read The Runes of Evolution and just had to cram in one more datum. Here's the paragraph, with the addition in the middle:
Whichever road it [evolution] used, it appears to have happened repeatedly, because swim bladder genes evolved and converged four times in teleost fish, providing many structures from which a lung could develop. Some estimate that fish overall evolved air breathing 68 independent times. These fish took evolutionary paths that differed in the details, but they reached the same destination dozens of times, predictably.
If I had space ... well, if I had space I would have put a lot more in, but if I had a few more characters I could have put in a big "NOTE ADDED IN PROOF" in from of the "Some estimate that fish overall evolved air breathing 68 independent times." And, perhaps due to my own haste and newness to this whole writing thing, the citation to that 68 times reference was dropped! So let me provide it here. In The Runes of Evolution, Simon Conway Morris writes on page xxiv:
Graham concludes, “air breathing has independently evolved among the fishes at least 38 times and perhaps as many as 67 times,” a point that Karel Liem echoes in his analysis of ABOs [Air-Breathing Organs].

"Graham" is Jeffrey B. Graham, author of the aptly titled book Air-Breathing Fishes: Evolution, Diversity, and Adaptation. The book was published before high-throughput genomics techniques, such as the analysis that gives evidence for four convergences in teleost fish mentioned in the previous sentence. As such, it's based on classic biology: comparing lots of fish and noting just how many fish breathe air, using organs that have many, many different shapes with one oxygen-gathering function. You could rewrite Red Fish Blue Fish with all the different fish that breathe air in Graham's book (an idea I'm just going to leave out there for free considering the burgeoning children's convergent evolution market).

Notice also that I was content to use the hedge words, "Some estimate," and that's good because I made another slip of the keyboard, putting 68 instead of 67. (I try to type independently to avoid plagiarism and I must have fused the two numbers from the quote maybe? Sigh.)  But the important word is in the final sentence of my paragraph above: whether 38, 67, 68, or something else, these are big numbers and are all in the range of "dozens" (as in greater than 24).

That in itself was a dramatic surprise to me, and should be a dramatic surprise to most people. The very fact that we are so surprised shows us that our mental image of evolution should be changed. Evolution is not always an inefficient and undirected process that depends on lucky chances. Or, if it is, there are so many lucky chances that it can be counted on to increase resource efficiency and even complexity. Conway Morris refers to evolution as a "search engine" working on a planetary level, returning complexity and intelligence. That's not what most people think of when they hear "evolution" -- and yet that's what Conway Morris and Graham see, and it's one of the points of my book. Here's one more bit of evidence to back it up.

Book Review: Coraline by Neil Gaiman

Another Gaiman book read aloud, this one meant for young readers. I liked revisiting it and thought it was well paced, but it was a bit dark and "stuck in place" for the younger readers. I also like how Coraline struggles with fear, yet how she's not deceived by the beldam for more than an instant. She has the right kind of strength -- she chooses it. It's instructive to compare the villain in Stardust to the beldam here. Both have a similar modus operandi, but in Stardust she preys on general hospitality, when in Coraline she instead usurps family. This is a great read because it's so focused, but at the end my favorite Gaiman works have more atmosphere and explore more. A hero like Coraline who likes to explore should be given more to explore.

Tuesday, August 9, 2016

Book Review: End of Watch by Stephen King

This book is the third in a trilogy following the exploits of retired detective Bill Hodges. The upshot is that this is a well-plotted, functional little detective story. More than the previous two books, this one verges into more typical Stephen King territory what with telekinesis, hypnosis, and even possession. The plot also involves suicide, and it all comes together with an almost audible snap. Yet, in other Stephen King books, there's something more going on. This could've had genuine insights into suicide or old age, but I feel like it's less than the sum of its parts relative to other insightful works like King's Joyland or 11-22-63. The first book in the trilogy, Mr. Mercedes, had some of these insights about the nature of evil, but nothing new on that really comes out here, possibly because the plot gives the villain too much power over his victims. I'd prefer if the victims actually had to be convinced but they are more controlled here. Regardless, King moves the plot along, has enough character moments to keep you invested, and surprises you just enough in the right ways at the right time. If you're pressed for time, I recommend just the first of the three novels here rather than sticking it through to the end, but it's still hard for me to find fault with something so cunningly crafted that it's difficult to find the seams in the story.

Monday, August 8, 2016

Audio: ASA 2016 talk on How the Periodic Table Shaped Life (and the Brain)

Two weeks ago I gave a talk on my book at the American Scientific Affiliation meeting at Azusa Pacific. Since the theme of the meeting was the mind and brain sciences, I focused on the chemistry of the brain and why I think that chemistry would be similar on different planets. This is an extension of Chapters 9 and 10 of my book with some new research findings.

Here's the audio for the talk*, and here's a PDF of the slides (fair use pics only).

(* Sorry I walked around so much, the mike picked up everything but volume goes up and down as I pace!)

Book Review: Stardust by Neil Gaiman

I just re-read Stardust by Neil Gaiman, aloud for my kids, from the version with illustrations by Charles Vess. The illustrations are perfect and the story fits together just as it should. It was a little tricky to read aloud. I know Gaiman thinks that certain scenes will just fly past kids who aren't ready for them yet, and I know that you have to establish the Fairie parentage of the main character for the story to work, but I'm reading it to a group including a 5-year-old, so, yeah, I'm going to edit out the sex. I remembered the first scene and edited accordingly, but there were others that I didn't remember and had to improvise a bit clumsily. Anyone who's reading it aloud should know it comes with the territory, and don't use the audiobook if you're reading to young children. That said, it's got wonderful characters and a fitting ending and occasional early-20th-century verbiage that just makes it that much more fun. This book is more Princess Bride than the Princess Bride book! On my personal Gaiman ranking list, it's definitely below Neverwhere, American Gods, and the Graveyard Book, but that still makes it very good.

Wednesday, July 20, 2016

BioLogos Blog Post about Finding Fossils with Kids

Here's a blog post about finding fossils from the Cambrian Explosion with my four boys, and what I think about the chemical causes that could have got us there:

It's kind of like a real-life Pokémon Go, with a purpose!

More details (and more science) are in the three-part series posted earlier, starting here:

Thursday, July 7, 2016

Book Review: Reviving Old Scratch by Richard Beck

Today I'm under a massive weight of fear -- not all or mostly mine, but so many of my friends are afraid, and for real reasons. Traffic stops shouldn't make you fear for your life. Going to an Orlando club shouldn't make you fear for your life. Going to an airport shouldn't make you fear for your life. Going to Wednesday night church shouldn't make you fear for your life. The best review I can give for this book is that it offers what I think may be the only real way forward through this oppressive fear. This book by a Texas psychology professor (and Abilene prison study leader) addresses fear and economics and spirit and idols and capitalism and power and, yes, the devil and demons. I don't even know how to post about this in a short form that will explain things right, but Beck, as a self-described progressive Christian from a denomination not known for its progressiveness, approaches spiritual warfare in a very real way but also a very different way from the tired Frank Peretti way. I'm just beginning to process it. This kind doesn't come out except by prayer and fasting. But, as a Christian, I think that the only way out of this tangled cultural web of fear and escalation is through the gospel, through me as a white guy policing myself and my own sin before turning to others, and through the cross and its proclamation that the powers and principalities are defeated. I don't claim to have realized what that means, but all I know is that I start from there, and I pray our country will go somewhere with it this time. We can't stay here.

Saturday, July 2, 2016

Book Review: The View from the Cheap Seats by Neil Gaiman

The subtitle of this book is "Selected Nonfiction," but it runs to a full 500 pages, so there's a lot that made the cut. Be prepared if you read this book to read more than that 500 pages, because Gaiman is his usual generous self here, and points you to so many other works of art that you'll be making library holds and Googling public domain short stories as you go. Thanks to this book, I found "The Gardener" by Kipling and "The Door in the Wall" by H.G. Wells, two excellent short stories that show underplayed sides of each of their respective writers. When Gaiman says something's especially good, it is indeed especially good.

The Yankees' legendary closer, Mariano Rivera, would freely show other pitchers how to throw his special cutter. He would try to give it away (yet he was always the master of it himself). Gaiman is the same way here -- he's trying his best to give away the secrets to making good art, and he explains it clearly several times over. Here's to some of it sinking in.

The organization of this book is also very good. It is a little overwhelming, and I would have cut about one or two essays per section, but the most recent stuff is the deepest and is concentrated in the last section, which deals with life and death. Despite the fact that this may seem to be "just a collection," it has a definite arc and a worthwhile climax in the last 50 pages.

For all that, it's ultimately a scrapbook, like The Art of Neil Gaiman by Hayley Campbell but with words only and from Gaiman's own pen. It's as worthwhile as most of Gaiman's writing -- which is to say, very.

Wednesday, June 29, 2016

Book Review: Acceptance by Jeff VanderMeer

The Southern Reach Trilogy comes to a whirling end in Acceptance. I can't help but compare it to LOST, with the proper disclaimer that I'm one of those strange people who actually liked the last season of that show and what was explained vs. what wasn't. For this trilogy, I'll just say how I reacted at the end:
-- I'm glad I finished it but I did have to ask myself the question of if I was glad, which shows I wasn't entirely glad, right?
-- I'm fine with the explained-vs.-left-mysterious ratio, and think some interesting biological ideas regarding symbiosis and mimicry are brought into the mix.
-- It's the pacing and "editing" of the multiple storylines that bothered me most of all. I feel like there's more plot in this book than in the two previous, and it becomes confusing because it's jumping around in time through multiple points of view who are changing names and making secret excursions etc. etc. If some of this had been moved to the second book in the trilogy, both books would have benefited. The author seems to want to keep a certain geographical feature secret until it's revealed in this book, and I think that was waiting too long.
-- Finally, religious language is used to give a nicely creepy gothic element, but the religious character is unconvincing. I actually found the religious dimension of LOST, although less overt, much more convincing because it resided deep in the characters, and was as much about philosophy as religion. Here, the element feels painted on for vibe's sake.
For a fragmented book I give a fragmented review, I guess.

Friday, June 24, 2016

Book Review: Colour and Meaning by John Gage

An interesting read, if a bit disorganized. Gage is critical of Berlin and Kay, although the criticism seems more like nit-picking than a real takedown argument. Modern art discussions include Kandinsky and blue, and Matisse and black. There's no real arc to the book, and it sort of just ends, but it does focus on the substantial connections between color and meaning without getting caught up in academic rabbit-trails. Not as much science as the subtitle implies, too.

Monday, June 20, 2016

Book Review: The Mirror of Ideas by Michel Tournier

This little book is deceptively slight. Michel Tournier pairs opposite ideas and talks about the difference between each. Some of the essays fall flat or meander, but many more create a spark like flintrocks clashing. Every one is idiosyncratic and unique. Good airplane reading. A number of good quotes but a little less quotable than I expected. A few of the opposites took hold, especially Tournier's distinction between "Primary" and "Secondary" people. The subject matter becomes more abstract as the book goes on. There are insights throughout, but I give the edge to the more abstract concepts, including a excellent final essay on "Being and Nothingness" that is as good of a review of the topic in two pages as I've seen in two hundred.

Wednesday, June 8, 2016

Book Review: The Amazing Adventures of Kavalier & Clay by Michael Chabon

This must be the most beautiful novel ever written about comic books. Chabon integrates his fictional dynamic duo of comic creators into the '40s and '50s so seamlessly that I fully expect to be able to find old Escapist comics on eBay. He describes every emotion in the human experience, with apt and vivid metaphors that on occasion made me laugh out loud, not necessarily with their humor, but with the sheer rightness of it all. Nor is this overly rosy -- events are bizarre, unpredictable, disappointing, but never meaningless. This is sure to become a classic if it isn't already. I just wish it didn't move so fast through its events, which is odd to say for a book so long, but I only want more depth and connection to these amazing people.

Sunday, June 5, 2016

Book Review: Fragile Things by Neil Gaiman

I was hoping for a little more from this collection than I got. I think, since this is Gaiman's second short story collection and I had read his third recently, that he has simply matured as a writer in the time since this. The best stories are at the beginning and ending: a Sherlock Holmes plus H.P. Lovecraft mashup called "A Study in Emerald" and an American Gods sequel story called "The Monarch of the Glen." Both of those are especially unusual short stories in that they seem to open up new possibilities for the worlds they inhabit. Most of the other stories are indeed very good, but in the end seem more like writing exercises and leaves on the wind than fully developed like the other two. (Oh, there's also one called "Goliath" set in the world of the Matrix, also a cut above the rest.) Like all Gaiman, well worth it, but I have to admit it seems below average for his high level.

Thursday, June 2, 2016

A World from Dust (Plus): DIY Squid Beak

The squid beak is as sharp and tough as a knife, yet it contains no metal. How could such an amazing structure ever have evolved? The answer is it's surprisingly simple to make a material like squid beak in six words: "by oxidizing sugar and a neurotransmitter."

The recipe sounds like something from the witches' trio in Macbeth: thou makest beak of squid from strands of sugar and dopamine, once thou oxidizest it in thine cauldron. (Ok, so "dopamine" isn't a very Edwardian word, and don't even start about "oxidizest," let's just move on ...) That sentence is a fairly complete description of the protocol. Everything you need is shown on the left side of part b in this figure from the paper:

A few more details on the ingredients: The strings of sugar are strung-together variants on glucosamine, which you can buy in big jugs at Costco for your joints. I've even seen it advertised at the gas pumps, so it must be a big seller. The cross-linking agent is L-dopa, which is dopamine's cousin molecule. These molecules' cross-linking abilities are mentioned in A World from Dust Chapter 9 -- the same family of molecules that gives you a dopamine rush also defends algae with its cross-linking chemistry. And the important chemical activity is oxidation, which connects to the theme of oxygen and oxidation that runs through A World from Dust.

If you oxidize those two ingredients a little, you get a soft, white sheet. If you oxidize a lot, you get a stiff, brown ribbon, a lot like the Humboldt squid's sharp beak.

Evolution accessed the latent chemical power of sugars, dopamine, and oxidation (outside the cytoplasm, where oxidations are predicted to happen) to make a squid beak. In the lab, we can access that came power to make a stiff, sharp blade without an atom of metal in it. Sounds pretty alchemical to me.
For more, see the original research at Zhang et al., Journal of Materials Chemistry B, "Squid beak inspired water processable chitosan composites with tunable mechanical properties."

Friday, May 27, 2016

Blog Post on Replaying the Tape of Life at BioLogos

I just wrote another blog post for BioLogos titled "Replaying the Tape of Life and Finding a Chemical Sequence." (Warning: mild spoilers if you haven't seen Forrest Gump yet. And if you haven't, what's stopping you? It's a great movie!)

Sunday, May 15, 2016

A World from Dust (Plus): Neanderthal Chemists

In Chapter 11 of A World from Dust, I mention the evidence of chemistry at Pinnacle Point, where early humans used fire to cook food and make paint. Now there's evidence that Neanderthals were chemists, too. This recent study analyzes the black manganese oxide rocks found in France where Neanderthals once lived. Earlier scientists assumed these were used for their color as something like body paint. Heyes et al. point out that it's a lot easier to find other black rocks for this purpose, so the Neanderthals must have had another reason for collecting this special mineral.

Heyes et al. show that manganese oxide can spark flames (as mentioned in Chapter 7), and find evidence of combusted manganese in the Neanderthal fire pits. The Neanderthals collected this for its chemistry as a firestarter, not as a mere pigment. Personally, I didn't know that manganese had this use before researching A World from Dust, which means that I didn't know as much about this element as my Neanderthal ancestors. Guess there's always something to learn.

Saturday, May 14, 2016

Book Review: The Shape of the New by Montgomery and Chirot

I can't help but compare this book to Minding the Modern by Thomas Pfau. Both take a wide-angle lens to history and trace the evolution of thinking -- The Shape of the New through four thinkers' works (Adam Smith, Karl Marx, Charles Darwin, and the Jefferson/Hamilton dialogue), but Minding the Modern through about as many words (person, will, purpose, etc.). Pfau goes back farther, is much more critical of the Enlightenment, and in the end focuses his narrative on a single thinker, Samuel Taylor Coleridge. The conversation between The Shape of the New and Minding the Modern is valuable. The Shape of the New is much more conventional (and easier to read). Even so, it filled in a few gaps for me historically, especially with Marx. Montgomery and Chirot have found a useful "zoom level" for their approach. They lay out the horrors of Marx and Social Darwinism as succinctly as anymore. They also make a good effort to be fair to the Counter-Enlightenment thinkers, incorporating some of Philip Jenkins' work on the church in the developing world, for example. Despite these efforts, they remain fully pro-Enlightenment, reminding me of a colleague's remark that academia is inherently conservative. Pfau comes off as relatively revolutionary in his emphasis on critique. Although they know all the reasons why so many people are against the Enlightenment (or more properly want to reform it in some way), Montgomery and Chirot never seem to quite understand at a gut level why someone would be against the obvious gains of the Enlightenment, and as such, the closest the book comes to being revolutionary at the end is a daring call for more humanities education. Pfau's analysis is more fruitful, because it works better to analyze words rather than nebulous ideas, and because he ends with a specific, underappreciated thinker in the person of Coleridge. Montgomery and Chirot talk about how important it is to read the original texts, but they do so in a book that doesn't actually quote the original texts much -- Pfau quotes original texts much more than they do! In the end, I'll take Pfau, but better yet, I'll read both books and realize that it's Pfau's analysis that sticks with me and gives me a direction. Still, Montgomery and Chirot have written a fine book because it allows for this kind of deep comparison to other thinkers' works, and I think if we continue to debate at this level, there's hope of true progress in this discussion.

Friday, April 29, 2016

A World from Dust Argues Against Gould's Book, Not Gould

Sometimes the most helpful comments are the asides. One of these happened a year ago with the second reader to finish the full draft of A World from Dust (to whom I am eminently grateful, by the way). He finished his email with "BTW, you really don't like Gould!" plus an emoticon. That took me back -- it prompted me to make it more clear in the draft that I was arguing against Gould's specific book and his "Tape of Life" theory, not the man himself. I'm not sure if I went far enough, because there seems to be a default assumption that debating a person's ideas involves debating the person himself.

Now that I've published an entire book structured around that argument, I suppose if I could go back and do it again (second edition?) I'd make a simple edit: search-and-replace all the references to "Gould" to make them say "Wonderful Life." I'm not arguing with the man so much as I'm arguing with his book. In terms of most of Gould's thinking, and most especially in his writing style, I came to praise Gould, not bury him. I only want to bury the "tape of life" (like the Atari ET game cartridges in the New Mexico desert?). Gould's innovative and, to use a word that's on its way out, disruptive thinking about evolutionary paths and mechanisms made the field what it is today.

The fact of the matter is that Gould wrote a lot about evolution and contingency, and it's clear that his views were much more nuanced than were contained in Wonderful Life. For example, his masterwork The Structure of Evolutionary Theory is much more detailed and less polemic than Wonderful Life. In Chapter 5 of A World from Dust, I wrote that finding a chemical origin of life reaction would show that the tape of life could be replayed. There's evidence Gould thought so too, and that he thought the tape of life could be replayed to that point.

But, and here's the rub, whatever Gould's views in the rest of his writing, it's Wonderful Life that everyone remembers. He was too good of a writer in that book. His sweeping, magisterial conclusions and quotes were so effective and unnerving that they drown out the nuance of his other works. It's Wonderful Life that people go out of their way to refer to when they talk about this, it's Wonderful Life that the papers in the beginning of my Chapter 12 cite, and it's Wonderful Life that has so undergirded the discourse that its "tape of life" quotes have become an unspoken default.

That's what A World from Dust argues against. Chapter 12 is all about how there should be an open conversation on this topic rather than a conversation-ending default. As that chapter discusses, genetic drift and random flow have their place on the local, species level, but on the planetary level, things become a lot more predictable. I'm not seeking a Kuhnian paradigm shift so much as a Hegelian dialectic -- not a revolution but a conversation.

So I hope it's clear, I do really "like" Gould. But he was just a man, and in his own way a product of his time. He was right on a lot of things and wrong on some other things. And, by writing Wonderful Life, he moved this important conversation forward. That's why it's worth talking about.

Friday, April 22, 2016

Book Review: The Invention of Nature by Andrea Wulf

This book is itself shaped like a river delta. Alexander von Humboldt is its source, and his voyage to South America the catalyst that led to a life of pouring out words. Three-quarters of the book describes his life and explains why he is a lost hero of science. Then the book introduces major thinkers who were influenced by Humboldt: Darwin, Thoreau, Haeckel, Marsh, and Muir. Each of these stories involves travel (if you only consider Thoreau's Walden Pond experience to be a sort of inward parallel to the outward voyages of the other four). Wulf especially excels at summing up the impact of Humboldt on these five thinkers with economy and vivid description.

I wish there had been more about where Humboldt's ideas came from. The book focuses on the generation before Humboldt, and it's implied that the advances in travel technology led to the advances in thought (though it would have been interesting to explore this angle a little more, come to think of it). I want to go farther back, to the Greeks, because Humboldt's conception of nature seems awfully Stoic in its composition, and I wonder how much of his ideas had been around since the ancients and how they were carried through to him. Where did Humboldt get his style, and especially this vision of interconnectedness? I want to go deeper, and I could have traded some of the early detail about Humboldt's outer life for more on his inner life.

Also, now that I'm finished with the book I'm left with an interest in reading more of Humboldt, but I don't have a specific "in" to his writing. Part of his forgottenness is that he doesn't have the singular masterpiece that is Origin of Species or the vivid, short articles like Muir wrote. And why is that? Are we just too far removed from Humboldt's time, or is it because he wrote in German? Well, we still remember Goethe more than him. I'd like to think about why.

But these questions arise precisely because this is a good story about a little-appreciated chapter of history. Like the river delta, it opens up into an ocean.

Sunday, April 17, 2016

Book Review: The Sculptor by Scott McCloud

This graphic novel would make a great opera. The characters include The Lost Artist Boy, The Carefree but Struggling Girl, and, of course, Death Himself. The plot involves a deal the Boy makes with Death so that he gets the power to reshape matter with his bare hands, in exchange for knowing he will die in exactly 200 days. Even that great power isn't enough to result in good art, not without further struggle, and then there's the issue of falling in love with someone when you know you're going to die before the year does. McCloud's characters are excellent and multifaceted. Even Death has his internal motivations. My only quibble is with the setting, or more precisely, the author's exploration of the setting. In other stories like this, NYC becomes a character in itself, but I felt all along like it was just background. (Possibly the author spent less time in NYC than Helprin or Gilliam?) This isn't really about the setting, but it's about the triad of main characters and the power of art and death. In those areas it makes for a unique, affecting story, perfectly paced in the graphic medium.

Saturday, April 9, 2016

Book Review: Rosalie Lightning by Tom Hart

A graphic novel that's a searing, detailed account of what it was like for the author to lose his daughter suddenly, before her second birthday. Hart wends his way through the sorrows of loss, the joys of childhood, and the legalistic frustrations of adulthood as he finds a journey through his grief. As I read (through tears) I realized that I had no idea how you should end a book like this, a book that begins with Rosalie dying. But Hart ends it on the perfect note, an open chord in ink and an image of growth and hope. This story is every parent's worst fear, but also a meditation on meaning and symbolism. There's so much familiar in the story that it feels like I've lived through it with Hart for an hour. This book has the same effect as a sad movie or a storm -- it blows through, upends everything, and cleans you out.

Friday, April 8, 2016

12 Colorful Rules that Shaped Our World now online

Here's the 12 lectures I put together a few months ago. Each one has a rule and corresponds to a chapter in A World from Dust, and has a DIY chemistry experiment:

DIY: Simulate Mono Lake in a bucket
DIY: Dye fabrics using sticky metals

DIY: Make colored birthday candles – and predict a plugged-in pickle’s color.
DIY: Making white lead pigment.

DIY: Making a glowing green flowing pattern from fluorescein (from highlighters).

DIY: Making a striped Winogradsky column (and finding explosive methane at the lower levels).

DIY: Purifying different pigments from different red plants in your kitchen.
DIY: Making indigo dye (with the help of oxygen) and removing stains.

DIY: Making edible spheres from calcium chemistry through “spherification.”
DIY: Two Rothkos for the price of one.

DIY: Make your own colored nanoparticles like found in stained glass.
DIY: Look at life from a new angle.

Thursday, April 7, 2016

A World from Dust (Plus): How Calcium May Turn DNA Into an Antimicrobial Net

One of the ways immune cells catch germs is with a net made of DNA. The immune cells are called neutrophils, and the nets are called Neutrophil Extracellular Traps, or NETs for short. The nets work because of a clever use of calcium that underlines one of the central balances of life as shown in the figure above.

Note how calcium is ejected from the cell in the lower southwest portion of the figure. This is why Chapter 10 of A World from Dust talks about calcium signals that are instigated by opening up calcium doors in the membrane and letting the calcium flow in. A NET begins with such a calcium influx, like many other signals. Calcium floods the cell and uses its unusual charge to aggregate and reshape proteins, reconfiguring the cell in myriad ways, resulting in the formation of the NET.

But then something remarkable happens: calcium's chemistry builds a NET. The cell just turns itself inside out, and a NET forms. The reason why this works is because the NET is made from DNA, and when DNA is ejected into the high calcium concentrations outside the cell, the sticky calcium binds phosphate in DNA, crosslinking it into a dense net that engulfs and immobilizes the germs. I'm reminded of Spiderman on the Electric Company (see 2:21):

So because of the imbalance of calcium outside the cell, all it takes to catch a germ is for one cell to play Spiderman, turn itself inside out, and spill its DNA. Calcium automatically solidifies DNA and the immune system uses a fundamental aspect of biochemistry to make an automatic net. Long ago, calcium was ejected to avoid cross-linking DNA. Now, DNA ejected into the calcium-rich exterior of a cell automatically makes a net.

I'd expect a system like this to evolve wherever water-based life uses a periodic table like ours.

Book Review: Seveneves by Neal Stephenson

This is my favorite Neal Stephenson book. That's not to say it's without flaws, but his obsessive technical skill in plotting and engineering a story (as well as his high page count) finally fits the broad scope of his subject. Basically, this book is "Stephenson reboots the world." As you'd expect, there's everything here from problem-solving on the level of The Martian times a thousand, to philosophical and psychological ruminations on being the only ones left after the surface of the Earth is sterilized. I only wish that the emphasis was different -- a major shift that happens two-thirds of the way through the book should have taken place one-third of the way through the book, in my opinion. It feels a bit like Stephenson is cutting off the second half of his story early because even he can't figure out how to make some of his surprises work in detail given the huge nature of the narrative shift. Stephenson is no utopian, and parts of the story get very dark and desperate, but if you stick it out to the end things open up to glimmers "more things in heaven and earth than are dreamt of in your philosophy." First contact is here but it's inverted and subverted and, to me, felt fresh. I'd say more, but part of the point of Stephenson is the surprises that happen in the last third, where this novel really shines. File this one under "gets better as it goes along," and it starts out pretty good, at that.

Tuesday, April 5, 2016

Book Review: The Art of Neil Gaiman

Only now, after finishing reading it cover to cover, do I realize that this was a coffee table book. It's full of bright pictures and reproductions of Gaiman's nearly illegible scrawl. It goes through his productions, comics, stories, novels, movies, etc., about 3/4 of which I've experienced, and focuses on the one question you're never supposed to ask an author: "Where did you get the idea for this?" Well, that question gets answered once in a while, but with Gaiman the question is often more "How did you hook up with these people to collaborate with after you got the idea for this?" The book is a bit uneven, but I don't really care, I enjoyed finding out about Gaiman's life and artistic processes. I did feel like many things were left out, but that's the nature of this book -- the true place where the ideas come from would require a full biography. If and when that comes, I'll read it, but in the meanwhile, reading this was worthwhile, both to jog my memory of all the great things that Gaiman's done and to introduce me to some new things, especially, especially his "Writer's Prayer."

Tuesday, March 29, 2016

Book Review: The Big Question by Alister McGrath

This is the kind of book one should expect from Alister McGrath: pellucid, distilled, organized, somewhat reserved, and focused on, as the title would indicate, big questions. McGrath maintains his knack for finding a perfect quote -- one by CS Lewis summarizes a 600-page book I just read in a sentence -- and for pointing all aspects of big questions I haven't thought of. For example, I've been thinking a lot about how Christianity paved the way for science, but hadn't realized how the doctrine of Original Sin specifically led to an empirical, experiment-based natural philosophy. I appreciate this book but it isn't McGrath's best, because (as he acknowledges directly) he's not good at conveying his own inner sense of wonder and fitness. He's telling, not showing, because that's the kind of writer he is. I also wish his critique of Sam Harris's moral philosophy in a late chapter was a little more pointed. The fact of the matter is that McGrath focuses on explaining, not entertaining, and I appreciate how he does that once again here. I personally prefer his books written to Christians to ones like this written to a more general audience is all.

Sunday, March 27, 2016

A World from Dust (Update): Should the White Rot Story Change?

One of the hazards and joys of science writing is that what you write will change in some way after publication. The first one of these just happened. A paper just came out that may change one of the sections in A World from Dust Chapter 9, from what was explained as a biochemical cause to what is more a geological/climate cause. In the book, I put forward the explanation that so many plants grew so big in the Carboniferous Era because they invented lignin, and it took millions of years for fungi to evolve an efficient system for degrading that lignin, so it eventually turned into coal deposits till the fungi evolved. This is what most people thought, and it was backed up by a recent phylogenetic analysis.

But wait! M.P. Nelson et al. just published "Delayed fungal evolution did not cause the Paleozoic peak in coal production" in PNAS. The title speaks for itself -- Nelson et al. have produced an impressively integrated array of sciences to argue that most of the biomass wasn't lignin anyway and also that many lignin-degrading activities did evolve quickly. Rather, they propose that wet climate related to geological activity resulted in the unprecedented burial of carbon as coal. As a scientist outside the field, their argument seems compelling because it depends on bringing together so many lines of evidence.

My only hesitation comes from another paper I saw during the same reading session: Nagy et al. in Mol Biol Evol titled "Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities." This paper suggests that white rot evolved later than previously stated, although I don't find many dates to pin down just how much later they propose it evolved. If this activity is significantly better on crystalline lignin or some extra-sturdy form, the story might end up aligning in part with the book's explanation.

I'll have to see how the scientists in the field sort this one out. If, as I suspect, Nelson et al. end up with the winning story, then there is a take-home lesson that takes a story away from Chapter 9 but will reinforce part of Chapter 10: evolution tends to surprise us with how quickly it can solve problems. If Nelson et al. are right, then it didn't take many millions of years to crack the tough nut that is lignin, and fungi were able to respond much faster than I or others presumed.

I'll try to update this part as more info comes out. The book is in print, but the blog can change as science does.

Monday, March 21, 2016

Book Review: Minding the Modern by Thomas Pfau

If you want to ask the big questions, you're going to have to read the big books. At least, that's what I kept telling myself as I measured my progress through this book after a week of reading only to find that I was 10% done. Pfau is a professor of English, but I think that were this written a century ago, it would have been classified as philology. The focus is indeed on words (or, more precisely, the concepts behind the words): will, person, teleology, and purpose are traced through Plato, Aristotle, Augustine, Aquinas, Occam, Hobbes, Locke, Smith, etc. up through the time of the Romantics (with appropriate flash-forwards to the debates about these terms in the modern day). Considering the ground that Pfau covers, this huge book actually seems quite short, and I actually found its level of detail to be just about perfect to cover the evolution of the concept of what is a person.

For all that, much of the book seems to come down to what thinkers thought of as the strength and utility of one of the biggest of little words: the "logos." What is the nature of the structure "outside" us, and how does it relate to the structure "inside" us? Is the universe ultimately about material or about relationship? It is something to dominate or something to receive as a gift?

I found it fascinating and well worth the effort to read something this far outside of my discipline. I've found that I come down on the side that we can participate in the logos by telling stories, and that those stories aren't just constructed and contingent, but are in fact true.

The last fourth of the book turns its focus to Coleridge as a thinker whose ideas may offer a way out of the materialist cul-de-sac we seem to be trapped in as the default philosophy of the century. I've run into Coleridge before and, I agree, his philosophy of starting with the "responsible will" inside rather than the material outside does seem to be a way forward. My only complaint is that I would have liked more about Coleridge's thinking, because as it stands I have to do a lot more reading on my own to figure out how to go forward in my field following Coleridge's example. The good news is I'm colleagues with a Coleridge expert, so the fact that I work at a liberal arts university and have friends like that is a big help moving forward. But if I had my wishes, this book would have split off and expanded the third part (the one about Coleridge), because I want to know so much more. Even the third part didn't have quite enough about Coleridge, because it frequently talked about other thinkers like Schopenhauer for pages on end, when I more wanted to get away from the negative examples and toward the positive ones.

This fits with Barfield (and less obviously with Deacon), and provides a valuable intellectual scaffold for moving forward with Coleridge's thinking as we head into the 21st century. Well, well worth the read, even for a scientist like myself.

Book Review: The Man Who Was Thursday by G.K. Chesterton

First off, this was a good book to read aloud. Chesterton's sometimes convoluted syntax can be straightened out nicely for pre-teens by shaping the phrases and emphasizing the right words, with a few tweaks to the diction here and there. In that sense, reading it to my kids was a bit like singing, an analogy I don't think GKC would mind. Even so, they were left a little foggy and confused by the end, but I think that may be appropriate.

The broad strokes that GKC paints with come off better when read aloud, I think. There's always something unrealistic about his stories, but this one works very well because it is deliberately framed as a nightmare of sorts.

I keep dithering on whether this would have been better at half its length or not. Reading through it a second time, I think the evenly paced nature of the successive "reveals" as the plot goes on feels unnecessary. But still, if the underlying point is to help the reader think differently about creation -- both as a noun and as a verb -- I think the book accomplished this admirably, while daring to assail the fortress of the biggest of the big questions, asking why bad things happen.

As always, it's difficult to know how to rate a classic, but I'll rate my reading experience more than the book itself. I was even gobsmacked a bit by a plaintive, simple question near the end and had to collect myself, so you can definitely say this book dug deep.

Tuesday, March 1, 2016

Book Review: The Things They Carried by Tim O'Brien

This was in my queue a long time before I listened to it, because I knew it would be hard to hear. O'Brien's book must be one of the classic texts about the Vietnam War, and hearing it read aloud by Brian Cranston is the right way to experience it. Not only does this narrative (if I can call it that) transfer the chaos and maddening threat of that conflict into your experience, but it also jumps around in time and diverges into meditations on the nature of writing, experience, life, and death. Despite the harrowing, unfinished, nakedly evil depiction of war, there is life, which makes the evil more painful, if anything. The way the book ends surprised me with what I can only call its dark innocence or winter light. So it was a hard book to read but also, clearly, a necessary book to understand the war that warped our country. 

Saturday, February 13, 2016

Book Review: Black Earth by Timothy Snyder

Since I often show the movie Mr. Death, which is about Holocaust denial and science, in my biochemistry seminar, I have an interest in the history of this dark wound on the middle of the 20th century. From that interest, I stumbled into Black Earth, and didn't really know what I was in for. It was hard to read. Not only is it outside my discipline (written by a historian about Eastern European history when I hardly know Eastern European geography, to my own detriment), it is also simply difficult to read what happened. Civilization spiraled -- scratch that, was PUSHED -- into anarchy and death. But climbing this mountain of a book gives a perspective that is unequalled, because Snyder explains how we are pretty much missing the point in our common knowledge about how the Holocaust happened. Everybody knows and everybody's wrong.

The cliché is that Germany forced the Holocaust on Eastern Europe with its efficient organization, Blitzkrieging its way across an unwilling populace. The fact is that most of the bureaucracy and organization was in Germany itself, and there the Jews were actually safer than they were in Poland and the rest of Eastern Europe. Outside German borders, the Nazis destroyed the state structures and in the absence of those, perverse incentives were set up which twisted ordinary people into mass murderers. To use a bunch of -isms, National Socialism killed more by its libertarianism than by its totalitarianism, and a large majority of the deaths took place outside the walls of Auschwitz.

Just when you think you can't take another chapter of these horrors, Snyder expands on his thesis in a different direction and shows how the unsung heroes who saved Jews were not who you may expect either, but rather the brave diplomats who extended state power to the powerless, and the people sometimes called heretics, who were used to being outcasts, so they took in other outcasts from some hidden strength of spirit. The most prominent churchman who saved the most Jews was from the Greek Catholic Church. I didn't even know there WAS a Greek Catholic Church, but something in that situation gave him the strength to save others when no one else would.

At the end, Snyder discusses how the Holocaust could happen again today. This section is particularly chilling, yet I feel as if this section, because it is so important, should be expanded and nuanced. Snyder argues that scarcity sets up the people to be servants of atrocity, but leaves it for granted early in the book that the Depression set up a level of scarcity that led to the Holocaust. Once I finished the book, I wished there had been more about specifically how the people felt the fear of scarcity, because if Snyder's thesis is right, those conditions are the ones we should be monitoring if we really mean "Never Again." Yet this area seems de-emphasized in the early chapters.

Part of the problem is that I don't know much about Stalin's famines, which illustrate this point exactly and which Snyder mentions but does not explain. But this leads to another problem. Stalin's famines killed a lot of people, and that seems to fit the mold of the common knowledge about an organized state causing mass death that we unthinkingly apply to the Holocaust. Snyder's analysis at the end focuses only on the dangers of another Hitler -- what are the dangers of another Stalin? And why didn't the scarcity in the Soviet Union lead to the pure horror that is the Holocaust? Or are they more equivalent than I think?

More questions than answers here, but that shows how good of a book this is. For a different take on history that is horrifying precisely because it's so different from what you learned in school (yet so well-supported), read this book. Just make sure you set some time aside, because sometimes you can only take a page at a time.

Book Review: The Bazaar of Bad Dreams by Stephen King

Sure, some of these stories are better than others, like in any collection. But every story seems to have something in it that makes it worthwhile. One is a rumination on the fixedness of time in the vein of 11-22-63, and since that's my favorite King novel, I'm happy to return to it here (even if it is also a Kindle commercial?!). One is about how a fleeting sin for hire destroys a person from the inside. One is about an evil little boy with a beanie that somehow still communicates the depths of evil and the unfairness of life. And one's about a car that eats people. Can't really find the extra good in that one, but as for all the others, this is worth it, and may be a good sampler of King's plusses and minuses for someone who doesn't want to commit to a behemoth like 11-22-63.

Wednesday, January 13, 2016

Book Review: The Runes of Evolution by Simon Conway Morris

I've been hoping Conway Morris would write a book like this for some time now, since the past decade has been so eventful in terms of convergence. As a catalog of recent findings and a jumping-off point for further study and debate, it's excellent. It would be fun to teach a class on the different chapters and dive into the evidence with advanced biochem students. I have a nagging suspicion that maybe a quarter of the cases Conway Morris presents as scientific evidence for convergence may have other explanation, but as long as a majority of the evidence presented here "sticks," you have a pretty convincing hodgepodge of data that evolution has a deep structure that it repeatedly finds.

My main issue is with the lack of organization. There's so much here and it's presented at such a high level that some pages read like a list rather than a sustained argument. That's fine -- I could use a list like this very much, thank you -- but it makes for slower reading especially by a non-biologist. There are connections made from chapter to chapter, but they are abrupt and don't have a deep structure themselves, except that the more complex matters of brains and minds are put at the end of the book. Conway Morris is entertaining as ever, and the balance of writing far favors wit over clarity. There's a place for that. As long as you expect that, I think you'll find a lot to think about here. Not sure if it helps convince a hostile audience, but this non-hostile audience member is glad this book came out, and it helped point out a few dozen papers I was unaware of as well.

Book Review: Faith Within Reason by Herbert McCabe

This was a great find. Some of the clearest writing on knotty philosophy that I've read. McCabe taught the thought of Thomas Aquinas to his students, and over the years his teaching must have been refined to the highest degree, because here is the best summary of Aquinas applied to current questions (both theological and scientific) that I have read. As a lay reader of all this, I found it highly accessible and applicable (with the minor exception of a few pages that I found to be overly "philosophical). The essays in the first half of the book form a sort of arc, and then the second half is more scattershot. The second half contained some of my favorites, including a brilliant and comforting essay on the prodigal son. Good reading for both mind and soul (and a good definition of soul, while we're at it).