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!