Wednesday, December 23, 2015
Saturday, December 19, 2015
My only question is whether it would be best to start reading Sandman with this overture instead of issue one. I'm usually a purist when it comes to reading things in publication order, but this seems like it would be a very good introduction to the whole world, and it would resolve those nagging questions before they occur. I would say start here.
My only quibble is that the nature of the plot's resolution feels surprisingly similar to one of my favorite Doctor Who episodes, but it works better here than in Who, so I can only say that there's an echo there. Anyway, Gaiman's stories are never really about originality, they are about setting and character and beauty and terror and fitting cleverness, so I can say that this exceeded my expectations in all those.
Thursday, December 17, 2015
Monday, December 7, 2015
The timeline runs from Babbage's Difference Engine to Google. Steve Jobs is mentioned but there's not time to do more than allude to his ouster, comeback, and passing. Rather, Jobs is mostly explored in terms of his relationship with Bill Gates (even a bit more than with Steve Wozniak). There are filters placed on this history, as there must be: everything is simplified and every person reduced not so much to an individual as to various dyads. That filter coincides with Joshua Wolf Shenk's Powers of Two, reviewed a year ago here, and it would be interesting to compare and contrast the two books, which provide a corrective to the "lone genius" theme that seems to be the current default.
Here the glass is half-full, and the negative effects of technology are mostly left on the cutting room floor. You don't really learn something new and different like I did in, say, Godel, Escher, Bach. Innovation remains somewhat elusive. But really, that's what this kind of book The Innovators has to be, and it gives an overview that demystifies those ubiquitous data processors, and in doing so, performs a public service. If you can see how THEY did it, then maybe you can see how YOU might do it too. Once you read a lot more books in your area, of course, so you can figure out how this stuff really works.
Friday, December 4, 2015
Most of the characteristics of these extremely deep microbes are what we expected. For reasons discussed in Chapter 6 of A World from Dust, these microbes use nickel and heme to process their food, and they emit tiny clouds of methane. They seem slightly out of place, because a limited genetic analysis finds they look more like surface soil bacteria than shallow sediment bacteria, but they made have been carried there from when the sediments were first laid down.
The only real surprise so far is how few of these microbes live down there. There's plentiful food, including hydrogen that, for some reason, they eschew, leaving it on their plate like uneaten broccoli. Something else is holding life back down there. The authors note that proteins and DNA fall apart more readily at high temperature and suggest that the hot, high-pressure environment makes the constant repair too costly. If this is so, then a deep underwater coal seam would be like a planned community in Las Vegas after the housing bust of 2008: plenty of rooms but no one willing to move out there because of the heat.
What this says to me is that the limits on life look a little more stringent than we thought. Whether it's the cost of repair, or something else related to high pressure, or something else entirely, what we have here is a reasonably good environment for methanogens that they don't fully exploit. With more investigation, maybe we can find out what's missing, and that will help us figure out just how prevalent life may be in extreme environments, both on this planet and on others. If life can't live well in this environment, then the same thing may be wrong with other environments that right now look OK to us. This one clue makes the universe seem a bit more lonely.
Reference: Science, July 24, 2015, "Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor." DOI: 10.1126/science.aaa6882
Wednesday, November 25, 2015
You may have heard that the Internet was created as a radically decentralized system so that it could withstand a nuclear attack. You have also have heard the scientists who invented the Internet loudly proclaiming that it had no such purpose. Which purpose was it? Both are true, and Isaacson does a good job of showing how.
The engineers and academics working on the nascent Internet technology were building a new way to pass around information. They had no reason to anticipate its military use or purpose. Yet the higher up the chain of command you go, the more you find the military purpose layered on top of the basic communications purpose. The people getting the money from Congress justified its expense with the military purpose that it could withstand a major, disruptive attack. The scientists didn't need that purpose at their "layer" of knowledge; the politicians required it at theirs.
In the same way, a process that is for one purpose locally may serve an additional purpose globally. A chemical process may serve and shape a biological function. Random gene flow and change may interact with a chemically ordered environment to produce a predictable change and even increase in complexity. In fact, a random process can gain a function at a higher level. The genes and elements may not "know" that the network they're building has a biological purpose, but that in no way negates the biological purpose. (For more on how this might happen, read Terrence Deacon's Incomplete Nature.)
In A World from Dust I focus on the "politicians" of the process, the legislative branch of chemical law-makers that we call the periodic table. These chemical rules result in predictable patterns emerging from random flow. You can stand close to the waterfall to see the random flow, or step back to see that it inexorably flows down and looks similar from moment to moment. It's all a matter of the width of your scope and your point of focus on the chain of command.
Sunday, November 22, 2015
To find out more about what this surprising statement means, you'll have to read the book. Unfortunately (I say with irony), Jenkins is a careful scholar, and so at times the book reads more like a card catalog than a thriller. Only in the final chapter does he really expand on the central thesis that these alternate Christianities and heresies, however fuzzy the line between them may be, are emblematic of the eternal variation and struggle in Christianity itself, and in every Christian's heart. This conclusion means that the history of the previous centuries can apply to us, today -- but Jenkins is cautious in his application, so those connections are mostly left up to the reader. So much thinking to do, so little time. Here Jenkins brings new treasures out of old storehouses, and the result is fascinating and even, in an odd way, encouraging. Dan Brown is nothing new.
Tuesday, November 10, 2015
Narratively the sense of discovery is actually more natural in this second book, because there's less "hypnosis made me forget" artificial suspense enhancement, and some of the descriptions of the facility are creepy enough to evoke the Dharma Initiative from LOST in the best moments. But it ultimately doesn't pay off or answer enough questions to justify the time spent in telling it, and feels like a shaggy dog story. Some narrative jumps make the story harder to follow without building suspense, and the really weird reveals are mostly in the first half, while the second half seems more predictable. It might pay off in the third book, but reading it seems more like a duty than a pleasure at the moment. Don't get me wrong, I will read it, and the atmosphere itself almost makes this second book worthwhile -- I just think it'll be better if I keep my expectations low.
Thursday, November 5, 2015
Saturday, October 31, 2015
The biggest flaw in the book may be a result of its own success. Throughout the first half of the book it's not clear exactly why Dreher's crisis is such a big deal. In the second half, it becomes more clear what the precise conflict is, and yes, it is a big deal. Maybe the redemption Dreher experiences is so complete that he can't quite remember the cutting nature of the hurt in the first part?
Although How Dante Can Save Your Life is written to a reader who has not read Dante yet, reading it post-Commedia I still found it very useful to see which passages resonated with Dreher. My hope is that there would be a genre of "Dante books" in which people write about how Dante helped them. I'd read that.
Monday, October 26, 2015
The premise is what technothrillers rise and fall on, and this premise is a good one, pretty complicated to explain but it becomes clear soon enough. I wish other novelists would learn from Scalzi that you should just jump into your world and set the stage as quickly as you can rather than withholding information to build the suspense. Scalzi has surprises in store, but they are good surprises that come after his world is fully realized, and they take you to places you didn't think of that, after the surprise wears off, are logical enough that you kick yourself a bit for not thinking of it. In other words, good surprises.
The plot's not quite as well-paced as Crichton, because the urgency seems slow to unfold and a lot of action seems to happen all at once. Also, the scope feels smaller and isn't as audacious as Crichton, but the social and political implications are better thought out than anything Crichton's worlds ever concoct. It's deeper sci-fi (although I do doubt that some of the technology is actually possible), and if anything the book's too short. I feel like Scalzi can set another few stories in this world and still be far from plumbing its depths.
This book also isn't as funny or as touching as Scalzi's Redshirts, and it has a sort of oral history appended to the end, which I'm wondering if it would have been better up front or in chunks spread throughout (which is what I think Crichton would have done). But it's as snappy and solid as they come, and it does what it should, which is plenty.
Thursday, October 15, 2015
To elaborate, Paradise not always easy, but it's actually easier than Inferno, that most famous member of the trilogy. There's less politics and what's there is more comprehensible. It also focuses on describing beauty rather than torment. Dante's theological questions and issues still resonate today. Maybe these books shouldn't be read till mid-life, as Dante implies in the very first lines of Inferno, and maybe they shouldn't be read unless you have theological interests. Well, I'm that old, and those describe my interests.
Sometimes there are convoluted or what I think are incorrect passages. Dante himself describes changing his mind on points both theological and scientific, so I can imagine him changing his mind again. This isn't a description of Heaven, but a description of Heaven as seen through Dante's eyes and interpreted by his words. Those are two different things, and if you put the author in the center, as both the medievals and postmodernists would, then you see there's little point in arguing with him about theology. The bigger importance is the human experience living in a fallen universe. Dante is reluctant to speak out against the people he speaks out against, but he is encouraged to write by what he sees. It's his vocation. In the end, Dante isn't a self-righteous prig. Dante struggles with himself in all the ways that any artist or author who's trying to represent reality struggles. But he found a way through, with Beatrice (and Virgil, Lucy, and Bernard) as his Beatrice, and the Divine Comedy as his path.
In the end, I was surprised by the cumulative effect of this journey. Even though the translation takes a step down after Canto XX (Sayers' last canto) and the commentary isn't quite up to her standards, the later cantos have the best images and scenes for me. The superposition of images is paramount, and it's important that you descend through Hell and climb Mount Purgatory before you get to the final cantos. But once I did, they had me in tears just like an indescribably beautiful and sad piece of music -- such as Craig Courtney's "Sanctus."
The last three major images, the point of light, the river of light, and the rose of saints, are striking. After climbing through spheres which turn ever faster until they reach the Primum Mobile, which is set in the unmoving Empyrean realm of God's pure light, Dante sees another image of the powers of the universe in which, rather than an infinitely large Empyrean, God is revealed as an infinitely small, still point of piercing light, surrounded by spheres of angelic powers. It seems so perfect to say that God is both at once.
Maybe this isn't the time for you to read all three books. It wouldn't have been a decade ago when I read Inferno. But if you work on creating things, and if you like the big questions, and if you love the good you see around you but struggle with the hate, and especially if you're halfway through life -- try making it through the Divine Comedy, with the assurance that, for me, the higher I climbed the deeper it got.
Monday, October 12, 2015
Friday, October 9, 2015
There's some unevenness to the pacing and the way the narrative is presented. Information is withheld in the beginning. which ended up annoying me rather than creating suspense. In one case we don't know crucial information because the narrator doesn't remember his introductory tour of the facilities, which is almost a textbook use of amnesia to keep the reader going. There's enough going on that those sections could be streamlined considerably. The first half of the book drags in places and the reveals of what makes the biology of this planet different are placed toward the end of the book (if they come at all). And yet on a scientific level there must be some fascinating convergences that the author isn't interested in. The main biological divergence that sets up the drama is interesting and its consequences are pretty well thought out, but I doubt it could actually happen to such an extreme.
Normally this would frustrate me to no end, but in exchange for the lack of science we get a deep psychological study of faith, isolation, marriage, and the stresses of a mission, even in success. As someone who traveled to a distant land myself recently, much of the feeling of being so far from home is captured expertly by Faber. A few moments of faith don't ring true, which lead me to conclude that the author is writing about faith from the outside. If anything, that makes me like the book more and tend to overlook its overlookings. The main characters should have deeper spiritual resources than they are shown to have when crisis hits, and they should also have more vacillation and variation in their faith in the good times. They should doubt more; the internal life of a Christian is never quite so even and shiny. They also should depend more on the person of Jesus rather than the Bible stories in general, especially if the narrator has memorized Matthew as the book implies. The internal lives of the characters are not quite nuanced enough, but they come close enough to make the characters live and to remind me of my own time in the field.
By the end of the book, a subtle but thought-provoking contrast emerges between science and faith that centers around issues of safety and God's providence with shades of color and angles that I don't normally see outside of the typical great Christian authors. The way the story is left unfinished in terms of faith feels right, while the ways it's left unfinished in terms of science feels more wrong to me. But it's not really about the science -- so I can't help but consider this book a success and hope that more authors explore these questions and these kinds of characters. I know how I've reacted given my own surprising parallels to this story, so I'd like to know how others who don't share that history or faith react as well. But as for me and my brain, this strange little book did contain some new things, and some solid old ones as well.
Friday, September 25, 2015
Tuesday, September 22, 2015
Sunday, September 20, 2015
Saturday, September 19, 2015
So after our hike we found fossils. Or at least what I could pass off to the kids as possibly fossils? We took pictures of our putative fossils and left them in the field.
This looks like a leaf-shaped form with fuzzy appendages flowing out from it (found by my wife):
This looks like a bean with legs:
And these might be trails of something wormy (found by my 12-year-old):
Notice how, at least, these are all in a similar type of rock. This is the shale that used to be sandy seafloor. I think they might actually be something.
Finally, I looked up a little on the science of the area and pieced together some interesting leads for further study in the academic literature. First off, this appears to be a newer site than the others. At least two major sites are located north a few dozen kilometers, close to the town of Field and Kicking Horse Pass, including the Wolcott Quarry and the area where the first specimens were found.
It wasn't until 2010 that a paper came out describing the Stanley Glacier site. This paper discusses how the previous sites were part of a "thick" formation but the Stanley Glacier rock is part of a "thin" part of the formation. Previously scientists had thought the thin part wouldn't preserve specimens, but from our own exploration we can confirm that it did.
I imagine that someone may have been hiking the trail to the glacier, noticed the black-stained layered cliffs on the west end of the valley, and crossed over to the waterfall to check for fossils. Maybe other sites can be found by similar cliffs. We caught a glimpse of some in the area of Kicking Horse Pass, for example, where the older sites are located. Seems to be a good excuse for more hiking in the area.
Here is the map from the paper showing the site and how it relates to the other sites near Field, which are part of the Cathedral Escarpment:
In 2014, word got out that yet another site was found north of the Stanley Glacier site, across the road near Marble Canyon. This was a major find with many diverse new shapes, showing that buried in those rocks there are many, many lifeforms waiting to be discovered. Connecting the dots (or the "F's" in the map above), perhaps there are other sites located along this line. How many unknown shapes are stacked up in those black-stained cliffs?
I believe the other sites are rightfully kept off-limits to the public, so the Stanley Glacier may be the easiest way to play paleontologist and see for yourself what this kind of discovery is like. As we showed, even a four-year-old, with some help, can do it. There's nothing like a treasure hunt to motivate small legs to keep moving, and the likelihood of finding fossils seems amazingly high.
The trailhead for the hike is only about fifteen minutes west of the main highway through Banff, along Highway 93, just across into Alberta, so it's central and easy to get to from either the towns of Lake Louise or Banff. (We came in from Calgary and spent a couple hours in Banff, including a stop at the rock store to show the boys what fossils look like, before grabbing lunch from the supermarket and driving to the trailhead while eating on the way.) We left Banff at 1:15, started the hike at 2pm and got back to the car at 6:30. From there it was a quick hour's drive to Golden, BC for our next hotel stay.
The trail runs south from the trailhead, up to a hanging valley between ridges that you can see from the beginning. You proceed through very different stages, which can be used as goals to motivate the little ones. First you climb up through a landscape recovering from a fire maybe a decade ago:
You're climbing up a hill, and the grade is taxing on little legs, but actually easier than the grade on the Lake Agnes Tea House trail in Lake Louise that we had done the previous day. There's little shade on the slope, so an early afternoon start meant that the sun was getting easier to take as we went.
Early on there's a stream running to the east as you switch back and forth:
Once you get to the top of that slope, the trail flattens out and turns toward the valley. Soon you cross a stream that used to be spanned with just a two-log bridge but now has a wider bridge that you could cartwheel across if you like:
This is a view heading south into the valley. The glacier is ahead and up to the right. Closer on the right is a sheer wall of layers of tan and brown rock smeared with black. This contains the shale of the Burgess shale and forms the backdrop of most of our pictures. There's a waterfall running down it at the south end that had helped to pull down some rocks from the cliff for little fossil hunters.
The flat part lets you catch your breath until the trail starts to climb again. It's not nearly as steep as before but much more rocky. At some point you'll feel a wave of chilly air blowing in your face from the valley, definitely cooler than the air on the sunlit hill. We also crossed into shade and at this point, were more certain that we could actually do this thing.
When you see this rocky staircase, you know you're maybe half an hour from your goal (and if you have a four-year-old you're probably going to have to carry him):
The trail is rougher from this point on. As you get closer to the glacier, you will soon be able to make out the waterfall, tiny against the huge cliffs of rock. This is your goal.
The glacier is just beyond it. If you have the energy you can hike all the way up to it, but for us, turning off at the waterfall was certainly enough. Here you can see the glacier peeking out on the left.
Stay on the trail until you are almost directly across from the waterfall on your right. There's a place where it looks like the trail branches, and stay on the rightward, downward branch. This takes you right next to a rock field in the center of the valley that is your final challenge. Scramble across to the base of the waterfall and you're there. I think the littler ones had an easier time with scrambling than we did, but we all had to watch out for shifty rocks.
Once across (and even before), look for tan or beige flat ones with multiple layers, about the size of a dessert plate or a dinner plate (I may have been getting hungry by this point). Flip these rocks over and examine them closely. Just from a few minutes of searching ,we were able to find several tiny fossils.
The nice part about mountain hikes is that down is faster than up. It took us an easy 90 minutes to get back to the car.
In the next post, I'll show what our "fossils" looked like and describe some of the scientific literature about this particular site.
Right after Labor Day, we wanted to take a quick vacation that would take advantage of the fact that under the quarter system, school doesn't start till the last week in September. So we drove from Seattle to the Canadian Rockies for a five-day vacation.
Since I've written about the Burgess Shale fossils, I wanted to take the family to hike up and see a place where those fossils were found. The Burgess Shale contains evidence of life's Cambrian explosion, where diverse forms most wonderful suddenly appear in the rocks a little more than half a billion years ago. I wondered if there was anything special about the rocks up there and wanted to feel what it would have been like to find these fossils.
Before we went I found an official site for this hike and several trip reports indicating that it would work for older kids, such as this one. We also found the guided tours offered to the two other official Burgess Shale sites, but we were too late to sign up, had kids below the age cut-off, and wanted to be able to go at our own pace (and turn back if need be). The Stanley Glacier hike looked like the one we could do, and it's a public hike that we can try on our own.
We have four boys, age 12 (going on 30), 11, 6, and 4. I wasn't sure that we'd make it, but I promised them if we did, they might find their own fossils. And it worked -- here's the proof, with the fossil area in the background:
I'll describe the hike in detail in the next post, so you can decide if your kids will make it. Most kids ages 10 and up should have no problem with this hike. It was a challenge for our little ones, but it actually got a bit easier as we went along. I want to publish that it worked for us, so it might work for you.
We spent four and a half hours total on this hike: 2 hours up, maybe an hour looking for fossils, and 1.5 hours back. To get to the fossils, you don't go all the way to Stanley Glacier, but turn off after about three miles. The first mile or so is a medium-grade upward climb that went the slowest for us, then there was a flat, fast part before the trail roughened and climbed again for the last half mile (ish). Then you turn off toward a waterfall on your right, scramble over some rocks, and there are the fossils.
Next I'll describe the hike in detail and how to find the fossil site.
Friday, September 4, 2015
The other examples of "late Barfield" I've read were too much influenced by Steiner and anthroposophy, but this one manages to avoid those topics (except for a few mentions). Also, Barfield is not focusing on Barfield's ideas so much as Coleridge's, filtered through Barfield, to be sure. I got the sense that the two are enough on the same wavelength that Barfield's filter is more a good teacher teaching than it is a partisan lobbying. I feel like I "get" Coleridge more after this book and that strengthens my estimation of both Coleridge and Barfield. This also fits with the picture of Coleridge from the wonderful history Age of Wonder.
To be sure, Barfield can't get through a whole book without making some annoying absolute and contrarian statements about modern science. I do think that my reading of Barfield can accommodate most of his intellectual puckishness by interpreting Barfield's "matter before mind didn't exist" to become "matter before mind didn't MATTER" (not in the same way as it matters now). It all comes down to what you mean by "exist," see?
But in this book that move of "translation" doesn't have to be made that often. It makes sense that Coleridge and Barfield are sympatico given the influence of German philosophy on Coleridge, which goes right along with Barfield's love for Goethe (which I'm OK with) and Steiner (which I'm not).
In the end, I think Coleridge's "polar logic" as described by Barfield may offer a way to interpret Barfield's philosophy in a way that throws light on modern experience without throwing out all of modern natural history. In fact, polar logic may be incorporated into a narrative interpretation of natural history. Barfield's own statements about the natural fit between evolution and Christianity imply that this should be possible, even when his sweeping dismissal of science of the past seems to get in the way.
Overall, a fascinating and helpful book that I'm working on integrating, but not for the faint of heart. I'm not sure how that interprets into a star rating, but Barfield's against quantitation anyway, so I'm sure he won't mind my avoiding the five stars on this one, even though I think it may be stronger on the whole than previous works I've given five stars to. This is definitely worth working your way up to.
Friday, August 28, 2015
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
Sunday, August 23, 2015
Thursday, August 20, 2015
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
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!
"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
Monday, August 3, 2015
Sunday, August 2, 2015
The theory does appear to offer a possible ways forward on the first front, although I'm not as sure about the second, but that's not my primary area and I'm fascinated by the chemical possibilities. Deacon's take on physical chemistry and the nature of energy is solid enough and unique enough that I'm considering how to teach it in my physical chemistry course. Much better than I could do on neuroscience (Deacon's primary area), that's for sure.
As Deacon admits, this book is only a sketch, albeit a 545-page sketch. I could have used more. Since dynamical processes have particular structures, I could have used more figures to clarify some of Deacon's terms and "levels" of dynamics. Although the evolution and mind subjects are interrelated, I think we could have gotten one book on evolution and a second book on mind, and that would have left room to explore more side roads and give more examples. But I'm intrigued enough to come up with examples on my own.
The biggest ally left unenlisted may be theology. Apophatic theology involves double negatives and absential qualities like Deacon's work. Again, this is an open door for others to walk through. I think there's fruitful progress to be made in taking Deacon's ideas seriously and then using those as a basis for natural theology (a la McGrath, not a la Paley, of course!).
In sum, this is a book that I've only begun to soak in. It already makes the short list of "10 most influential books" in my life.
* Deacon and RJP Williams do both emphasize constraints, so much so that I'm already seeing new things by juxtaposing the two. My first public reflection on Williams was a lecture titled "The Chemical Constraints on Creation" no less!
Wednesday, July 15, 2015
The Zalekskis weave a narrative from four strands that meet in mid-20th-century Oxford: J.R.R. Tolkien, C.S. Lewis, Owen Barfield, and Charles Williams. My book reviews include numerous examples of all of the above. Of these, Tolkien and Lewis are preeminent and the obvious draws. Barfield and Williams are the ones you discover because of their association with the better-known duo. Barfield's story is more active near the beginning and end (he lived until 1997!) and Williams only gathers the equivalent of a chapter or two in the middle, fitting with his firework-like entrance and exit.
The sharp-eyed reader will notice that a key part of this story is left out. Human and bacteria proteins have the same basic chemistry, being made of the same CHON atoms. If bismuth is sticky to bacterial proteins, it must be just about as sticky to human proteins. So if bismuth kills bacteria, it should kill human cells as well. So why is it that we can drink the stuff? Why is there a novel titled Arsenic and Old Lace but Bismuth and Old Lace doesn't scare anyone?
Human cells can survive a dose of Pepto because they have an extra layer of chemical protection. Our internal chemical shield is built from sulfur, in the form of the molecule glutathione, mentioned in another part of Chapter 2. How this shield works is shown in a 2015 PNAS paper titled "Glutathione and multidrug resistance protein transporter mediate a self-propelled disposal of bismuth in human cells" (which, incidentally, is so well done that other scientists would do well to pattern their metal-life investigations on it).
As shown in the diagram above, purple bismuth (Bi) approaches from the left. It crosses the cell membrane and sticks to yellow glutathione's (GSH's) sulfur atoms. Bismuth is so sticky it collects multiple glutathiones, then the cell takes the assembly and tucks the dangerous metal away into a small sulfurous bubble (or vacuole) shown in gray on the right. This is what glutathione is for -- to preemptively stick to the sticky things before they can stick to something else.
The really nifty part of this is that as this process depletes glutathione, the cell senses that and turns on the machinery for making more glutathione. The more bismuth abounds, the more glutathione super-abounds to fix it. Excess glutathione is then available for sticking to other toxic metals as well, so that Pepto may incite a more general protection.
The bacteria killed by Pepto-Bismol don't have a complex glutathione system like this, so its stickiness turns their insides to solids, and they die. Human cells can resist internal petrification because of the chemistry of sulfur as corralled by glutathione's structure. Our cells sweep the sticky bismuth into a side chamber and our proteins remain nice and fluid.
This has implications for cancer therapy. Some forms of chemotherapy kill cancer cells with sticky, toxic metals like platinum. Cancer cells resist the chemo by turning up their glutathione production. Understanding how that system works should allow us to find a way to turn it off, which would make metal-based chemo much more effective. More details can be found in this summary article related to the research article above.
This is also why understanding the chemistry is so helpful. Bismuth-sulfur chemistry may lead to more effective chemo. So support your neighborhood chemist -- you never know what she'll find next.
Friday, July 10, 2015
This expands on the narrative of A World From Dust in two important ways:
1.) The problem with being warm-blooded is not just making the heat, but keeping it. To insulate its precious heat from the cold waters around it, the opah pumps its blood through intricate and efficient blood vessels in twisted hairpin shapes. This structure is called a rete mirabile and can be built using Adrian Bejan's engineering theories for how heat flows. This hairpin structure is optimal for insulating a circulating fluid, so it is found repeatedly in warm-blooded animals. Bejan's Constructal Law could have been used to predict that a warm-blooded fish would have a complex rete mirabile structure before that structure was found in the fish -- it is a consequence of how heat moves. The opah is generating more heat, so I believe it would have a higher Energy Rate Density and Chaisson's ideas may apply, too. It has a more complex internal structure to match its higher energy throughput.
2.) Other fish that look like the opah and have genes like the opah are not warm-blooded, but a few very different fish (for example, tunas and lamnid sharks) have the biological spaceheaters that are halfway there. These fish obviously have different shapes and different genes, but they have independently developed similar systems for heat generation and insulation. In very different species, evolution has converged to produce similar and predictable warm-blooded temperatures and structures. Which species get it may depend on random rolls of the dice at the gene level, but that some species will get it and fluorish, that is predictable, given enough time.
So, not only is a warm-blooded fish very cool (see what I did there?), it also shows that evolution solves similar problems with similar features (warm blood) and similar structures (rete mirabile), in tuna, lamnid sharks, and opah, repeatedly producing predictable complexity.
Note: The audiobook reader is really excellent, changing tones to indicate different characters artfully, and throwing himself into King's over-the-top dialogue with gusto. I recommend listening to this rather than reading it.
Tuesday, July 7, 2015
Saturday, July 4, 2015
There's three basic plot lines: a tennis academy of high achievers (including a flawed but fascinating family at its center), a halfway house of addicts and ex-addicts, and political/sci-fi satire of where we're going as a society. Before reading, I would have thought I'd prefer the poli-sci-fi most and the halfway house least, but it was precisely the opposite. It's the halfway house through the story of Don Gately that was compellingly horrifying and hopeful in all the right ways. In the other storylines the satire occasionally stepped so far out of reality that I laughed but with a smirk rather than the laugh of recognition (and/or the shudder) that I got from Gately's desperate circumstances.
For this reason, I actually look forward to The Pale King. Given what I like most about Infinite Jest, DFW writing about boredom and the IRS is going to be amazing.
DFW is a generous writer. Perhaps too generous at times. But on every page there's a well-turned phrase or touching insight, and since there's more than 1000 pages, that adds up to a unique experience.
Some of the plot turns on a movie that is more compelling than it should be, somehow reaching into your soul and changing you, narrowing you and reducing you to a mindless addict. The book itself is also more compelling than it should be, but it changes you to broaden your perspective and take in more than you saw before.
In the halfway house especially, the story descends to the bottom and also goes the farthest, and though the resolution remains at a distance, from the top of the mountain the veil lifts, and it (the resolution) can be glimpsed even if, for now, it can't be touched.
Monday, June 22, 2015
As a piece of extended technical journalism, it's fabulous at explaining complex subjects that most people in the field don't understand. As a piece of general writing, it's a little too quick to assign white hats and black hats, especially when one of the main "black hats" (Goldman Sachs) actually gains quite a bit of gray by the end. (Don't worry, they're still a vampire squid, but they're an old and sometimes self-contradictory vampire squid. Gödel's Vampire Squid.)
The most surprising value of this is that you understand more of how computer programmers work, so if you love someone who codes and want to understand more of what they do, by the end you've have a few glimpses into the universalities of coding life -- distorted by the financial greed of the markets, which is the book's main subject, but computer programmers seem to be much the same in whatever field.
The book jumps around a little too much, trying to make a narrative out of disparate stories that don't really go together. It would have worked better as a collection of essays with a short intro and extro, I think. But it's an education in modern economics and computer science, with a good dose of old-fashioned morality thrown in. I would welcome a theologian's reflection on the nature of evil after reading this book, in fact.
Inside Out is not just an entertaining movie, it's also a worthwhile movie. It had enough bright colors and pratfalls for my four-year-old and enough deep psychological subtext for me. I may never look at certain thought processes the same way again. The subtext is sturdy enough that it provides another dimension to the movie: it forms a framework for understanding brain science. As Exhibit A, I submit a recent Cell paper that Inside Out can illuminate.
(Before I continue, let me say that this contains MILD SPOILERS for a location visited relatively late in the movie. If you want to discover this location for yourself, go see it right now and come back!)
The paper I'm thinking of is titled "Sleep Facilitates Memory by Blocking Dopamine Neuron-Mediated Forgetting." Like any good title, it contains the key point of the paper, which can be illustrated using the imagery of Inside Out.
Researchers started from the knowledge that sleep helps build memories. In the Inside Out world, the sky turns black during sleep time and the memories roll out to Long-Term Memory storage, which fits precisely with this knowledge. Some memories don't fit in Long-Term and are rolled down to the Memory Dump. By studying memories of smell in fruit flies, the researchers dug into the tubes and found one gatekeeper who determines which memories roll where.
Imagine an Inside Out Forgetter (as pictured above) who sits at the entry to Long-Term Memory, kicking some memories out of the rolling chute and down into the black funnel that is the memory dump. This Forgetter is Dopamine -- the same molecule that gives you that euphoric dopamine rush so many people talk about. Maybe this particular Forgetter is moonlighting, constructing pleasant sensations by day and working as a Forgetter by night.
What the scientists did is they kidnapped the Dopamine forgetter, and more memories rolled into Long-Term storage. The science is a lot more detailed and complicated, mostly because dopamine has so many jobs, but the basic message is smaller than a Pixar short.
Speaking of which, can we enlist the Inside Out crew to make some educational videos for psychology courses? Something tells me profs teaching next year's courses will have a whole new set of references in them thanks to this movie. Which provides one more small reason to see it.
Friday, June 19, 2015
As for what she's really saying with her language, the closest thematic analogue I can think of is Neil Gaiman's American Gods, which is one of my favorites of Gaiman's. The reason why Tempest writes what she writes intrigues me in the same way as American Gods did. This seems to be like what Owen Barfield called "putting things back together" but from a standpoint of polytheism and ancient Empire rather than from a standpoint of monotheism and ancient community in rebellion against Empire. Although I come from the latter standpoint, I'm fascinated and want to see what Tempest will continue to build with her words, because her poems are as tangible and feel as lasting as bricks and mortar.
I would build differently -- but I can't wait to see where she goes with this bringing mythology into the heart of modern life. It feels like a grand beginning to a brilliant career.
Friday, June 12, 2015
Complex I of the respiratory chain is one of the crucial enzymes that ultimately helps you use the oxygen you breathe. It is the first funnel through which electrons are poured on their path to combining with oxygen. Part of this funnel is shaped by oxygen's unique chemical properties.
Enzymes like Complex I, called hydrogenases, first show up around Chapter 6 of A World From Dust, well before oxygen fills the atmosphere in Chapter 8. Still, if any oxygen is around at all, they are shaped by it, because they must avoid oxygen's negative power. Oxygen reacts with stray electrons to form Reactive Oxygen Species (ROS) that shatter the insides of a cell.
If a hydrogenase drops too many electrons out of its "funnel", they are picked up by oxygen and make havoc-wreaking ROS inside the cell. Avoiding the negative consequences of oxygen shapes life as much as running toward the positive consequences of oxygen's energy.
This was shown in the recent study "Reactive Oxygen Species Production by Escherichia coli Respiratory Complex I" in Biochemistry. This study is built on a previous experiment in that increased the amount of electron-carrying "electron boxes" inside the cell called NADPH. Normally Complex I only gathers electrons from the NADH electron box through its funnel, but when there's high amounts of NADPH, it will evolve to accept NADPH as well. It does so precisely at the green sticks at the bottom of this figure: