Tuesday, October 25, 2011

Book Review: Green River Killer: A True Detective Story

If you've been waiting for CSI: Seattle to come out, maybe this book will do the trick. Or maybe not. Because although both this book and CSI are about a complicated case with police work and science, and this book (being a graphic novel) can be read in about an hour like a CSI show, the similarities stop there. This book is realistic to the point of being boring at times. The capture of the killer is not particularly dramatic, and much of the book concerns a long interrogation in which he can't remember anything precisely. But the value of this book is that it is real. It certainly was real for Jeff Jensen, the author, considering his father is Tom Jensen, the detective who at times was solely responsible for the Green River case. This book is about the small joys (and wearing grind) of perseverance. One of the small joys is the way Jonathan Case, the artist, captures the exact aging of the characters as the narrative skips back and forth from the early 80's to the early 00's. That's something you can only get from this medium. On the whole, it is so realistic that you're left to make meta-connections on your own; ultimately, this is a procedural at heart. But it's a good example of what graphic novels can do, and evidence that the genre has really grown up.

Monday, October 17, 2011

Crayola Sculptures

I want one of these. I mean, how hard can it be to make a crayon sculpture? On second thought, those are really BIG:


Saturday, October 15, 2011

Evolution is Not Simply Divergent

So I just wrote about how I enjoyed the little but formidable text Graphs Maps Trees, which applies scientific visualizations to literature. But there's a problems with the science, and once again, the trail for the misconception can be traced to Stephen Jay Gould.

Gould's point, repeated by Moretti, is that Darwin's original tree of life (yes, I know he was too smart to use that specific term, but it's what we call it now) was more to show divergence than simple common descent: in his diagram, only the most extreme branches continued from generation to generation, and he used to to account for species diversity. That's very true. Gould goes on to say (in a block quote in Moretti's essay) that evolution is a story of proliferation (this same branching of extremes), very different from cultural transmission in which an idea can be carried by a single human from one culture branch to another, and so the branches cross and weave and converge instead of just diverging.

The problem is that the real tree of life is indeed both convergent and divergent, like the cultural tree. The worst offender is this quote by a historian of technology, George Basalla:

"Different biological species usually do not interbreed, and on the rare occasions when they do their offspring are infertile. Artifactual types, on the other hand, are routinely combined to produce new and fruitful entities" (p.137). a.) e.g., the internal combustion engine was merged with the bicycle & the horse-drawn carriage to produce the automobile (p.138)

Um, no. As a biochemist looking at the tree of life, I see exactly this same repurposing of old parts and combinations to make new parts everywhere. Even the process of making antibodies is a shuffling of old parts to make something new. Basalla's quote only works for a limited set of macroscopic species, and I think it's the exception rather than the rule. Bacteria trade genes and build new things by combination all the time. Just because a mule is infertile doesn't mean convergence never happens.

This is a major point of the argument, and it actually helps Moretti, because he's arguing that convergence is the normal state of affairs in literature, and I'm happy to say I think it's the normal state of affairs in science as well. Conway Morris and Dawkins agree with me on this. Fascinatingly on p.81 Moretti argues that if divergence is king then randomness is running the show, but in human affairs like literature, convergence is dominant. Since I'm arguing that convergence is the characteristic of all evolution, then am I arguing that the ecosystem is more "human" than we may have thought? A provocative phrase, and I'm content to think about it for now.

True, the branches of the tree of life can never fully converge, but they can functionally converge. Moretti points out on p.85 that the branches of the tree of literature can never fully converge either, but always remain distinct. The more we talk the more I think we're basically talking about the same kind of tree.

In a nice summary of the branching diagram for literature, Moretti concludes that "literature moves forwords and sideways at once; often, more sideways than forwards. Like Shklovsky's great metaphor for art, the knight's move at chess." (p. 91) Do DNA trees of life imply that life makes similar knight's moves?

Book Review: Graphs Maps Trees

Graphs Maps Trees by Franco Moretti may have the highest thoughts-inspired-per-word ratio of any book I've read recently. Of course, it helps that there's not many words. This is basically three essays (one per word from the title) and an afterword by a geneticist for the scientist's perspective. Moretti argues that we should employ scientific techniques to assess trends and cycles in literature. Before visions of the graph from the first page of that textbook in Dead Poets Society start running through your head, I should point out that Moretti clearly puts this as complementary to traditional analysis oriented on a single text. Rather, this looks at each novel as a leaf on a tree, or a point on a graph, so overall trends may be seen, necessarily simplifying and missing something to see something else.

In Graphs, Moretti shows how genres tend to have a lifespan, and admits he doesn't know exactly why, but it may have something to do with broad patterns of social cohesion often called "generations." (He's puzzled, as am I, by why groups would organize like this when babies are pretty much born constantly, but that's just a tangent).

In Maps, Moretti shows how plotting the events in a series of village novels according to their location shows that the events eventually fragment and dissolve away from the village itself.

In Trees, Moretti shows how the way clues are treated in Sherlock Holmes stories can be sorted into categories that branch off like a tree. I have trouble seeing the real utility of the tree structure in this, it's more an if-then than a tree necessary, but his next tree shows how the person and tense used in different types of novels can change even within a sentence to show certain kinds of branching, and this is very interesting.

I have some bones to pick on the way science is used in the tree chapter, but I think that deserves a post of its own. On the whole, I like Moretti's approach, and I'd like to take some of it myself. The most important thing I learned from him may not be the techniques or ideas, but the sense of humility and openness, that this "scientific" approach is only one possibility while the traditional analysis still holds. Good to remember.

Sunday, October 9, 2011

Life's Solution: Specific Notes and Quotes

Here I'm just going to make a record of my dog-eared pages from Life's Solution for future reference for myself. Feel free to look over my shoulder:

p.120-126 "Play It Again!" section.If anything, the role of convergent paths in evolution of E.Coli has been enhanced since this book same out in 2003. I'd like to do some of this myself ... How is it that Figure 6.3 can separate out adaptation from chance from history?

p.230 "Interstellar Nervous Systems?" section. Sodium pumps are found all over the place. This has been pinned down for the electrical eel recently. I wonder if there's more to see with this particular molecule's convergence.

p.266 Conway Morris directly addresses the point of qualia that Douglas Hofstadter mentions as well. It's worth noting that Hofstadter and Conway Morris (ahem) converge on this point. What do similarities in neural structure say about the question of "the redness of red" for philosophy?

p.288 Oxygen transport proteins convergence: I didn't know hemoglobin/myoglobin was found in so many places. Could that be a convergent structure? How would we know?

p.295 The Molecules Converge: Basically a 2003-era list of what I'm really interested in: convergent proteins. So many references, so little time!

p.297 "If convergent evolution is an 'eternal return' to the 'attractors' of functionality, then we cannot be surprised that history repeats itself." Then the fact that the hammerhead ribozyme is convergent.

p.307 "Yet, when within the animals we see the emergence of larger and more complex brains, sophisticated vocalizations, echolocation, electrical perception, advanced social systems including eusociality, viviparity, warm-bloodedness, and agriculture -- all of which are convergent -- then to me that sounds like progress."

p.313 A GK Chesterton sighting! "Reason and justice grip the remotest and loneliest star." (From Father Brown's first story.) The following description of planets made of gems sounds like a passage from Doctor Who! My "anglophilia" brain area is lighting up.

p.325 Eugenics and the morally ambiguous nature of progress, again in line with GK Chesterton. I'm going to have to keep assigning his book in Biochemistry ...
quotes John Green: "To the very end, [Darwin] failed to appreciate the morally ambiguous character of human progress. He failed because, like many social scientists today, he had no adequate conception of Man." I think Gould and Dawkins are keen to decry "progress" in evolution because they can only accept an unambiguously progressive formulation of progress. If progress is seen as ambiguous, then yes, you can say you see it in the natural world and the evolution of man.

For more on progress and anti-Gould rhetoric I should look up McKinney, Science, vol. 237, p. 575, 1987.

p.329 The six-point outline of "what salient facts of evolution are congruent with a Creation." Let me try my hand at summarizing them:

1.) Biochemical simplicity (building blocks)
2.) A method of navigating the vast possibilities (a mechanism like protein folding)
3.) The sensitivity of the process
4.) How life rearranges and adapts the old rather than building something brand new
5.) Many paths/branches but converging again and again on certain characteristics/structures
6.) The inevitable (and broad occurence) of intelligence, coming from complete sensing of the world.

Book Review: Life's Solution

Life's Solution is a rarity for me: a book I knew I had to own before I read it. I couldn't wait for it from the Library book sale, and I couldn't just check it out from the library. I've read several articles by Simon Conway Morris in different formats (for example, see the previous review of Real Scientists, Real Faith on this blog), but this is the book in which he takes 332 pages to write about what he sees in evolution as a scientist who discovered big parts of it (the Cambrian explosion) and an Anglican Christian who is friends with Richard Dawkins but doesn't agree with him on the question of God. For one thing, Conway Morris thinks there is a question in the first place! I was about to say this is a big, sprawling book, but in truth, my only quibble is that I wish it would've sprawled a little bit more. The last few chapters in which he tackles theology have nice turns of phrase but don't really seem to fully flesh out the theological implications of the convergent patterns that Conway Morris sees in evolution.

As a catalog of a bewildering array of convergences, this book is entertaining. Again, it left me wanting a little more, especially in the frequently repeated "This feature evolved at least 31 times," because this is such a central thesis of the book I'd like to know how we know that. But honestly, that's what the footnotes are for. Conway Morris focuses on the organism rather than its molecules for the most part.

The fundamental question this raises for me may sound a bit strange, but here it is: If indeed all these features, from bipedality to camera eyes, have evolved repeatedly and in a converging pattern, does this mean sin emerged in multiple ways, but convergently? That it happens in every young life with a different path but it ends up looking the same? I think this point can be a platform on which we can understand a theology of the fall of man in light of this science. But, of course, however we define the origins of sin, the important thing is that we agree on its destiny: summed up and healed by the cross of Christ.

This is what I mean when I say I want more theology at the end! But that's not really the purpose of this book. Even at the end, Conway Morris chooses a subtle turn of phrase when he could be more direct, and I think there's a method to his madness there. Ultimately, I think everyone who's interested in the deep structure of biology should find a way to read this book, it is a fascinating catalogue of a new way to look at the world that fits both science and faith. It's the biologist's counterpart to R.J.P. Williams's The Chemistry of Evolution, and anyone who knows me knows I don't say that lightly!

PS: I know there's tons of arguments out there about "evolution or not" and "what does it mean", and to those who don't have time to parse every argument, I say to just pick up a copy of this book or Williams's and flip through it. Then flip through The Signature of the Cell, the flagship Intelligent Design book. The books are about the same length but even a cursory glance at the content will show that Conway Morris and Williams are interested in looking at the world in truth, in all its glory. That kind of specificity is, I'm sorry to say, absent from Meyer's Signature of the Cell. You don't need to read the whole thing -- you just need to flip through a few pages. If Intelligent Design was a viable theory, this is the kind of book it would produce. I'm still waiting.

Thursday, October 6, 2011

Book Review: When You Reach Me

This is children's literature, which I read aloud to Sam. It's very good children's literature, and all along I was hoping it would be more, but in the end, I have to put it on the children's shelf. There's a lot to like here: a time travel puzzle, a late-70's setting, tons of L'Engle references, the $20,000 Pyramid, and some nice sixth-grade emotional politics. It all has a purpose, even Dick Clark, and comes together in a really nice way. The climactic scene is very well written, for one. And the title character learns important stuff in a subtle way, so there's a moral but you can ignore it easily enough, which is important. Still, for all the intricacies of the plot, it was just a hair on the side of condescending (do children really need to be told how you can be in two places at once with time travel THAT many times?), and as an adult I was able to pick up on what was going on rather early. It was good for Sam to be forced to read through a book that looks at the world the way a girl looks at the world -- he got a little antsy sometimes but the nice plot convergence at the end made it worth it for him. Some people have overrated this book. I still think A Wrinkle in Time was better.

Book Review: Hannah Coulter

I listened to this book, by Wendell Berry, on my commute (got it as a free audio book through a promotion). It's the life story of a woman born in the 30's who lives on farms through World War II and up through the turn of the century. It sneaks up on you eventually that this isn't just a story: Berry is really saying something here. I've been aware for a while that he is a sort of Christian radical of a sort, as radical as you can get being an intense proponent of the small-farm way of life. His characters are beautifully nuanced, the voice of the narrator is consistent, simple, and profound, and there are lots of implications for science and technology-minded folks like me. I actually considered assigning this for Biochemistry reading but it's just a little too far. But it is as thought-provoking as the G.K. Chesterton I do assign about how to live life. I don't read many novels but this one may change my mind.

HIV as music

The video at this blog post from the Scientific American site has a sample of the HIV genome translated to music. But instead of just random-sounding four-tone melodies, the composer went a step further and included the amino acids that the genes represent, with a separate scale for those 20. It actually all comes together to sound like music -- sad music, which is appropriate, but definitely music.

LUCA Was Complex

I'm said I'm going to start collecting examples of complex ancient life, and here's another one: a study of particular structures in archaea (a branch of microbes) suggests that the Last Universal Common Ancestor (LUCA) was more complex than previously thought.

This is the article, and this is the science news story about it.

If J.R.R. Tolkien's ideas are right (and Owen Barfield's, whom he got them from), then we'll be seeing more and more of this. I'll be collecting them here for my memory and yours.

Lots of implications: from the simple "life is not an easy thing!" to the complex concept of "have we assumed too much about what constitutes 'progress' in biology?".

Great quote from the news article:

"You can't assume that the whole story of life is just building and assembling things," Whitfield said. "Some have argued that the reason that bacteria are so simple is because they have to live in extreme environments and they have to reproduce extremely quickly. So they may actually be reduced versions of what was there originally. According to this view, they've become streamlined genetically and structurally from what they originally were like. We may have underestimated how complex this common ancestor actually was."
File this with Brain Proteins Before Brains and the thioredoxin urzyme (coming soon, to a Day of Common Learning Lecture near you).

Monday, October 3, 2011

Historic Photographs in Legos

Would this be a good way to teach the boys history? Probably not, but they are pretty cool, and most of the photos are instantly recognizable:


HT: Paste Magazine