Monday, June 22, 2015

Book Review: Flash Boys by Michael Lewis

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

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

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

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

Understanding Brain Science with Inside Out

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

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

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

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

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

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

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

Friday, June 19, 2015

Book Review: Brand New Ancients by Kate Tempest

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

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

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

Friday, June 12, 2015

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

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

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

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

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

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

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

Tuesday, June 9, 2015

Book Review: Hold Your Own by Kate Tempest

Now this is poetry. Vivid, fast-moving, rhyming effectively (until not-rhyming effectively), allusive and grounded in ancient mythology, in this case the blind seer Tiresias. You can tell that this is poetry that respects the spoken word and is written without pretension -- both muscular and heartfelt. There's only a few missteps and easy outs throughout, but for the most part this does what I always felt (deep down) poetry should do. It lives.

Monday, June 8, 2015

A World From Dust (Plus): This is Water, and the Answer is 20

This is part of a series of posts expanding and updating the book A World From Dust: How the Periodic Table Shaped Life.

David Foster Wallace wrote an amazing graduation speech titled "This is Water"* that opens with a parable that has become part of the Millenial Internet Canon:

"There are these two young fish swimming along, and they happen to meet an older fish swimming the other way, who nods at them and says, “Morning, boys, how's the water?” And the two young fish swim on for a bit, and then eventually one of them looks over at the other and goes, “What the hell is water?”
"If at this moment, you're worried that I plan to present myself here as the wise old fish explaining what water is to you younger fish, please don't be. I am not the wise old fish. The immediate point of the fish story is that the most obvious, ubiquitous, important realities are often the ones that are the hardest to see and talk about."

DFW goes on to talk about the inward things: compassion, empathy, and generosity. Read that first. But after that I want to build on his parable and look outward, at the water itself. What is it? There's something in the water that is obvious, ubiquitous, and important: it flows downhill.

Because you can predict that water flows downhill, you can expect that a hillside will develop a branching tree-like network of streams that becomes a river that flows down to the sea. One of the key arguments of A World From Dust is that life is both built from liquid flow (like water) and evolves in a predictable "downhill" pattern (like water). Some parts may be unpredictable, like whether the flow will turn right or left on a flat part of the mountain. But the shape of the downhill flows and the overall path of the flow can be written down beforehand.

At the molecular level, water is moving randomly and unpredictably, but its fluid dynamics are more predictable. Life that moves through water must adjust and adapt to water's physical properties. Very different forms of life strive to move through the water more quickly and/or more efficiently. Since the water is the same all over the world, these different forms of life will find that certain patterns of movement work better than others, all over the world. Once evolution allows them to adapt to water's flow, these different lifeforms will converge on similar movements, whether they are silver or orange colored, whether they have a backbone or not, even whether they are made of carbon or metal.

This is shown in a paper titled "Convergent Evolution of Mechanically Optimal Locomotion in Aquatic Invertebrates and Vertebrates" in PLoS Biology. (An intro to that paper written at a more general level can be found here.)

Very different fish swim in the same way. In particular, the ratio of undulation along a fin to the amplitude of undulations is always 20. The ratio is 20 even for a robot built to look like a fish:

The water is built from the chemical formula H2O. Its unpredictable random motion develops into predictable flow and a predictably optimal way of moving through that flow. Any fish swimming through the oceans on this planet, or on other planets, would move most efficiently using a fin-motion ratio of 20. The fish have found this rule repeatedly, and now we're catching onto it.

If swimming motion is predictable from physical laws (themselves built on chemical structures), then other parts of biology may be predictable as well. The rules of geology and chemistry even set a sequence by which the elements in the periodic table are used. The book describes how this predictable sequence made the world.

A theme of this series will be that different levels of life have different predictabilities. Many levels, like the level of swimming motion, are shaped by physical/chemical rules. Other levels, like the level of fish shape, are less predictable. Which level truly reflects the "nature of history"? That's a big question and will require a lot more data to decide -- which is what the book and this blog are going to be for. When it comes to moving through water, chalk this one up to "predictable convergence."

* If you haven't read the speech, do so right now. I mean it:

Tuesday, June 2, 2015

A World From Dust (Plus): Introducing a Virtual Appendix

I have a special arrival to announce: I have written a book, and it should be on the shelves in about six months! The book is titled A World From Dust: How the Periodic Table Shaped Life.

A World From Dust is a popular science book about the chemical sequence behind the evolution of creation.

It's about how geology, biology, and chemistry worked together over billions of years, providing a hidden order under the random flow of genes and lava and water.

It's about the chemical job that each element takes up in life, and how that job is predictable from its place on the periodic table.

It can be told as the story of many elements: how iron and sulfur gave a spark of life; how manganese was a key for oxygen; and how copper and zinc formed the basis for your immune system and growth patterns.

It can be told as the story of one element: the story of how oxygen was hidden from life, then killed life, then gave new energy and new shapes for life to become more complex than before.

It's also about how, if we rewound and replayed the "tape of life", what we would "hear" in evolution would be much the same the second time around. It's about how, at certain levels, life is predictable and ordered -- and at other levels, it's not.

To use big words, it's about chemistry, convergence, and contingency. To use little words (that are probably better), it's about fate and free will.

Just this morning, Pixar released the first teaser for The Good Dinosaur, which asks "What would have happened if the asteroid that killed the dinosaurs never hit the Earth?" Pixar's answer is that dinosaurs and humans would coexist. It's a nice premise for a movie but it's about as realistic as The Lord of the Rings (not-that-there's-anything-wrong-with-that, since Tolkien himself shows up three times in the book). I think, if the asteroid did anything, evidence says it accelerated evolution and was ultimately creative as well as destructive. But that's another argument for another post, probably after the movie comes out ... right about when the book is published? We'll see.

A World From Dust engages in argument with several scientists and connects their ideas. For example, the "tape of life" reference above tags Stephen Jay Gould's Wonderful Life as a sparring partner. Readers of this blog will also recognize the late RJP Williams, and possibly Simon Conway Morris, Eric Chaisson, Adrian Bejan, Robert Hazen, and Stuart Kauffman, all of whom have been reviewed in the blog's book reviews.

To that end, even in the week since I've emailed the manuscript to the publisher (Oxford University Press), I've found several papers that have to do with the central argument of the book, whether supporting its premise or challenging certain points. What's an author to do when it takes half a year to publish a book but science keeps moving at the same clip as ever?

That's where this blog comes in. I will blog about these new papers as they come in, and talk about how they fit with the argument of A World From Dust. This will be, in general, more technical than the book itself (which is written for a more general reader), but it will be a good resource for those who read the book and want to know more. And it will allow for back-and-forth discussion in the comments. These are big questions, and the point is to hash them out, not to come to an absolute and universal conclusion.

A few papers are lined up and I hope to post a couple times a week. I'll also post a few, ahem, reminders about how you can buy the book when it hits the streets. This blog will provide another layer for detail and discussion both before and after the book is on the shelves.

The best thing about this is that I don't know what's coming. I've been writing the book for a year now, and in that time some points have been both challenged and supported by new papers. That roller-coaster should continue, in public, here. That's one of the great joys of science and one of the reasons I'm a scientist. It will be recorded here for the curious and the questioning, so watch this space.

For the rest of the series, click on the tag A World From Dust, or start at one of the following posts:
Biology: "This is Water, and the Answer is 20"
Biochemistry: "How Oxygen Stress Steers a Protein"