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!

Wednesday, July 15, 2015

Book Review: The Fellowship: The Literary Lives of the Inklings by Philip and Carol Zaleski

The easy access of information through the Internet has made some books smaller. These are the popcorn books, with large fonts and big colorful pictures. On the other hand, the Internet has allowed some types of books to grow larger and better, taking in more with their more expansive view brought in by artful integration of all this easy information. The Fellowship must be one of the latter category, and it pulls off some tricks of intellectual breadth that I didn't think were possible.

 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.

It's a lot of ground to cover, but I read it in just a few days. This book succeeds because it takes the Inklings' orientation toward story to heart. The narrative is told as stories that make a single story, at times even with suspense-building tactics on the part of the Zaleskis. I stayed up late reading it even though I knew the ending.
Much must be edited out, but what is kept in is what most Lewis and Tolkien fans want to know. What did Lewis and Tolkien really believe? How did they sharpen each other? This provides the deep connective tissue of the narrative.

Only real flaw I can put my finger on at present is that of proportion: there's too much bio that can be gleaned elsewhere, and too little of the interaction between the Inklings. So little is recorded about the actual meetings that this is completely understandable, but I focused on anything about who influenced whom and what came from where -- the chemistry. I think that some factual detail could have been sacrificed for more conjecture about the connections between, for example, Middle Earth and Narnia, or Williams and That Hideous Strength.
For example, the Zaleskis mention tentatively that Tolkien may have been influenced by Barfield. and quote Vernon Flieger. In my mind this is such a proven, sensible, and foundational connection that it underlines the importance of Barfield to the group -- but here, it is mentioned as peripheral. I don't mind such speculation; it's what makes a book like this sing! This book is about the connections, not the nodes, and a shifted focus more toward the connections would have allowed more integration of the minor Inklings as well. As it is, many works are mentioned with little speculation on possible cross-influences. However, I have already read several books on and by each of the authors here, so a more general approach may fit the audience this is really for.
On the whole, the juxtaposition of the authors allowed me to glean some of the connections that I crave, and to relate it to my own work and writing, so I must highly recommend this unique and highly readable book to anyone with any interest in how creativity works, or how faith works, or how Oxford worked in the mid-20th century.

A World From Dust (Plus): Why Pepto-Bismol Kills Bacteria but not Humans

Chapter 2 of A World From Dust explains how Pepto-Bismol works. That pink stuff kills ulcer bacteria because of its chemistry -- the bismuth in it is so sticky that it sticks to and jams up proteins in bacteria.

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

A World From Dust (Plus): As Predictable as a Warm-Blooded Fish

This is a body-temperature scan of a fish. It should be dark blue because most fish are cold-blooded. Some have evolved biological spaceheaters next to strategic tissues that would show up as orange dots above. But the opah (Lampris guttatus)spreads its warm blood around, even keeping its heart warm, resulting in warm blood throughout its body, shown as yellow and light blue. This allows it to eat at depths other similar fish can't reach.

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.

Book Review: Battle Lines: A Graphic History of the Civil War

I picked this up to see if I should recommend it to my early-teen kids and ended up engrossed for myself. The basic idea is of seeing the Civil War through the lens (in one case literally) of ordinary objects. The graphic novel medium is used incredibly well, with the only problems coming when more exposition is needed to connect the dots, or in the case of the second episode, when trying to cram 100 years of legal history into a dozen pages. You won't get a bird's-eye view of the war from this, you'll get snapshots -- but some of the snapshots are incredibly moving. A graphic panel is worth 1000 words. One episode in particular uses the triptych style to tell three stories in parallel and accomplishes what no other medium can. It's a slight mixed bag, and if you're familiar with Civil War documentaries and movies, some of the episodes essentially recapitulate those. But a large majority of the episodes are creative, insightful, and tragic. I can only hope that the makers of this can return to the era and fill in more episodes based around other objects in the future. This is a fantastic way to teach and learn.

Book Review: Finders Keepers by Stephen King

Even though it's essentially a self-contained story, Finders Keepers suffers from the mid-trilogy blues. It's still a cracking read and finely crafted, as King weaves together several stories with nice parallels just on the right side of coincidence and characters that seem just a touch more human than other writers' characters. The motivations in this case are literary, as a reclusive writer's Moleskin notebooks play the MacGuffin. But Mr. Mercedes was better: more happened, with more twists, the evil was scarier, and the setup more unusual (just read the blurbs and tell me which story you're more interested in reading). A few foreshadowings of the third book, End of Watch, interested me more than the present story did. When all three are out, the shortcomings of Finders Keepers will probably fade and the trilogy should be considered as one big book. For now, it feels a bit too much like running in place, but I have a feeling King will make it pay off in the end.

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.