Monday, August 18, 2014

Does a Contingent Foundation Imply an Unpredictable House?

Fascinating new paper in Nature by Joseph Thornton's lab titled "Historical contingency and its biophysical basis in glucocorticoid receptor evolution." In my opinion, Thornton's one of the best scientists out there and this paper shows why. It looks at the history of evolution with a biochemist's eye for detail and also speaks to the big-picture questions. This paper is going to require some repeat reading and digestion, and for now, I'll start at the end, with big-picture thoughts. I find the experiments illuminating and important -- but I disagree with some of the interpretations of the experiments.

The experiments leave no doubt that, for this hormone binding this receptor, there are only a few small roads through the forest of possibilities that led from the original, less-picky receptor to the later, more-picky receptor. Also, there were no signs leading to those roads, that is, no evolutionary pressure that could have helped pick these rare mutations out of the crowd of possible mutations. This is similar to how DNA can change randomly if a water molecule hits it the wrong way. The specific hormone-receptor interaction we have is shaped by randomness and it very well may have a different shape if the tape of life was run again. (The surprise for me is the tight relationship between overall protein structure and the specific hormone structure, which is more intense than I thought it would be -- in other words, I expected proteins to be able to do more with the multitude of shapes they could adopt.)

But, as Simon Conway Morris might say, so what?

The key to the interpretation of this study is that the evolution we're talking about is the specific arrangement of oxygens around a constant, central 4-carbon-ring sterol core. What separates cortisol from the other hormones is the placement of an oxygen over here and not over there. In a dance of co-evolution, this specific arrangement of cortisol's oxygens was chosen out of a welter of possible arrangements and the protein changed alongside, taking a very limited number of roads to do so.

But if those improbable permissive mutations for our cortisol system never happened, then a different arrangement of oxygens on the same carbon core could easily send the same cortisol signal. The specific molecular structures may be unpredictable and contingent, but the fact that some specific arrangment of oxygens will send a specific signal like cortisol can be predicted and repeated. Presumably that's why we have so many signals built around 4-carbon-ring cores decorated with oxygens at different places. The variation in the oxygens isn't as interesting as the constancy in the carbon core, and the fact that all these hormones sending very different signals follow this same, predictable pattern.

Also, the fact that there are only a few roads (2 out of thousands or even millions) that can develop into this specific system doesn't account for the variable speed with which the system can develop to explore those roads. If mutations can be accelerated by stress, could they be accelerated enough to make this improbable path probable? After all, there are only a handful of mutations that are required to change the specificity, and if the rate of mutation for this receptor gene speeds up, the improbable becomes more probable.

Other carbon-based, water-loving organisms on other planets therefore probably have a very different cortisol shape. But although the oxygens may be differently placed in their cortisol, I would predict that there would still be oxygens placed around a carbon-ring core.

The oxygens can flit around the central carbon core and the receptors can mold themselves to those oxygens in many different ways, reshaping the circuitry of the hormone system. But from a more distant perspective, where the exact placement of oxygens can't be seen, the system would adopt much the same shape, using oxygen and carbon in much the same way to send much the same signal. The shape of the foundation is contingent, but the overall style of the house is predictable.

What this paper does is that it clearly places hormone-receptor interactions (within the sterol class of hormones) in the "contingent" category, but I maintain that the chemistry of the signaling system would remain much the same, whichever path the hormone-receptor interactions took. The hormone may be contingent, but the overall shape and chemistry of hormone system is predictable.

All A-Twitter

I finally broke down and opened a Twitter account. You'll find me there at @BenJMcFarland. Still learning the rules of etiquette there, but it seems to be a great format for passing around science news and quick conversations. I'll focus on science and books on Twitter, while here I have the space to hold forth at more length. From this starting point, let's see what evolves ...

Thursday, August 14, 2014

The Art of Eden

Check out this article about an exhibition at the Museum of Biblical Art build around the theme of the first three chapters of Genesis. Most of the pieces are very interesting and gain a lot from the synergism between faith and science. I especially like the Explosion picture at the top of the article. However, the "Serpent Before the Fall" sculpture seems underwhelming to me. It's like I always envisioned and doesn't seem to add anything. Perhaps it's different for someone who imagined the serpent in a different way. The artist and I may simply see the world in ways that are too similar.

Wednesday, August 6, 2014

Book Review: The Hitchhiker's Guide to the Galaxy

Read this aloud to my 11 and 10 year olds and it worked surprisingly well for that age. (Had to do far less verbal "editing" than with Ender's Game, for example. If this was a movie it'd be a solid PG.) The first chapter was funnier than I remembered, and the next quarter of a book was less funny than I remembered -- it's hard to make light of the destruction of the Earth when you're reading out loud to children -- and then once we got to the Babel Fish it picked up again. My favorite part still must involve the sperm whale and pot of petunias, which even made it into the movie.

If you want evidence for how the Dawkins/Adams/Doctor Who crowd is a mirror of the Young-Earth/Ken Ham crowd, this little book actually provides it. There's even a literal young earth involved in the plot! Also, bits about the proof of God show that the reasonings of the two groups run in parallel. The difference is that Adams is intentially hilarious, and he never takes himself too seriously.

When I was in high school and still of the young earth persuasion, this book actually didn't challenge me at all, and may have even reinforced my erroneous belief that old earth implies an disordered and irrational universe. The humor that bothers me the most is the humor that verges on nihilistic and pessimistic, not the humor that takes on religion. But when it's all taken lightly enough -- when you fall and forget to hit the ground, as from later books in this "trilogy" -- it works overall and may turn into one of the best uses of humor. And there's something kenotic about that.

In fact, I would argue that there's more depth and compassion in this book than in all of Dawkins' writing. Behind all the truck about probabilities and irrationality is a yearning for the certain and rational, wrapped up in a human narrative. The theme of falling and humanity that runs throughout the trilogy is one example of a strand that could provide some interesting literary analysis. But no time for that -- for today, I just enjoyed having a laugh with my boys.

Thursday, July 31, 2014

Why I Teach Where I Teach

I teach at a small Christian liberal arts school for a number of reasons. One of them is given in this probably overlong but still entertaining and pretty much right article titled "Don't Send Your Kid to the Ivy League". For example, I'm working with a nation-wide group that is trying to bring real knowledge-generating research into the teaching laboratory for ordinary science classes. None of us is at an elite school, and I think all of us are teaching our students in ways that the elite schools don't attempt.

But even at my institution, especially in conversations with those "above" me in the administrative order/Great Chain of Being, I find myself slipping into technocratic, job-focused justifications for what I do. It's one of those things where the playing field is so tilted that unless you put forward active effort you slip into the default pattern of thinking, even if you've consciously built your career around thinking differently. Don't be conformed -- be transformed.

Here's the quote that stands out to me:

Elite schools like to boast that they teach their students how to think, but all they mean is that they train them in the analytic and rhetorical skills that are necessary for success in business and the professions. Everything is technocraticthe development of expertiseand everything is ultimately justified in technocratic terms.
 
Religious collegeseven obscure, regional schools that no one has ever heard of on the coastsoften do a much better job in that respect. What an indictment of the Ivy League and its peers: that colleges four levels down on the academic totem pole, enrolling students whose SAT scores are hundreds of points lower than theirs, deliver a better education, in the highest sense of the word.

Wednesday, July 30, 2014

Book Review: The Crying of Lot 49

Here's another short classic of science-related literature, but I just didn't get into it. The main problem may be that it just doesn't make a great audiobook. The story is deliberately disjointed and even hallucinogenic at times, and while I felt the visceral descent into paranoia and doubt, and then doubt of doubt, I could recognize that it was expertly done and yet don't feel I got much more than that out of it. I like how the ending twists in on itself, and I like what's left open and what's closed ... when I step back and look at the elements of this book I liked a lot of leaves on the tree, but the tree itself was surprisingly sparse and disconnected. I prefer Vonnegut, I suppose. Pynchon didn't cohere.

Monday, July 7, 2014

Book Review: Beowulf by J.R.R. Tolkien

For years I have wanted to sit in Tolkien's class on Beowulf and hear him talk about the poem and culture he knew so well. If only they had MOOCs back then! But now I feel that my wish has been granted. Christopher Tolkien put together a book of his father's translation of Beowulf and the accompanying lecture notes.


This is actual academia, so it may be an uphill battle for those without a deep interest in Tolkien. But I found an invaluable window into the mind of Tolkien between the lines of these notes. In addition, at the end is appended Tolkien's own fairy-tale version of Beowulf (without all the Geats/Swedes/Danes history stuff and actually beginning "Once upon a time ... ). I just read that to my older boys and they enjoyed the parallels with Rohan in the Lord of the Rings, although neither they nor I were expecting quite so many decapitations in a fairy-tale.


My favorite part of all this was reading Tolkien being a professor, discussing academic claims and translations and historical debates. Ultimately, academic discussions are very similar, and even if I didn't care about the debate, I did care about the debater.


Tolkien had a sharp mind and an amazing grasp of Anglo-Saxon literature. For example, he could tell you if a word was used or a name alluded to anywhere in the literature, such is his love for the field. But for all his ability to parse out the trees, what truly amazes me is Tolkien's ability to always remember the forest as well. Tolkien often solves tricky translation problems by appealing to the piece as a whole and how this part works within the entire poem.


He also spends a lot of time talking about the faith of the author and how that author applied his own Christian theology to the pre-Christian history/myth he was writing in this poem. There's some fascinating theology in there for someone interested in that to chase down with a dissertation, in how that aligns with Tolkien's Catholicism and Biblical passages on this topic like Romans 2. Most important, Tolkien never checked his faith at the door, but brought it in robustly, with academic skepticism where appropriate, but with the obvious conviction that this matters. And he's right -- those (to me) are the most interesting parts of the lecture notes.


So I'm not sure how someone else would react, but I loved the chance to sit under Professor Tolkien. I just wish I could have heard him in person declaim the opening "Hwaet!" of the poem. Some things books cannot do.