Merry Chemical Christmas!

Two wonderful Christmas trees from Chemical & Engineering News' Newscripts column.

Book Review: Logicomix

Not sure where to file this one. It's a biography of Bertrand Russell, focusing on his work in logic and mathematics, ending up in World War II, written by Greeks with a bit of ancient Greek tragedy thrown in for good measure. Although Russell is the main figure it's really about the other characters as well: Cantor, Wittgenstein, and Godel. Godel's Incompleteness theorem is presented right (far as I know, since it goes along with what I read in Godel, Escher, Bach long ago!), but there's just so much logical depth one can achieve with a comic book! It really is about the characters, and I enjoyed going with the flow. Although I wonder how much of the story is colored by what the authors want to say rather than what is really there. For instance, did the computer really win WWII for us? I think it was a factor but a lot more factors were more important. Radar, for instance (was the computer necessary for radar, in the sense that without Turing there would be no radar?). The book puts forward democracy as a solution against evil and skates on by the fact that Germany in the early 20th century was pretty democratic! As a thought-provoking way to learn some math history and to start a line of thinking this is an excellent book. What it doesn't do is resolve the issues it brings up -- but I wouldn't expect that anyway!

Book Review: Tales from Outer Suburbia

This is another book by Shaun Tan, who wrote The Arrival completely without words. Since that's one of my favorite graphic novels I was looking forward to this. It's a collection of (very) short stories, often punctuated with large illustrations, but it is still more about the words than the pictures. I read this one together with Sam and it was interesting -- I don't think he's ever been exposed to fanciful fiction like this before, in which every story is matter-of-factly told, and everything is familiar, except for one outlandish fiction in each (say, an alien exchange student, or a deep-sea diver wandering around the neighborhood). Each story has some deep current underneath it. There's two that still stand out to me -- one in the middle about marriage and one toward the beginning about a sad child. The former is not what I expected from a young-adult book like this but it is very well done. Bottom line: it's like a box of chocolates, and if one story is semi-normal I guarantee the next one will surprise you. Great for introducing what fanciful fiction can do to a young boy.

Symposium Lecture Posted

This summer my colleague in psychology called together a few of us interested in science and asked if we'd like to give a symposium for "Darwin Day" (depending on who you ask, either the anniversary of Darwin's birth or the publication of the Origin of Species). The thing grew to five hour-plus sessions and even then felt like it didn't have enough time. My 15 minutes of semi-fame are in the "biological sciences" section, and I'm in the middle, between Eric Long's talk and Tim Nelson's. I probably am focusing on a scientific audience a bit much but am trying to make my case for a general audience!

I just regret that the Q&A isn't on there (although that's partially my fault -- long story!), because that's where we really addressed the faith/science overlap. Here it's (mostly) all about the science. Discussion of the overlap will come in the upcoming Weter Lecture!

Here is the link to the iTunesU page with all the sessions.

Book Review: What the Dog Saw

[piclink]

It's very obvious that Malcolm Gladwell tried to get his start in advertising, then "fell back" to writing, as he decribes in the introduction to this, his latest book. He's at his best in short snippets, like ads, just enough to make his point (which usually results from two or three who'd-a'thunk type connections) and then get out of Dodge before the reader starts to think up objections. (This is why this book is definitely better than Outliers.) He's very good and very original, but it would be nice to see him in conflict with ideas rather than promoting them. (The ideas he sets himself up as being in conflict with are usually conventional wisdom "everybody knows" semi-strawmen ... but, to his credit, they usually ARE something everyone knows that he then shows is wrong!)

This collection gets stronger as it moves along. The first few articles feel almost like informercials, but later he has some very good essays, and my favorites usually involve some science. The problem with Gladwell is he's never faced peer review and it shows. In the introduction he says he hates it when someone reads something and says "I don't buy it" because writing's supposed to be entertainment. Well, I've said this before but ... I don't buy it. Every piece of writing is an argument. It's making an argument that you should take the time to read it. And Gladwell's actually very good at making that argument implicitly in his writing! So, sorry, Mr. Gladwell, I still don't buy it, but I will read it.

(Besides, "igon value" instead of "eigenvalue"?! That's just embarrassing.)

Regardless, there are enough good essays in this book that I think I may assign it to my students to buy for a seminar class for which his essays will be good introductions to the topics I'll discuss. But they are only introductions, good for getting the conversation started, surprisingly weak at commiting to practical conclusions that will change the way you go about life. (Maybe it's the underlying philosophical assumptions that mold everything else, assumptions that I may not "buy" into?) As a current article-writer and verbal welder of disparate ideas, Gladwell is unparalleled. Let's just get some real intellectual conflict in there and we'll have real depth.

Free RJP Williams!

A lot of people are interested in the chemical stories of RJP Williams, but mostly they are behind some kind of expensive "wall." But wait ... I just found this 2007 article from the Royal Society and (God save the Queen) it's available free to all (I think ... ). This seems to be a pretty good summary of the 2006 book I reviewed earlier. Check it out here:

http://rsif.royalsocietypublishing.org/content/4/17/1049.full

Han Solo: Game Theorist?

You have to see this blog post from the Freakonomics blog for yourself. It's about Star Wars Episode IV and Han Solo's decision to fight for the Rebels. I'm trying to figure out how to integrate into the boys' math curriculum. There are advantages to home schooling.

Here's the link.

Book Review: What is Life?

[pic link]

This is not Schrodinger's What is Life? from before the DNA structure was solved. (The phrase is also used all over the 'net from the diversity of a quick Google search.) It is Lynn Margulis and Dorion Sagan's What is Life? from the mid-90's. (Yes, it's that Margulis, the famous one who proposed the endosymbiotic theory of mitochondria, but no, it's not that Sagan, it's his son!)
.

It's also an example of the blessed serendipity of the semi-annual Library Book Sale. This year I went to the book sale and found several books on origins (of life and/or the universe) that I was looking for, for a dollar each: the book by Martin Rees I reviewed earlier and this one topped the list. This is a beautiful edition, big pages with full-color pictures of microbes and rocks. It was deliberately formatted after the "old science books" of earlier centuries, and even has some full-page hand-drawn biological specimens like those old books had. It feels like an old book, and I love that about it.

.

The topic of the book is a history of life told by Margulis (I gather she's the driving editing force, what with the book's emphasis on symbiosis and reproduction). What I like about it is that the thermodynamics of entropy and energy dissipation is pretty much there, and the vignettes about certain bizarre microbes are wonderful. Well worth it just for those. It complements some of the other stories, like the RJP Williams one I keep going on and on about because so few people can find it!

.

Where it goes off the rails in my opinion (and since this is a book review it's all my opinion but let's just re-emphasize) is the final chapters in which man is discussed. The authors argue that Darwinian reductionism and directionlessness is wrong. They bring up Samuel Butler's ideas and expand on them to suggest that there is a direction to evolution and that direction is guided by "choice" -- a property that everything living (able to respond to its environment, I would reduce that to) shares. So this is the "microbiological existentialist's" version of creation. I'm still trying to figure out exactly what this "choice" is and where it comes from. I can't get away from the worry that at its heart it's just randomness magnified, whether a certain environmental element is sensed or not, that organism survives, and goes on to reproduce. That's the "choice" they're talking about, and is it any different from a computer's "choice" if a subroutine that ranks options and takes the best one is included, maybe with a random Monte-Carlo element built in? It's just a question of how much randomness happens. I'll have to think about it more but I can't find any way out of that mess, and I don't see how it's fundamentally different from the position they say is wrong. The central question is: Where does the "choice" come from?

.

I see a parallel here with Signature of the Cell by Meyer (although this is definitely debatable and incomplete): in both cases we have a fuzzy concept that's given a quantifiable backdrop, but the core of the concept is not correctly quantified (not for me at least!). Meyer gives probabilistic calculations of "design" that calculate these huge astronomical numbers, but if the starting assumptions are off the numbers don't matter. "Choice" in What is Life? has a similar role, although the authors stay away from quantifying what "choice" is, they argue as if it were quantified or a clearly defined part of the system. But the best I can gather for its definition -- if it is environmental sensing and response -- is that the only "surprising" part of choice would be random error in either sensing or response. That could even improve the system, sure, but it's not really any less "random" than the Darwinism you're arguing against in the first place. Meyer's calculations assume/quantify too much, and Margulis and Sagan's don't seem to assume enough (or they assume their "choice" is different from selection when it seems to me to be random noise).

.

Of course, this is off the cuff and I have to think about it more to tamp it down, but I'm not satisfied with either "design" calculations or "choice" philosophies.

.

The big difference with starting with chemistry (the approach that appeals to me) is that we start with quantifiable terms: energy, entropy, and enthalpy. (The complexity is in the APPLICATION of those numbers to the system!) The sun provides an excess of energy to the system that the system converts. On the individual level there's a lot of variation. But the way energy moves gives a direction -- perhaps contingent but a direction nonetheless -- to the system, suggesting the universe is "set up" to do this, to have this result.

.

Again, off the cuff. I'm probably going to regret the shortcuts in some of these statements, but that's kind of the point. I slap this online as a rough draft and you, dear readers, help me find the holes in it. There will be holes, oh yes.

.

So the concept of "choice" that the authors put forward, I "choose" not to integrate it into my thinking.

.

And this makes some of the more outlandish statements in the final chapters -- that science is creating a story that will replace the old time religion/creation myths, that man's capacity for self-deception is what sets us apart from animals, etc. -- it makes them ring hollow because I don't know what this "choice" thing is. An emergent property? How is that different from randomness? If self-deception is the key to humanity then why are we here in such a perverse universe? And why is the universe knowable at all if self-deception is our foundation? (Seems like cutting off the branch you're sitting on ... )

.

Regardless, this book is well worth it for its beautiful pictures and stories. Just make the "choice" to complete your own synthesis of those and take the final chapters with a big grain of salt.

We Three College Professors

Because the word "magi" leads directly to "magician," it's straightforward to think of the Magi as the 1st-century equivalent of David Copperfield or Harry Houdini. Indeed they were astrologers. But back then there was no such thing as astronomers, and the people who carefully scanned the skies, with surprising sophistication? Those were magi. So I think of them as astronomers, college professors from Iraq, absent-minded and oblivious to political realities, rich and able to travel and risking a LOT to go to this country Israel they really didn't understand. It's easy to dismiss the silliness of academia sometimes, and rightfully so. But God reveals himself to those who seek him, even cloud-headed academics. I take comfort in that. Those who seek, find. So let's keep seeking and knocking.

Maslow's Hierarchy of Video Games

I just realized that video games satisfy different fundamental needs. Imagine a pyramid, with more common games at the bottom:

Most games have a Darwinian/Athenian-Olympics emphasis. Tap the buttons faster than the other person (ah, Summer Games for the Commodore 64!). Beat them in head-to-head tournaments. The irony is each person, playing alone, can be master of his own domain and top of his own food chain. But then we have millions of food chains, each an illusion. It works until you turn the power off (or until the interminable credits are scrolled off the screen). Or you can get online and be better than someone you don't know in a country far away.

Then there's rhythm music games: This involves following complex instructions precisely (no real tone control, only timing). If you hit the notes you get the reward of the music. It feels like you're creating something but the real goal is parroting. Yet you can learn about song structure from these. I have a new respect for Ringo Starr after realizing some of that drum stuff he did was actually pretty hard.

Then there's The Legend of Zelda: exploration (which is like foraging for food and recreating maps of the environment in your head) The joy of getting food in the form of hearts and fake money is supplemented by the joy of solving puzzles and getting new tools, a eureka moment, like doing well on a final exam. Mario and other platformers generally fall below Zelda in exploration, and are closer to the pure competition/repetition of button-mashing, but can include puzzle elements that move them up the hierarchy. Little Big World has a considerable creativity element from what I understand but I've never played it.

I've never been able to play The Sims but it seems to be social: some interaction with others (real or not), putting the self in context. Most games just don't put a high priority on this one but the success of this series suggest it's a good idea to try to build on. The complexities of this and what it can reveal about you means it may be the highest on the complexity of purpose list. But I still don't have the patience to figure out how to play the darn thing. I rented it once for the GameCube and gave up after 5 minutes. What does that say about me?

... And yet, and yet, don't you feel there must be something more? (I assume it's not the Playstation 4!) (It must be James Cameron's Avatar!) (um, maybe not.)

Handy Blog Cheat Sheet

Welcome new visitors of all stripes and persuasions. Apparently no one wants to debate a book review of Odd and the Frost Giants (or even Knowing Christ Today) but ID is on everyone's mind. The main point I'd like to make here is that there's LOTS of posts on this blog and if you have questions about me or what I believe or why, here's a road map for where to start:

1.) "What do you know/believe about creation?"
On the sidebar you'll see a series of posts titled Eight Days of Creation that address this. If you can make it through all that ... you'll get a certificate. :) The RJP Williams book I am thinking about now is called The Chemistry of Evolution. It's cool. But it's expensive. Try a library, I did! Another good book is The Open Secret by Alister McGrath. It's reviewed somewhere here too.

2.) "What do you know/believe about Jesus?"
Funny, this comes up in Day Eight and the final post of the Eight Days of Creation. (Day Seven has some useful stuff too.) I recommend reading them all in order but if you're pressed for time, give it a try. (Snarky comments about religion are most appropriate for those posts, if you'd like to save time and avoid reading something new. Anybody wishing to be taken seriously in a debate about religion should at least familiarize yourself with N.T. Wright's amazing book Resurrection of the Son of God. It's long but it's a great (and surprisingly readable) academic work.)

3.) "Why are you doing this?"
My very first post ("This is not a blog") has something along these lines, but I suggest clicking randomly. If you get a large enough "n" of posts you'll probably find something that annoys you. But you may find something you like, who knows?

I ask myself question #3 myself sometimes. I'm going to have to be a bit hands-off for the next few days as I grade finals and write lectures/presentations and build some proteins, so please don't take lack of personal response personally. I'm just throwing this out there and seeing what happens, as Bill Mallonnee sang: "You sew your heart onto your sleeve // and wait for the axe to fall."

Could Your Car Run on Vitamin C?

[from C&E News Nov 16 2009]

OK, not like putting vitamin C in your car and having it run on that, but with a middleman: vitamin C feeds a molecular engine that makes hydrogen, and THAT fuels your car. Here is the outline of events:

1.) Vitamin C (ascorbate) gives electrons to cytochrome c. (It has enough "energy" that this would work.)
2.) Cytochrome c gives electrons to photosystem I. (That's its job after all!)
3.) Light excites the electrons in photosystem I. (Again, that's its job.)
4.) The electrons move to platinum clusters on the other side of the photosystem.
5.) Platinum catalyzes the conversion of acid protons to hydrogen gas.
6.) Hydrogen gas carries the "light energy" anywhere it goes (and when burned in a car produces water vapor as the waste!).

The especially good news: this scheme (shown above) self-assembles and runs for months without help. Not sure how much platinum it needs ... but at least as a catalyst it's not consumed.

I'm getting more and more keen on hydrogen as a versatile fuel, if we can just solve the storage problem. This shows just how easy it is to make it. Storing it is a bigger problem, but it doesn't seem insurmountable (easy for me to say, I don't research that!).

Comments on the East Anglia Climate Research Unit (CRU) Emails

I'm hoping to put this together with other thoughts on other topics but I think something needs to be said now since it's on a lot of people's minds.

Basically, several emails were hacked from the East Anglia Climate Research Unit (CRU), which has been the source of a lot of climate history research. What this means is the reality TV cameras have been turned on for the scientists in that their private emails have become public, with all the politics clearly exposed, and some data presentation discussions. Does the data presentation become data distortion? Are they trying to hide some of their research to put forward what fits with their theory?

So if the camera adds ten pounds, I think it also takes away 10 IQ points. Some of the stuff that's said is just plain tribal and I'm sure there's sociologists of science talking about how it show "groupthink." There's two responses: 1.) This proves climate scientists are frauds and 2.) This proves climate scientists are just human but it has no effect on climate science.

Of course, I'm going to come down firmly between those two straw men. (What else are straw men for?)

There is a deep problem here, with the authority of science. When scientists want to use the authority of science, they emphasize how it's monolithic, how those who disagree must have other interests, that the science is somehow neutral. When the scientists themselves are revealed to have non-scientific interests ... the monolith falls over.

Look, if you spend your life's work on something you will want to defend it. Just because someone is defensive doesn't mean they're wrong.

The fact of the matter is, the science is not monolithic. There are some things that are near 100%: old earth, evolution, HIV causes AIDS. Then there are some things that are more 75%/two-thirds, where you have a clear majority and then some reasonable dissent. Climate change is in this category, and the most reasonable argument I've heard on it is the "driving in fog" argument: we're not sure if there's a cliff out there, but just in case there is doesn't it make sense to put on the brakes?

Another analogy may be cancer. We've found a lump. It could kill us. But hacking off the limb with the lump could hurt us too. So this is the time for reasonable prevention and "watchful waiting." (See recent mammogram advice shift!)

So I'm in favor of inexpensive, straightforward solutions to this problem. The rubber-meeting-road conclusions are:

1.) Cap-and-trade as it stands now seems too close to a shell game. Let's get something simpler on the table. I'm not usually for taxes but a gasoline tax may be in order. That's better than a convoluted system that seems more like medieval indulgences than a true solution. The point of the tax is not to generate money but to let other things that are now more expensive cost less relatively ... which can lead to lower costs in the long run.

2.) Research, research, research into solar/hydrogen cells and build, build, build nuclear. Also work, work, work on transportation with alternate fuels and try some geoengineering on a small-scale basis. It's not time for geoengineering yet, but if we get a decade of data that suggests it's time let's get ready. There's positive things to do with energy that as a chemist I'm really excited about.

3.) Stop pretending there's a 100% consensus about the future. Instead argue that a clear majority of scientists think there's a problem and that should be enough for now -- try inexpensive or innovative options now and keep a close eye on temperatures and weather patterns and species extinctions. There may be a cliff out there in the fog, but if stomping on the brakes causes a 15-car pileup I may still end up hurt. Instead, can we slow down and at least try to watch things like this recent cooling?

What's really needed is probabilistic thinking. I still think there's a majority chance that we have a problem but we need to watch more to be sure. There are simple ways to try to cut down -- I've noticed that car miles are down and bus miles are up. This is important enough that all the stops should be pulled out for low-impact, low-cost solutions. I don't see a clear justification for drastic costs yet.

Let's watch this lump and see if bad stuff happens; in the meantime, let's "eat healthier" with our energy choices and try to see if energy research hits the jackpot.

All I Want for Christmas is Some Borax

Here's a great recipe for making sparkly Christmas ornaments from pipe cleaners and a Borax solution, from the Houston Museum of Natural Sciences Blog.

This year, we're putting off getting a tree for another week or so because it means less trouble keeping ornaments out of a certain rugrat's mouth.

But that just means I'll have time to get together the ingredients. I just need to ask my wife if we already have Borax or if I'll need to get some from the store.

Name Chart

Here's a figure from a recent Proceedings of the National Academy of Sciences showing how frequently babies were given certain names in certain years. The message of this graph is "the faster they rise, the faster they fall." Which means Aidan as a name should pretty much disappear in the next few years!

Book Review: Knowing Christ Today

Dallas Willard, author of this book, is a professor of philosophy at USC and a friend of Richard Foster (author of many books on the spiritual disciplines). At first this may seem on the list of "combinations we wouldn't think of offhand," but Willard's writing makes it perfectly natural. He is one of the best writers at conveying heavy philsophical concepts without you even knowing it; the writing is so sharp you don't even feel it. This book is about "epistemology" on that level, but he makes a strong case that knowing Jesus is a category of knowledge as strong (or stronger than!) scientific knowing. What he has to say goes right along with the Weter Lecture (although I hope to approach half his heart for the practical "application points" for the reader). Some post-its that didn't make it into the lecture:

"When we have knowledge ... we are not just guessing, and the anxieties, hesitations, and vacillations that prevail where knowledge is absent no longer control our lives." p.45. (From those three characteristics I take is that knowledge is very much absent 'round here.) A correlation between Idols, Ignorance, and loss of Identity (Israel's national identity at the very least) is provocative. Contrary to this is the Real stuff that one can Rely on (and know).

His chapter on natural theology is great on evolution but not so helpful when it comes to quantum physics. The problem is he builds a lot on the statement that something never comes from nothing. This is fine on our level, but the quantum level has the uncertainty principle in which something does sometimes come from nothing. The philosophical edifice can still be built I think but it changes the equations importantly. This is in some ways the most disappointing part of the book. There's just a lot of complexities he skates by.

p.118: The Apostles Creed is a list of knowable, historical events. It's no good to just pretend they're mere "spiritual truths"; they are events that can be known. Not just facts either, but events that happened to a person who can still be known.

p.137: The story of R.A. Torrey is retold (it's even in VeggieTales now). He counted on God's provision through prayer to extreme levels. Reading this alongside the Jubilee rules points out that God put sabbath and Jubilee rules in the law to try and codify this kind of radical reliance.

p.153: Willard's conception of the Kingdom of God is very interesting. He says your kingdom is what you can control with your will. So if the kingdom of God is near/at hand, does that mean your choices can be made, can be given to God? I'm trying to see how this fits with NT Wright's historical explanations of what that phrase meant to second-temple Jews. I think there's overlap but there's some things to explain too.

p. 158: The most challenging part of the book: Willard reminding me that my job is to seek the best for others, the first thought, love. Let's just say this doesn't exactly come naturally to me...

p.160: Another simple but mind-blowing quote: "Prayer is God's arrangement for a safe power sharing with us in his intention to bless the world through us."

p.207: For those teaching at Christian colleges: Willard suggests that because the scriptural knowledge is reliable and real, it is therefore testable. This is where the rubber meets the road. What does this mean? It's a huge challenge. But I think it's valuable. The knowledge taught at a Christian college should be different from that taught at a secular college. Scary but true.

Book Review: Odd and the Frost Giants

What's better than a movie with the kids?

A book with the kids.

I read this book to Sam in the space of about 2 hours. It's a story about an impertinent 12-year-old boy in old Norway who meets three talking animals who turn out to be rather important entities. I was able to use my Norse mythology to predict who they would be. What's funny is these same characters are in The Ring so Sam has a better idea who's singing when that opera's playing. It's typical Neil Gaiman: a brisk, original story told with confident broad strokes. Great for a 7-year-old boy to hear.

Sam says (verbatim): "I really loved it! In fact, I've started reading it by myself."

Now I've got to decide: When's he ready for The Graveyard Book and Coraline? (The book, not the movie!)

Book Review: Signature in the Cell

An Open Letter (ok, a review) to Stephen C. Meyer, Author of Signature in the Cell:



Dear Stephen (you may call me Ben),



I believe what you do: In one God, almightly creator of heaven and earth, and Jesus Christ, his only son ... you know the rest. I have worked in science, too, and have a big interest in the questions of how life started. In both of these matters, I am on your side and am also theoretically predisposed to accept your arguments about Intelligent Design. I have no philosophical opposition to it, in fact, I believe, no, scratch that, I know that the creator stepped into creation as Jesus and gave us a glimpse of the future with the physical resurrection on Easter morning, an act of new creation unexplainable any other way.



So w/r/t this whole book you've just written, about how the Creator must be inferred to explain the origin of DNA? I very much wish you were right.



But you aren't.



I don't say this because I fear for my job. I have a feeling I could have a very nice job at the Discovery Institute if I pushed for it, speaking to churches and other groups across the land, defending Intelligent Design. After all, you're in town here, I could just commute. Here I've already got plenty of grant money and tenure, and I'm at a place where I could defend such a defense of ID as part of my job, even if all the rest of that was not true.



I say it because, as a scientist who prays and studies scripture, I do not buy your argument.



Let me offer some incoherent bullet points that I would organize and maybe will someday:



-- First off, if you want to convince someone like me, writing a 600-page book in which you take 200 pages to walk me through the Watson and Crick model of DNA and other details before you get into your argument is off-putting from the beginning. It's clear this book is not pitched to scientists who may have counterarguments. This book is pitched toward the general public who do not have counterarguments, which is fine for reporting, but does not work for the kind of close detailed argument you suggest is lacking. I have seen several sites that report the 600-page length of the book as if it were some kind of indication of its quality. But there's really about 200 pages of argument in it all. Of those 200 pages, about 100 pages or more were arguments that I've seen before in similar literature, repeated here without reporting on the context (some of which I provide below). I just read a 400-page book on the origin of life (see earlier review) that had me reading slowly and re-reading, making connections, illuminating other things I had read or learned earlier... this book, despite being longer, was read in about 1/10 the time (and only had, alas, 10 post-its compared to >100 for the other book!). It just didn't do what science does in that respect. Again, I understand, maybe the creator did it this way. It's just a bad sign when the length of the argument puts me off before I even get into the meat of it.



(So I'll basically go through the post-its now!)



-- The argument about the earth's early atmosphere is tantalizing but seems a case of cherry-picking, of finding old references that call things into question and leaving them at that. Whatever the low number of oxygen that started out, it was low and went up. There's a graph with more than 10 independent measurements of past oxygen levels vs. time, and though there is scatter, there's a line going up through it all. So oxygen was at least rather low, and it makes sense to a chemist that it reacted with a lot of the metals and non-metals to be absent from the early atmosphere, because oxygen is reactive, there's no getting around that. What kind of chemical reactivity do you propose for your assertion that there was some around, enough to interfere with the reduced chemicals? Why DIDN'T the oxygen react, if there was still some around? (Post it pg. 224)



-- Later you claim that DNA is information-neutral, that is, that there is no way one pair of base pairs will be favored over another. Of course, this is true, and is one of the reasons DNA actually works as an information-carrying molecule. But then you claim that because of this there can be no bias toward information in the bonding of DNA itself. Of course there can't -- DNA wouldn't carry as much information if there was a bias. But this doesn't mean DNA can't ever gain a bias in combination with other things. This tunnel vision on DNA shows up in the very way you structure your argument: you first argue it wasn't DNA, then it wasn't protein, then it wasn't RNA only. But what if DNA is brought together in triplets by another molecule -- then the other molecule confers its binding onto the information-neutral DNA template. Three DNA basepairs can be held together by another molecule in a triplet. This pattern holds through the book: the argument is made that it can't be this alone, or that alone ... but what about the recent findings that things can work together? That's a later bullet point. (Post-It Page 242)

-- There are frequent distortions of the biochemical facts. You write about "the discovery of seventeen variant genetic codes." But most of these are in mitocondria and they consist of a few exceptions to the hard-and-fast general rule. The writing implies that they are totally different codes, when actually they are a change in 1 to 6 out of 64 code units. The equivalent is that of an alphabet with one changed letter. Yet you imply that these are totally different codes. It is moves like this that highlight that you are not looking at the data and then coming up with an explanation (even one with God as a causal agent) but are rather starting with your explanation and then making thing fit into it. These are alternate codes that are exceptions that prove the rule: there is really one code and everything else is a slight variant of it, at most. Claiming that there are 17 different alphabets when you have 24 letters the same and 1 or 2 different, 17 times, is something that weakens your case rather than strengthens it. (Post-It pg. 248)

-- "Then again, it simulates a goal-directed foresight that natural selection does not possess." But the RJP Williams book I just reviewed, and my upcoming Weter lecture, are both about how chemistry gives biology a direction through the second law of thermodynamics! So if chemistry provides a "teleos" to biology is your argument undermined? I don't agree with the biologist's caricature of life as meaningless randomness either. But I think the rules for the emergence of life may be encoded, not in an irreducibly complex DNA molecule, but in the rows of the periodic table of the elements. You keep making the point that information must come from somewhere. Well, the pattern of bonding of the chemical elements (which influences the availability of each on Earth and the structures they can form) would provide some sort of information by this definition. The second law, not natural selection, would drive these chemical cycles. You use the second law only as a source of confusion, a Babel-like curse on the universe. But the second law can drive cycles of life, bringing life together, as described by Williams and as is a major point of my upcoming lecture. I can find no reference to the books and articles by RJP Williams and co-authors, and this is an unfortunate omission. (Post It pg. 284 also 336 and 332)

-- The claims that nucleotides are hard to assemble are outdated in one fell swoop by the recent paper in Nature by Sutherland's group that nucleotides form from a mixture of simple constituents, growing more complex with irradiation and cycles of wetting and drying like evaporation and "rain." Not only is this a problem for your argument because we now have a pretty good path by which nucleotides can form, but it also points out the failure in your "divide and conquer" reasoning. You attack DNA on its own, RNA on its own, protein on its own, for instance, and then you say because each of these is improbable we can just multiply the probabilities together and get a huge number. But that argument fails to account for the possibility of cooperation. This is what allows the nucleotides to form; that they mixed everything together in one big pot and these nucleotides spiraled out of it, self-assembling (by the chemical rules of bonding). I have a suspicion that a similar "working together" makes the other myteries work: that of the "central dogma" or the original (non-coded) cell itself. (Post-It pg. 302)

-- On Douglas Axe's work, I'm still a little annoyed that Axe spoke at the recent ASA meeting but no audio was posted for his talk. Do you want scientists like me to believe your work or not? Whatever the reason for that, the published work by Axe is fine enough on its own, and it does show up those who claim there are no peer-reviewed manuscripts in your libraries. But it misses something huge, something again from RJP Williams. You're only using one corner of the periodic table. You're arguing that a protein must be 150 residues long and made only of amino acids to work. I agree, that's improbable that something like that would just come together. But metals and metal ions can catalyze reactions by themselves! What about Fe or Fe-S or Ni or VO4 or whatever? One third of enzymes have metals in them, often for explicit catalytic use, in which the protein helps with binding but the metal does the chemical work. And even today some metal clusters (like nitrogenase's) will catalyze reactions without any protein at all. All Axe has proven is that proteins alone are unlikely to have been a beginning. But metals are better at chemistry and they could have been the starting point. There is no mention of this possibility anywhere in the 600 pages.

The bottom line is that I want your work to be in conversation with mainstream science. Your set of predictions is a good step forward (though you overstate your own success in the accuracy of the junk DNA predictions, you have an OK point). But reading this book after reading Williams is like reading Twilight after reading Lord of the Rings. It's just not in the same ballpark. Look, I want to believe, but you have to help my unbelief by demonstrating something, not by just taking the most difficult thing we can find, saying it's unexplained, and saying "now you have to believe what I say." No, actually, I don't.

I hope one day ID can publish a book that will get 100 post-its from me as I read it (and not from frustrations!). I will keep trying to read these books if you and your colleagues keep putting them out. I believe in your freedom of speech and, again, if I believe in a real God that really makes a difference I must allow for the possibility that you may be right. But you've got to do a better job if you're ever going to have a prayer of convincing me. And you've got to convince me if you ever want to convince someone who doesn't believe in any rationalities greater than their own.

But this book? This isn't it and I'm a bit frustrated at that.

This is not censorship or ignorance. It is grading an effort, and testing an argument, things I do every day. I gave it a chance and am beginning to think that the persistent effort of ID scientists to ignore the other developments (such as Sutherland's) that conflict with their views are seriously leading the church astray, and when you lead the church away from truth you are walking where angels fear to tread.

Yours (truly), BJM

Poe: More Lewis than Darwin?

One of the talks at this summer's American Scientific Affiliation meeting was Harry Lee Poe, "Edgar Allan Poe's Big Bang Theory and the Power of Imagination." H.L. Poe is a relative of Edgar Allan Poe's who argued that Poe's personal faith trajectory was like C.S. Lewis and opposite to Darwin. The big difference between Poe and Lewis would be that Lewis lived decades after his conversion but Poe died soon after.

At first blush this seems crazy. Just proposing the mash-ups between the two stories is fun: "The Raven, The Witch, and The Wardrobe," or "Surprised by Death" ... but look a little closer at Poe's own story. He was interested in science and known more as a humorist than a horror writer in his time (the horror brought in the money that he lived on, and he was good at it; he would often START with the horrific stuff and work his way out from that). It is established that Poe joined an intense reform movement (the "Sons of Temperance") shortly before his death, and his science book Eureka is very open to the idea of a Creator. The circumstances of his death are contradictory and mysterious -- the newspapers implied he died of alcoholism but several people who knew him denied this -- yet that newspaper explanation was what I had in my mind. The good thing about Wikipedia is it immediately shows the confusion on this account, and that the "conventional wisdom" about Poe's death is confused. His death is just a mystery. But the idea that he was headed in the direction of crediting the creator with existence and following up on what that means ... that "Sons of Temperance" membership is the one solid piece of evidence here, and it points in that direction.

Well, I simply don't know, but there's loose ends here that may never be tied up. I didn't even know such a case could be made. I do have a personal connection to Poe and science: my very first paper that I actually wrote was based on research I did proposing that Poe is actually in an old archival photo of the Philadelphia Academy of Natural Sciences. Nothing ever came of that and I had started to assume it was just off base, till this relative comes out talking about Poe's huge interest in science and how it may have led him to understand creator from creation.

Still a mystery, but fascinating possible connections. Who knows?

Flu Chart

This chart was recently whipped up by a doctor in a few seconds with a tool called Amalga. It shows total visits to hospitals for "Influenza-Like Illness" for different years. I don't think you need to be told that 2009 is the gray line:

This is from the Freakonomics blog, which also includes a link to a "screening algorithm" from Emory that tries to tell people when they should just stay home and when they should go to the hospital. (link)

I better keep washing my hands ...

My New Favorite Website ...

... is Strange Maps, which posts maps like this chart of who is where when in The Lord of the Rings. Just incredible. (Click to enlarge and see what I'm talking about.) Find more at strangemaps.com.

Book Review: Just Six Numbers

I find this book fascinating, not just as science but as a window into the mind of a scientist. Sir Martin Rees is an astronomer who wrote this book to describe how six particular numbers appear to be "set" so that life will have a chance to emerge from the cosmos. Since he's an astronomer he writes very well about the laws of physics and once the periodic table is set up he assumes that takes care of everything (as a chemist, I start where he ends!). He is not a theist apparently, but he quotes St. Augustine twice and has the good sense to include a "summing up" chapter where he explains the tuning of these six numbers by invoking the multiverse, in which an infinity of possible universes exists, and we happen to see this one because there's no one around to see the others.

To which I say: great! You believe in something infinite. Why is an infinite array of universes preferred to the idea of an infinite creator? You gotta choose your infinity. And an infinite personality creating other personalities is at least logically connected. It comes down to, do you want to believe in someone bigger than you or not? And I suspect that we'll always be left at precisely that point, on the verge of a leap of faith but never forced over it, no matter how much science we know.

The six numbers are (that is, my understanding of the six numbers given my limited physical knowledge is):
-- N, which makes gravity so much weaker than the other physical forces, which allows atoms to form at all.
-- Epsilon, the nuclear efficiency, which is the energy released when matter is converted to energy in the heart of a star. If this was different (0.006 or 0.008 instead of 0.007) we wouldn't have a full periodic table.
-- Omega, the critical density, related to the ratio of dark matter to visible matter. If there weren't a lot of dark matter galaxies wouldn't form.
-- Lambda, the cosmological constant, a cosmic repulsion that pushes things apart (not well understood yet at least in the year 2000!).
-- Q, the number of ripples in the expansion, allowing galaxies to form from unevenness in the universe (1/100000 rather than 1/1000000 or 1/10000).
-- 3 + 1, that is, three dimensions of space and 1 dimension of time, which allows the inverse-square law to work so gravity can actually hold planets in stable orbits.

Needless to say my Weter lecture builds on all this and from a different perspective. But I'm grateful for Rees's forthrightness and clear statements, both for science and philosophy. This is an example of where the discussion of faith and science should be, for those scientists without a faith background.

Book Review: The Gathering Storm

This is Book 12 (out of 14 ... I hope) in The Wheel of Time, a series I've been reading since high school. I met the author once at a book signing, and have read the series on and off again, and just when I got back into it with Book 11, the author passed away. Fortunately he left copious notes and half-written scenes behind. The work was passed to a new author and now everyone wants to know how it worked.

Well, it's just fine. The action moves along about twice as fast as previously, and though there's an occasional false note of a moment (particular when things just sound too much like a movie to be true), the plot is definitely authentic and the writing works for me. There's a climactic battle that I was slightly disappointed by, and another character's descent into darkness that impressed me the other way (though the resolution of that was, again, just a little too cinematic for me). I'm just happy to know what happens and to finally see it happening, even if it's not perfect, and see it heading toward an endgame after two decades. This one worked and I'm confident the next ones will too.

12 X 800 pages = 9600 pages down, about 1600 to go.

Book Review: The Chemistry of Evolution

This book by R.J.P. Williams and J.R.R. Frausto Da Silva is a little 450-page version of a chemist's story about evolution. I have tagged and marked it up and thought about it so much all I can say is for the review wait for the Weter Lecture!

The only additional thing I have to say is that, you know how sometimes some people say there's hole in that plot (of a movie or something) big enough to drive a truck through? There's no such holes in the substance of this book, but the implications are so vast that I feel like there's holes in that sense to drive through -- questions to answer, and freeways to drive down. So in a book of science, a discussion of "holes big enough to drive a truck through" doesn't have to be pejorative -- in this case it's a very good thing because there's a lot of thinking left to do.

Now for the time to do it ...

Glad to Have that Johjima Shirt (Again)

We bought the boys two Mariners shirts a few years ago: one was #51 Ichiro and the other was Johjima. Since then Ichiro's been as consistent as always but Johjima's lost a bit of power, been injured, and been in a sort-of-spat with one of the starting pitchers blaming him for some bad starts (in my assessment not really Joh's fault, more the other player-who-will-not-be-named-later). He was already showing signs of decline when suddenly he was signed to a big three-year contract that has the fingerprints of "forced by the ownership" all over it. I was still a fan, but it didn't seem to be working out, and I was hoping for a turnaround.

The turnaround happened in an altogether suprising way. Johjima walked away from the guaranteed two years' salary to return to Japan, be with his family and play every day. Worries of an albatross contract turned into that all-too-rare feat in baseball: a graceful exit.

When you look at the numbers you see we got more than our money's worth out of Johjima. And now that I see his own sense of honor in the face of imperfect circumstances, I'm happy to have my kids wear his shirt again, just like I still wear John Olerud's All-Star shirt from 2001. Nice job.

Now, if we can start talking to Carlos Silva about just pay ... (Don't tell the player's union!)

Tea Notes

Just some bullet points:

-- Lipton Black Label Tea is actually Not Bad. Not fabulous either, but it might be better than my standard cheap black teas.

-- Teavana's Dao Ren is the king of green teas. They say it's grown in a fruit orchard to take up fruit scents. I think it's grown in a poppy field which may explain its addictive nature. Of course, they're running out of it soon ...

-- Teavana doesn't stock unflavored Rooibos anymore. This wouldn't be a big deal except I just figured out how to make a tea latte that taste just like the Starbucks Rooibos Vanilla from Rooibos + vanilla syrup + half and half AND it's caffeine free. Republic of Tea and Twinings both make OK Rooibos but I want loose leaf whole leaves!!!

-- Got a Dragonwell from the tea festival that looks like little flat green rosemary leaves. It's very good (better be 'cause it's expensive), and it's quite novel to be steeping actual leaves rather than curled up things.

Book Review: The Music of Life

[Pic Link]

This was a nice, short book with some real things to say, yet it still felt a little inflated. The central metaphor is wonderful, and the basic thesis is that life and even consciousness emerges from the physical interactions of smaller parts, that it is more than the sum of its parts and cannot be identified with any single one or type of part. The author is a Nobel laureate for figuring out how the heart beats, that there is no central oscillator but it's a cooperation of small, relatively simple pumps that creates the sophisticated sequence of the heart beat. There's some fascinating truths here, and the author starts out by taking Richard Dawkins to task for his metaphors that genes control everything. They don't. (Although a little later he goes out of his way to praise Dawkins to compensate.)

A section late in the book about consciousness points out how a "brain transplant" would NOT be a "self transplant," that the body is an integral part of the self. The author goes on to suggest that this means there IS no self when you get down to it ( ... but isn't that just returning to the original idea that there must be a small region of self and if you can't pinpoint it to a small part, then it doesn't exist? What about if the self includes the body??). I think the body-mind integration is important and is reflected in the way the Bible insists on physical resurrection, not a "transmigration of souls" or whatever. I think it confirms the self as a physical thing with spiritual dimension, not that it destroys the self. That's because I'm a Christian and the author is drawing parallels to Buddhism. But the bottom line is that this is a place where further conversation can start, and it's a lot more interesting to talk about what this says about the self and consciousness than to follow after Francis Crick or Richard Dawkins attacking straw men all day. Here's to more books like this ... hopefully with a little less padding in the stories and more meat in the conclusions.

Book Review: Mendeleyev's Dream

This one's a history of the periodic table. Since the Weter Lecture I'm writing is about how the periodic table relates to creation, I thought this might have a nugget or two. I think the beginning and the end of the story (the Greeks and Mendeleyev himself, respectively) are done well, but the middle takes way too many detours into alchemy and physics to stay on task. Is it really so bad that Aristotle's four elements were wrong? Weren't they right in some way? And if you're going to bring up Galileo in a book about chemistry can you at least bring up something new about him? There is a pervasive air of "scientific orthodoxy" hovering over this book in which the Middle Ages are just an intellectual backwater (except for THIS exception, oh and that other one, and the other one there ... until the number of exceptions make you skeptical that such a cliche was true in the first place), and little acknowlegement that Aristotle was also "lost" for much of the middle ages, until Thomas Aquinas at least. There's still a lot to be done with the popular science vs. religion cliches. But as for history, this book could have used a little more organization and discipline in the middle ... like the periodic table itself gave to chemistry!

Brendan's Song

I don't think I ever posted the song we dedicated to Brendan back when he was born in January. (It's really an epiphany song which coincides with Brendan's birthdate, but I thought I should post it while thinking of it!) It's available to listen to online at last.fm, just click here and find the black box in the upper-right part of the screen and click on play to listen to "Nothing But a Child" by Steve Earle. (And, um, that video is NOT Steve Earle, click at your own risk.) Here's the lyrics:


Nothing But A Child (Steve Earle)
Once upon a time in a far off land
Wise men saw a sign and set out aross the sand
Songs of praise to sing, they travelled day and night
Precious gifts to bring, guided by the light

They chased a brand new star, ever towards the west
Across the mountains far, but when it came to rest
They scarce believed their eyes, they'd come so many miles
And the miracle they prized was nothing but a child

Nothing but a child could wash these tears away
Or guide a weary world into the light of day
And nothing but a child could help erase these miles
So once again we all can be children for awhile

Now all around the world, in every Iittle town
Everyday is heard a precious little sound
And every mother kind and every father proud
Looks down in awe to find another chance allowed

Nothing but a child could wash these tears away
Or guide a weary world into the light of day
And nothing but a child could help erase these miles
So once again we all can be children for awhile

iTunesU Autumn 2009 Biochemistry

I just think it's cool that if you type in "biochemistry" into the iTunesU search box, you get this link on the top of the first page.

At least, it works that way on my computer. Feel free to listen in. I've changed quite a bit of the "entropy" lecture this year, for example, thanks to my R.J.P. Williams research.

(And, yes, one of my lectures is named after a They Might Be Giants song. I'm hoping people searching for that song will also see my podcast, what can I say?)

How Hard is This Really?

I mean, just talk to your kids. They're kind of important. The kingdom of heaven belongs to such as them. And they make funny noises when you blow raspberries on them.

Here's the article that prompted this thought, although I just read the first part before mentally throwing up my hands in dismay:
http://www.nytimes.com/2009/09/29/health/29brod.html?em

Call of the Year

This is too funny. Usually I find Mariners' announcer Mike Blowers annoying but apparently on Sunday he turned clairvoyant. You need to listen to both audio clips in order to understand what's going on. Oh ... and make sure your volume's turned down for the second clip ...

http://mynorthwest.com/?nid=374&sid=218287

TV Review: The Lost Room

The Lost Room is a 6-part miniseries that showed on SciFi (now SyFy) network, and its real title should be Lost for People Who Don't Have Time for Lost. It's got a similarly interesting premise and of course isn't nearly so convoluted or referential as Lost but in the wait till January for the final season, this miniseries fills in the "weird TV show" slot nicely. And it's only 4-5 hours of watching to commit to. The first hour is actually a bit weak but it really picks up steam with the second hour, when the "rules" by which the several "objects" operate begin to be combined in really interesting ways. The show was like a good comic book, very plot-driven and if anything a little thin on the characters but if it took more time on characters it'd be more than 6 hours long, now, wouldn't it?

Some have complained that it's great till the very end and I can't figure out quite why. The end is a little bit stock, but there's some things about it that are different that I liked. The ultimate "reason" for the strange happenings isn't explained, but it's an open universe. The character arcs are all nicely tidied up, which is really all you should expect.

So -- it takes about as much time as watching 2 long movies, and it's more inventive than most. Highly recommended.

Book Review: Empire of Illusion

All through this book I was trying to think of where I had heard of its author before. Then in the final chapter he admits, "As I was writing my book American Fascists on the Christian Right ... " and everything fell into place. This screed, at times spot on but just as often over the top and vague, was written by the same fellow who used to be a foreign correspondent and now likens conservative Christians to fascists. I'm glad it took me that long to figure out why his views were so extreme, because I'm well aware of his previous work and I may have listened a bit less if I knew he was the type not to really listen to conservative Christians. I'm not all that conservative myself but I am tired of those on the left who will not really listen to them/us. And Hedges is one of those.

So this book is a mixture of easy targets, good honest jeremiads, and old liberal tropes dressed up in the latest news of Spring 2009 when the book apparently went to press. In the past few months things have turned around enough -- while they are still shaky -- that the apocalyptic pronouncements in the last chapter about the coming systemic collapse ring hollow, although, he's right, you never know. I just find the book format to be too unresponsive, and the last chapter itself colors the rest of the book as not taking the long view.

An outline of the criticized institutions:
1.) Wrestling/television/celebrity culture: I thought the comparison of celebrity worship to ancient gods is actually useful and helpful, and there were some things I didn't know about wrestling, but you know, I really don't think the "uncensored" episodes of Jerry Springer are anything but the most extreme edge of TV ...
2.) Pornography: The thrown-away too-old actresses are the angle here, and the absolute abuse that is endemic to the industry. Probably the most-agreed with chapter on my part, although the repetition does get absolutely sickening. I think a stronger theology of sin and the body would strengthen this chapter.
3.) College: Even Berkeley's too hung up on football. Well, there is a reorganization of priorities going on right now, and if it's not a real re-org, colleges will go the way of the newspapers. But I have hope that there's lots of things we do better than anyone else in this area.
4.) Positive thinking: Now that Dan Brown has revealed he is on the side of the "positive thinkers" I am absolutely sure I'm against it. Some useful observations in Hedges chapter but also an easy target.
5.) Politics: By the time he started quoting Nader extensively I started reaching for my David Brooks as an antidote. The good-to-not ratio was way down in this chapter and the citations of Spring 2009 data way up.

So Jeremiads are always readable, but not always right. I really wish this had more about where to go with all this beyond three pages about love tacked on the end. Too many times it doesn't offer an alternative after trashing what rightfully should be trashed and the end is downright alarmist. Hedges, you had me for the first half but then you lost me. Too bad, because I think if you'd stop calling them fascists that the church would agree with you on quite a bit. Up until you get to decrying elites while at the same time deploring pretty much everyone else in politics. Isn't that a bit elitist?

St. Elmo's Fire 30K Feet Up

Patrick Smith in his airplane column on Salon.com posted a link to this picture of what St. Elmo's Fire looks like to an airplane pilot. Check it out!

(He reiterates that, yes, it does actually look like that.)

The Lost Symbol Spoiler of All Spoilers

So I haven't read Dan Brown's new one, The Lost Symbol, but I've read several reviews and can tell you it's probably a valiant effort but will not match The Da Vinci Code in societal impact. Which, um, I also have not read. But in my field you trust others to run experiments and report the results. I've read the reviews of three different reviewers and also the Wikipedia plot summary and that's amusing enough for me.

By the way, Laura Miller's review in Salon.com is by far the best review as in most informative and most appropriately skeptical of Brown's entire philosophy.

Since I think any readers of this blog have better things to do than to read 500 pages of Dan Brown's writing, I just have to pass on the cornerstone of Brown's theory this time, the secret Word of Power that characters are pursuing through Washington DC. So don't read if you don't wanna know. Straight from Wikipedia, here is the Word:

With the night's events over, Peter decides to show Langdon the true Word. He shows Langdon that it is hidden in the cornerstorne of the Washington Monument, and that the Word is actually the Bible. Peter reveals that the true Ancient Mystery is in fact the realization that people are not God's subjects, but in fact possess the capability to be gods themselves. Once they realize this fact, they will open the gateway to a magnficent future.

So Dan Brown reveals his Gnostic roots again. "Go ahead, eat that fruit, you surely won't die, you will know good and evil and will be like him!" This is just as wrong as the Da Vinci Code, but it appears to be hidden so deep this time that hopefully most people will just skate on by it. Still ... sigh ...

Living in a Lego House

Would it be a Bungal(EG)ow?

http://www.dailymail.co.uk/news/article-1210206/James-May-set-live-Lego-house.html

Book Quotes: GKC on Science and History

I just finished G.K. Chesterton's The Everlasting Man, which I've been meaning to read for a long time. It's a response to H.G. Wells's own science-based history of the universe and man. G.K. Chesterton aims to show how man stands out among nature and how Christ stands out among religions. Some good quotes in there, and instead of a review I just went through the trouble of typing them all out (hoping some of the wit will rub off through the keyboard), and so here's my greatest hits:

“I do not believe in dwelling on the distances that are supposed to dwarf the world; I think there is even something a trifle vulgar about this idea of trying to rebuke spirit by size. And as the first idea is not feasible, that of making the earth a strange planet so as to make it significant, I will not stoop to the other trick of making it a small planet in order to make it insignificant.” – GKC Everlasting Man Ch. 1

.

“Nobody can imagine how nothing can turn into something. Nobody can get an inch nearer to it by explaining how something could turn into something else. It is really far more logical to start by saying ‘In the beginning God created heaven and earth’ even if you only mean ‘In the beginning an unthinkable power began some unthinkable process.’” – GKC Everlasting Man Ch. 1

.

“The simplest truth about man is that he is a very strange being; almost in the sense of being a stranger on the earth. In all sobriety, he has much more the external appearance of one bringing alien habits from another land than of a mere growth of this one. He has an unfair advantage and an unfair disadvantage. He is at once a creator moving miraculous hands and fingers and a kind of cripple. He is wrapped in artificial bandages called clothes; he is propped on artificial crutches called furniture. His mind has the same doubtful liberties and the same wild limitations. Alone among the animals, he is shaken with the beautiful madness called laughter; as if he had caught sight of some secret in the very shape of the universe hidden from the universe itself.” – GKC Everlasting Man Ch. 1

.

“For clothes are literally vestments and man wears them because he is a priest.” – GKC Everlasting Man Ch. 1

.

“Among the more ignorant of the enlightened there was indeed a convention of saying that priests had obstructed progress in all ages; and a politician once told me in a debate that I was resisting modern reforms exactly as some ancient priest probably resisted the discovery of wheels. I pointed out, in reply, that it was far more likely that the ancient priest made the discovery of the wheels. It is overwhelmingly probable that the ancient priest had a great deal to do with the discovery of the art of writing. It is obvious enough in the fact that the very work hieroglyphic is akin to the word hierarchy.” – GKC Everlasting Man Ch. 1

.

“Indeed the Book of Job avowedly only answers mystery with mystery. Job is comforted with riddles; but he is comforted. Herein is indeed a ‘type,’ in the sense of a prophecy, of things speaking with authority. For when he who doubts can only say ‘I do not understand,’ it is true that he who knows can only reply or repeat ‘You do not understand.’ And under that rebuke there is always a sudden hope in the heart; and the sense of something that would be worth understanding.” – GKC Everlasting Man Ch.4 p. 230

.

“Father Christmas is not an allegory of snow and holly; he is not merely the stuff called snow afterwards artificially given a human form, like a snow man. He is something that gives a new meaning to the white world and the evergreens; so that snow itself seems to be warm rather than cold. The test therefore is purely imaginative. But imaginative does not mean imaginary. It does not follow that it is all what the moderns call subjective, when they mean false. Every true artist does feel, consciously or unconsciously, that he is touching transcendental truths; that his images are shadows of things seen through the veil.” – GKC Everlasting Man Ch.4 p. 237

.

“The truth is that the Church was actually the first thing that ever tried to combine reason and religion. There had never before been any such union of the priests and the philosophers.” – GKC Everlasting Man Ch.5 p. 243

.

“I mean the primary and overpowering yet palpable impression that the universe after all has one origin and one aim; and because it has an aim must have an author. … Atheism only became possible in that abnormal time; for atheism is abnormality. It is not merely the denial of a dogma. It is the reversal of a subconscious assumption in the soul; the sense that there is a meaning and direction in the world it sees. Lucretius, the first evolutionist who endeavored to substitute Evolution for God, had already dangled before men’s eyes his dance of glittering atoms, by which he conceived cosmos as created by chaos.” – GKC Everlasting Man Ch. 6 p. 294-5.

.

“It is no more inevitable to connect God with an infant than to connect gravitation with a kitten.” – GKC Everlasting Man Ch. 7 p. 302.

.

“We must grasp from the first this character in the new cosmos; that it was larger than the old cosmos. In that sense Christendom is larger than creation; as creation had been before Christ. It included things that had not been there; it also included the things that had been there.” – GKC Everlasting Man Ch. 7 p. 309.

Best Science-Themed Bar and Grill in Boston

Just up the street from M.I.T., and next to the M.I.T. museum (which expressly forebade me from posting pictures on a blog on the ticket, so sorry about that), there is a small bar and grill called "Miracle of Science." This is its menu. If you have to ask what I ordered then you don't know me very well. OK, one hint: It's near to where rubidium should be. :)

Asphalt and Moses

The Dead Sea is possibly the most unique place on Earth. Not only is it incredibly significant historically, but it is also unique in its chemistry: the high salt levels and low sea levels most people know about, but even more so it has large mats of strange microbes living in it, and it produces asphalt, of all things. In fact, there was a lively trade set up between Canaan and the surrounding countries for the stuff. The cool thing about asphalt is that we can date it and place it, and we can see that this trade is very old. We find asphalt went from the Dead Sea to Egypt in mummies dating back to 200 B.C. and may have be traded long before that. Did trade caravans passing through Canaan pick up asphalt as well as the occasional slave (say, one sold by his eleven brothers)?

Exodus describes how the baby Moses was set out on the river in a basket lined with "heimar," probably asphalt just like this. The Egyptians didn't use asphalt for bricks like the Babylonians did (they used stone, or evidently straw-based clay). In Egypt asphalt was used for waterproofing royal baths and making mummies. It would be just the thing for turning a basket into a tiny boat for a tiny boy. Did it require a royal connection to obtain? Did that royal connection also allow Moses' family to know when and where the princess of Egypt bathed? That would be just a conspiracy theory. The certain thing is that the future of Israel was saved with some special chemistry that could have come from near the Dead Sea, just like Israel itself.

(This story from the book Echoes of Life by Gaines, Eglinton, and Rullkotter, p. 261.)

Book Review: Planet Narnia

I read a lot of books this past month, and this is the one I enjoyed most. I've known about it but avoided it for a year or two now, because it seemed like a fanboy kind of book, or a blog post (horrors!). To summarize, in this book Michael Ward proposes that the Chronicles of Narnia has a hidden internal structure, almost a "code" behind it all. That sentence raises the hackles and defenses of most scholars/scientists. It makes it sound like there's a Dan Brown-style conspiracy behind this well-known but also polarizing set of children's books, one step removed from the "Bible Code"-type of nonsense. The amazing thing is, after reading this book, I'm convinced he's right.

Ward knows Lewis inside and out, and uses all his knowledge to cram in tons of information to build his case. No stone or poem left unturned. And the key to it all is Lewis's interest in the planets, both the modern and medieval conceptions of them. I agree with Ward, it looks like C.S. Lewis built the seven books of Narnia around the seven medieval planets, just like he built his "Space Trilogy" around three medieval/modern planets. The Lion, the Witch and the Wardrobe is Jupiter, Prince Caspian is Mars, Dawn Treader is Sol (the sun), and so on.

What makes this work is how it makes things "fit" that never fit before: Father Christmas showing up in LWW (he is "jovial"), all the death and destruction in the Last Battle (it is "saturnine"), the sets of twins in The Horse and His Boy ("mercurial" reflections), for example. The really cool thing is that his whole point is that science, mythology, and the worship of the true triune God are all fused and used together in C.S. Lewis's work. I did not expect to find much in this book for my Weter lecture, but I found much after all, thoughts that go to the very heart of what I'm trying to do with the lecture. So ... wow.

This book started off with me evaluating the case. It ended up with me re-evaluating (positively) my impression of Lewis. I had always had the impression, compounded by Tolkien's own dismissive quotes, that Lewis threw together the Chronicles in a slapdash fashion. (After all, Father Christmas?!) I had always thought of myself as a "Tolkien" kind of guy more than "Lewis." The best review I can give of this book is that now Lewis makes complete sense to me ... and I'm not sure what "kind of guy" I am any more.

Book Blurbs

Well, mostly placeholders to remind me that I read these when I look back on the year. All three will be cited in my lecture, I'll tell you that.

Echoes of Life: A book on biomarkers and geology that tries to tell the personal stories behind the scientific stories but is too technical for the normal reader. Which is too bad, because this is fascinating stuff and great examples of chemical reasoning. The problem is the author is a novelist who used to be a grad student in the area. So while it's well written and precisely written, it is not clearly written. Nonetheless it is the perfect book for me at this point, I just hope it sells more than the one copy I got through interlibrary loan ...

State of the University by Stanley Hauerwas: I think I can actually "read" Hauerwas in real time now. Always challenging, and now I'm beginning to see the solid Scriptural basis to many of his arguments I have a harder time disagreeing with him. Reminds me of Scott -- WWSD? And once in a while laugh out loud funny. That reminds me of Scott too.

The third book deserves a "real" review post of its own, it's that important. More on that to come.

Weter Lecture Announced

Click here for the Weter Lecture announcement, proof that yes, this will really happen, February 2, no less. A short synopsis follows. I've been reading, reading, reading, and have found that C.S. Lewis and Stanley Hauerwas are always good at giving me both quotes and things to ponder.

Quick Thought on Infinity for the Day

(From Richard Swinburne's talk at Oxford last June:)

One of the primary reasons scientific atheists are just that (atheists) is that they believe that God is an extra, needless layer on complexity overlaid on the natural order. But in some ways they need to brush up on their philosophy, because they're combining categories. Instead of allowing a God with infinite power, they postulate infinite universes in the form of the multiverse (or something else like that). The problem with this is that infinite power is simple, but infinite universes are complex. Power is filling to a maximum of ability or possibility, but universes are additive in their complexity. This kind of philosophy is why you can say things like God is the simplest kind of "person" there could be. In some ways, infinity is simplicity, if the infinite being is very much "other." If you're reaching infinity by just multiplying the current universe by infinity, that is the truly needlessly complex thing!

Let me quote the question Swinburne started his lecture with:
Q: What do we have that God does not?

Give up yet? It's a related topic ...

Book Review: The Best American Spiritual Writing 2006

Yes, this is one of those anthologies, but I think of it as having a friend who reads a lot of magazines tell you which articles she liked best. Somewhere since 2000 they changed the adjective from "Christian" to "Spiritual," but 75% of the writing is still Christian or general theistic. A few short essays deal with Buddhism or the Norse Gods, and one detailed story describes a traveler in present-day Afghanstan going to the place where the two huge Buddhas were destroyed by the Taliban in March 2001. Malcolm Gladwell describes Rick Warren's Saddleback Church. John Updike has a haunting poem about the Cathedral at Rheims. I got a few pages here and there to use in my Weter Lecture, and a list of rules given to those who paint icons for "how" to paint. I'm going to put that up next to my desk for when I write.

Book Review: Tolkien's The Legend of Sigurd and Gudrun

http://www.washingtonpost.com/wp-dyn/content/article/2009/05/04/AR2009050403462.html

I was wondering a few things as I sat watching the 18 or so hours of The Ring Cycle recently. I was wondering what the source material was for these stories of heroes, dragons, fallen goddess brides, and betrayals, what Wagner had changed from it, and what someone else with a different worldview would make of that. Especially someone with a passion for Norse legends and a knack for storytelling, say, J.R.R. Tolkien. I'd love to have some of Tolkien's lectures on these stories. Maybe even a translation where he puts everything together.

As I was wondering that, this book was sitting on my shelf. I knew it was some of these things, but in actuality it was all of them.

It was also very dense reading. You have to see it to believe it. Most lines on the page only have four words, and so each page is a column of text with white space on either side. Don't be fooled: every word counts, more so than anything I have ever read. This writing is the neutron star of density. Tolkien follows the Old Norse poetic style of matching up the beginnings of words rather than their ending and is very good at following it.

I liked Seamus Heaney's Beowulf. But I think I actually like these poems more. Tolkien describes the source poetry as "flashes of lightning" and I think he captures lightning in a bottle here.

Just like the Ring Cycle, it's not easy going, but it's very rich and rewarding.

Using Music to Run Your Scientific Instrument

This is a neat one. Many scientific instruments have a complicated setup to move liquid through tangled channels. After all, your house has all these pipes to move water around, most instruments are like that on a small scale. The trick is how to push the water around those complicated paths in the way you choose, on such a small scale. So far the most useful solution has been to make the "floor" of the pipes with rubber and run little air hoses up to the floor, and when you want to close off a pipe, you send air pressure down that hose. It works OK but has it limitations, especially because it's hard to make an instrument smaller than, say, a washing machine with this setup.

So, what if instead of air, you could use music? The idea is to use different tones to move the droplets around the pipes. Say, pipe 1 responds to C natural, pipe 2 responds to E and pipe 3 responds to G. Play a G and the drop will move in pipe 3 only. It's not clear yet to me, but I think you may be able to use chords too. The cool thing about chords is you can superimpose notes and send them across the whole setup, and transmit complicated information that way.

This may allow many scientific instruments to be as small as a handheld, like a Star Trek tricorder. An iPhone that you sneeze into, it moves the drops around and analyzes them to tell you if you have the flu. And they will literally run on music. No word on if the iTunes software will be required.

Click here for a press release with a video of drops of water moving around to the U of Michigan fight song.

Still Ringing in the Ears

Since last Saturday night I have watched a grand total of 2.5+4.5+5+5.5 = 17.5 hours of opera. This was my third time seeing Wagner's Ring Cycle, and my first since finding a complete box set of the operas on LP at the Library Book Sale (for $4!!!!). It gets better each time, and rewards the effort put into it. Not only am I beginning to identify the major musical motifs Wagner uses for different characters or emotions, but I'm also connecting the dots between this and Tolkien (and, a little less, C.S. Lewis and Neil Gaiman). Tolkien's curt dismissal of Wagner's work is often quoted ("Both rings were round and there the resemblance ends" or something like that). But there is an important way in which Tolkien's work is a direct repudiation of Wagner's, each a collection of four stories based on Norse myth. Tolkien writes during World War II and sees a Germany saturated in Wagner's myth, to the point that Hitler killed himself while listening to Gotterdamerung and his death was announced with Siegfried's Funeral March. The importance of pity, and not killing, and not being strong, is perhaps THE underlying theme of Tolkien, and it stands in direct opposition to Wagner's need to end with basically killing everyone.

Yet there is a lot of beauty and genuine emotion expressed in Wagner better than anywhere else. It helps me that C.S. Lewis liked Wagner quite a bit! What's funny is how, as a parent, you project a bit onto what's going on for the sake of your children rather than yourself. And there is a lot of parent-child emotion in The Ring, that's one of the reasons it's better than, say, Tristan und Isolde or Wagner's usual focus on just the romance.

Another interesting connection is, if Tolkien was reacting to Wagner, my favored author Tad Williams was reacting to Tolkien! So things continue ... who will react to Williams?

Parables and Protein Crystallography

[picture link]


To find the structure of a protein, once you purify and stack it up in an ordered crystal, you shoot X-rays through it. X-rays are important because they are spaced the right distance apart that they interact with the electron clouds in the protein. The electrons cause the X-rays to shift and coalesce into discrete points on the other side. By measuring the intensity of the X-rays at each point you can mathematically reconstruct the shape of the electron cloud. The interesting thing about this is that every point in the X-ray pattern contains information about the whole electron cloud, but you have to take tens of thousands of points together to be able to figure out the exact shape of the electron cloud (and therefore of the protein).

So look at that X-ray pattern above. Each point contains information about the entire protein. But you'll get nowhere if you try to draw a protein based on one, or even a few, points. What you'll get will be too fuzzy. The more points you collect the sharper in focus your picture will become.

It's the same way with the parables told by Jesus about the Kingdom of God. Each is a point: a picture, with a lot more texture than the points above, but still, just one picture. To see the Kingdom of God through these parables, you need to take them all together and somehow integrate them (this is the work of the Spirit). By looking at all the parables at once, suddenly the Kingdom of God comes into bright focus. It is a mustard seed, and a pearl, and a woman who finds her quarter. It is all these things and more. The more your thinking is shaped by these stories the more the Kingdom of God will structure your very thoughts.