Thursday, December 24, 2009

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.

Wednesday, December 23, 2009

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.

Sunday, December 20, 2009

Book Review: What the Dog Saw

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.

Thursday, December 17, 2009

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:

Tuesday, December 15, 2009

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.

Monday, December 14, 2009

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.

Friday, December 11, 2009

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.)

Thursday, December 10, 2009

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."

Tuesday, December 8, 2009

Could Your Car Run on Vitamin C?

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!).

Friday, December 4, 2009

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.

Wednesday, December 2, 2009

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.

Tuesday, December 1, 2009

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!