Friday, August 29, 2008

Science Myths

History is starting to frustrate me. That's because for every easily told story about science history there seems to be a deeper, more confusing, less scientifically orthodox explanation. And this is for four major personalities in the history of science discussion.

I've heard:

1.) Galileo's imprisonment was more about politics than geocentrism. Galileo also remained faithful to his idea of God, in his way.

2.) The debate between "Darwin's Bulldog," Thomas Huxley, and Bishop Samuel Wilberforce about evolution did not include many of the most quotable parts to it -- those were made up or exaggerated after the fact for effect. (Side note: I was able to visit the room where this debate took place, which is now a storage room at the Oxford Museum of Natural History. It wasn't as big as I had imagined, meaning I had probably exaggerated it in my own mind!) Huxley may have wanted to promote warfare between science and religion because there were too many of the clergy doing science! Back then before grants and all, if you wanted to do science you needed someone to give you money to live on. A few rich patrons supported science, but the biggest patron of them all, the one that gave people money and time that allowed them to ask questions about the natural world? It was the church. Huxley wanted to sever that connection so he could be a scientist without being supported by the church. Looks like it worked.

3.) When Copernicus placed the sun at the center of the universe, it did not imply to everyone that humanity was dethroned. The center of the universe wasn't considered the best place to be -- after all, it's precisely where Dante placed Hell. At the time people were worried because placing the sun at the center of the universe dethroned the SUN! (An excellent talk on this topic, one of the best I've heard all year, is available here in mp3 format or as text here.)

4.) And now, there's even footnotes to the story of Giordano Bruno, the philosopher who was (according to CW) burned at the stake for suggesting the universe was infinite and that there were other worlds. A book reviewed here says he too was more a victim of politics and bad personal choices than scientific censorship. The description of the character from the book sounds like some people I've met: someone who's looking for a fight and then uses science as the weapon. That some of the science ended up being right is actually beside the point. He wasn't burned at the stake for having heretical ideas; he had heretical ideas because he was a misanthrope and was burned at the stake for that.

So, not being a historian and being unable to fully investigate these four claims, I'm left with the sense that some of them are right and some of them are wrong. But even if only half of these are right, there's still some major myths being taught as truth in science class. I'm not talking about evolution, I'm talking about the place of science in the history of ideas, and I think that is more important than the specific biological mechanism of creation.

Chili Peppers are Good for You

Not only is the capsaicin in chili peppers anti-bacterial, it's also anti-fungal and can increase metabolism by changing the shape of a protein pump in the muscles, making it release energy as heat instead of pumping calcium. Is there a hot-pepper diet on the horizon?

Thursday, August 28, 2008

Book Review: Ghostwalk

Ghostwalk by Rebecca Stott is a semi-supernatural semi-thriller about Isaac Newton and alchemy. One of the revelations of the novel is that Isaac Newton spent much of his life being an alchemist, not really being a scientist. I'm fascinated by this man so I was hoping this book could shed light on him. But it's not really about him. It's about a semi-historical argument that someone committed a set of 5 murders in Cambridge at the time Isaac Newton was there. Trying to be all Da Vinci - codish with real history. And it just doesn't fly.

The author's strategy is to try to recreate alchemy by doing what alchemists did in her writing: by juxtaposing things, allowing time and characters to bleed into each other, etc. It ends up doing what most alchemy did: it makes a big mess.
The accuracy of the history is above par for this kind of novel, and the depiction of a 21st-century research scientist is passable, although I really doubt a bigshot research scientist would have the time to do what he does in this novel while keeping a lab running! Some passages actually work well in spots, and I found some insightful connections and vivid images.
But the dialogue can be terrible. What's supposed to be a white-hot clandestine relationship just seems self-absorbed and pretentious to me. The historical mystery is solved not by deduction but by turning to a medium for connections to the spirit world. The point can be made that there are things outside the usual definition of science -- but it needs to be made better than this.
Maybe part of the problem is that Newton's theology is downplayed. Sure, he wrote a lot about alchemy, but he wrote a lot about theology too. It's just as much of a distortion of his character and his history to downplay that as it is to downplay his alchemical interests.
Is Newton just too big of a man for one person to describe? I don't think I've ever read a truly convincing description of his entire life. I just don't "get" Newton, and maybe we never will.
James Gleick's book on Newton is better than this, as is Neal Stephenson's Baroque cycle (I've only read the first book but it covers the same timeframe as this). Ultimately Ghostwalk is just a silly story with an unusual historical accuracy that ultimately doesn't change or illuminate anything.

Thursday, August 21, 2008

My Three Sons ... What are the Odds?

I finally found an article that doesn't just assume that each time you have a baby there's a 50/50 (or technically 51/49) chance that you'll have the same gender again. This is a tougher search problem than it sounds, because so many science explainers take the easy way out and refer to pregnancy as a coin flip. Obviously the previous coin flips don't inform later ones. But how do you know birth is a coin flip? I suggest that the immune system + reproductive system + parental choice + environmental factors = something more complicated than a coin flip, something with memory potential. SO ... I finally found this article, which references an earlier one done by actual statisticians:

It turns out there may be a slightly increased chance (up 2 to 6%) of having a fourth boy if you already have three. Maybe not the same for girls, interestingly. I'd guess if we have another child, there's a ~55% chance of having a boy, based just on this survey of actual family birth orders. And that sounds about right: nothing too different from the "coin flip" explanation, but something revealing a system that's more complex and interesting. Personally, I wonder if my NKG2D or MICA immunoproteins might not be involved?

Introducing Baby #3

... Now at 20 weeks and counting, we got an ultrasound of our third baby boy today:

Wednesday, August 20, 2008

A Natural History of Internet Trolls

This is a highly amorphous post about trolls.

It's been a while since this NYT Magazine article came out ...
... but I've been thinking about it since then. They don't live under bridges but between servers. Their ethical dilemmas concern whether it's OK or not to hack into an epilepsy website to put flashing graphics on it to induce seizures. I'm fascinated by the alternate morality of this world, and what kind of invisible assumptions they base their actions on. It's not always possible to take them at their word but sometimes you have to read between the lines. Then again, sometimes they flat-out say what they mean.

Trolls have absorbed hierarchies based on strength and weakness, and do seem to have a fundamentally Darwinian midset. They conceal their own weaknesses and put on shows of strength to cow other people into respecting them. And it's all about virtual strength. About the strength to ignore what other people say about you, to be self-sufficient, to take a joke however crude or rough. No man is an island but these trolls would like to be.

The NYT article is interesting but really not deep enough. It's mostly about interviewing them and taking their words at face value. But there's really a spectrum of trolls online. There's one baseball website that I like the main page but never read the comments because it's just a lot of doctored photos and loud obscenities flying back and forth. Trollmanship in training, focused on a baseball team. I really don't see what the point is, but the full-fledged troll grows out of this environmental free-for-all. And none of it works on a large level. It needs to be a niche ... it takes a village, but if that village gets too big it falls apart. Troll communities are important to them as a place of combat as well as refuge; they aren't that individual after all.

If you meet a troll in the wild, don't stare him in the eye. Just walk on by, slowly.

What happens when a troll (or troll-ish strategies) moves into another environment? Did Ernst Haeckel develop troll-like characteristics in certain arguments? Does Richard Dawkins? Does Ken Hamm? Does this poison the well for discussion? How do you detoxify the environment once a troll has passed through? (Sulfur-chelating compounds?)

And why is it so easy to absorb the normal model of strength and weakness, of talking big and pushing back, without even trying, but it takes a person like Jesus to show us what God is really like? (And then 30 minutes later stuck in traffic I've forgotten again.) Why is the creation so different from the creator? Now we're back to Genesis 3-11.

In any case, thinking you're being all original, and successful, by being strong and powerful is the trolls' biggest self-deception. It's the most common, non-original thought of all. And ultimately, the most successful troll is boring. You've been able to rent a Rolls-Royce for your interview with the NYT reporter -- good for you. But what do you really think about that? Why do you want to impress the reporter that badly when you don't own your own bed? Can't tell, you're too busy pushing people away with your words.

There's a lot going on here. Sin, strength, the grain of the universe, what we're made for ... there's something in the story of trolls that's fundamentally modern and ancient. It's about what really matters and how to live life together when you come down to it. Something to chew on at least.

Friday, August 15, 2008

Video Sermons

Why is the central charismatic preacher so important for having a big church? It doesn't help the church and it weighs stress on the preacher disproportionately. Slate had an article about the "video franchise" services that are popping up across the country:

And as an engine of church growth, video preaching poses problems for even the most ardent evangelicals. Some fear it will allow well-known pastors to swoop into new territories and roll up struggling locally led churches while rolling over smaller ones, especially those tied to mainline Protestant denominations, such as the Presbyterians and Baptists, that are already losing adherents to nondenominational megachurches—and talented pastors to other careers. "Where does a man or woman who feels called to preach get practical experience if their local church is a video venue?" says Bob Hyatt, founder of the Evergreen Community, a small evangelical church that holds services in two pubs in Portland, Ore.

Saddleback Church's Rick Warren, perhaps the best-known megachurch leader in the country, has said for years that he never broadcast his services on television for just that reason. But he has evidently softened his stance: This spring, Saddleback opened the first three of 10 planned video venues in and around its Orange County, Calif., home. "We're not reaching out because we need to be bigger, we're reaching out because more people need Jesus," the church's Web site says. Try telling that to the small-time minister when Mr. Purpose-Driven Life comes to town.

And it's not just a problem for other pastors. In fact, says Shane Hipps, author of The Hidden Power of Electronic Culture: How Media Shapes Faith, the Gospel, and Church, using video goes against a critical tenet of Protestant faith: the priesthood of all believers. Instead of a real experience, it offers a mediated one that inherently puts the pastor in a position of greater power over the masses. "It's actually undermining their theology," he told me recently. Hipps, who worked in advertising for Porsche before entering the seminary, says the small Mennonite community he leads in Glendale, Ariz., asked him to consider "going multisite," as it's called. He refused. Even podcasting his sermons makes him uncomfortable. He started doing it for the benefit of elderly members who couldn't make it to church, but a year later, his own minor celebrity has helped him acquire 6,000 subscribers.

The bottom line is that people keep coming to these video franchises, and as long as that's our criterion we'll keep offering them. That is a good thing, because different people come to these different services. Our church misses the "video cafe" we used to have because it allowed us to set the service up like a coffeehouse and dispense with things like pews. Many people were more comfortable with that. But why as the years go by does it seem like my church is focused more and more on that one central speaker? Is the problem societal and there's nothing to be done about it? Or can something change it?

I don't know, so I'm asking.

Tuesday, August 12, 2008

Book Review: The Cell's Design: How Chemistry Reveals the Creator's Artistry

[Note: I have been asked to review this book by the American Scientific Affiliation journal Perspectives on Science and Christian Faith. This is a first draft for an eventual published review, so if you post comments they can help me refine/expand!]

The Cell's Design is both new and old at the same time. It represents a new line of argument for the Intelligent Design hypothesis, and yet the argument itself is as old as William Paley's Watchmaker Argument. Fazale Rana, vice-president at Reasons to Believe and co-author of Origins of Life with Hugh Ross, describes his strategy in the preface: "Instead of arguing for creation by relying on the perceived inability of natural processes to generate life's chemical systems, this approach frames the support for intelligent design in positive terms by highlighting biochemical features that reflect the Creator's signature." Rana uses "Biochemistry as Art" as a consistent metaphor for design throughout this book, beginning most chapters with a famous painting and inventive links to a school of art. Often "Biochemistry as Engineering" is used as a secondary metaphor, with analogies drawn to quality assurance steps in manufacturing and other similar processes.

As a practicing biochemist, I welcome this change in strategy and tone from the increasingly narrow confines of the Irreducible Complexity argument found in Michael Behe's Darwin's Black Box (referred to passingly but approvingly by Rana). The complexity of DNA Polymerase III, for example, deserves our admiration, as do other complex biochemical processes. As much as half of this book is spent explaining these biochemical workings for an audience assumed to have no prior experience with biochemistry. As instruction, it is adequate, although a book centered around the beauty of nature should itself be beautiful, while the cartoons depicting these processes are simplified and drab. Standard biochemistry textbooks convey the complexity of these machines better, although for a different audience, as does the online video “The Inner Life of the Cell.” The level at which Rana describes biochemical mechanisms seems chosen to support the underlying argument, which compares biochemical assemblies to cogs in a watch. This is most easily accomplished by depicting the proteins simply, minimizing their fluid nature. Most importantly, this depiction elides the fact that all these proteins are polymers of the same 20 amino acids, in every species, on every continent, a fact that allows for adaptation and transformation.

Often Rana’s arguments boil down to describing how molecules work and calling it “fine-tuning” -- when it very well could have been simple adaptation to available conditions. Chapters include discussions of minimal genomes, assembly of protein machines, production of proteins from DNA, gene structures and organization, membrane structures, and rebuttals to previous claims of poor design. A few strong arguments are mixed in with weaker ones. The speed of the development of the genetic code is indeed astonishing, occurring just about as soon as the Earth cooled enough to support life. The finding that DNA replication machinery may have 2 origins instead of one is also "too wonderful for me" to fully describe. But maybe it evolved twice – that is too quickly glossed over, as is the counter-argument that out of millions upon millions of organisms, we can reduce DNA polymerases to only 2 possible ancestors.

Chapter 11, on evidence for convergence of biochemical function, is a prime example of the missed opportunities in this book. Several fascinating examples of convergence are listed, but in a list that tells little more than the titles of papers that could be obtained from a perfunctory PubMed search. Stephen Jay Gould’s argument that evolution is contingent is recapped and rebutted, but the ideas of Simon Conway Morris, who has made a career out of collecting examples of convergence, are not mentioned. What could be a strong point for the book becomes little more than a laundry list.

To Rana’s credit, some alternate evolutionary explanations are described, such as in the case of the formation of the genetic code. Most times, however, possible evidences for common descent and divergent evolution are not included. The most complex examples of biochemical machinery are cherry-picked and described in detail, while similar, simpler prokaryotic versions that accomplish the same task are omitted. Much is made of the precise location of a few specific amino acids for protein function, while it is left unsaid that these crucial amino acids are only 1-2% of the total, while many others can be changed without significant loss of function. Overlapping genes are emphasized as evidence of deliberate design, while the fact that these genes are a tiny minority of cases, often at the very ends of genes in genomes under extreme pressure, is left unsaid. No mention is made of the endosymbiotic theory for formation of mitochondria, although that event would hold several possibilities for discussing artistry, theology, and the methods of a creator.

I would like to know what specific predictions are made by Rana’s model of creation, in which separate species are designed and accumulate only deleterious mutations over time. Why are bacterial and human polymerases so similar if they were created separately? Why are there no designs that are clearly impossible without a Creator, such as a species that uses 20 unique amino acids or a different genetic code? (Surely not everything must be optimized exactly the same exact way for life to exist!) What phylogenetic patterns should be deduced if mutations are only harmful, reducing proteins from an optimized starting point? What old, optimal proteins can you identify, and what stepwise progression downward is observed?

The wonder of biochemistry and what it may reveal about the Creator is indeed a worthy topic, and Rana often tells us how elegant and efficient these protein machines are. But if it is a possibility that the Creator chose to form a universe where all life sprang from a single point, and one in which chemical changes could cause life to adapt itself to the world around it over millennia, it does not substantially decrease the wonder of biochemistry, which is the main point of this book. In fact, if He chose to do so through chemistry rather than direct manipulation of atoms, that is a more elegant and efficient solution than having multiple, directly manipulated starting points. It also would give a book like this more to say if the evolutionary processes could be detailed. Such arguments would be more aesthetically satisfying and would reveal a creator more worthy of praise.

As a statement of biochemical wonder, this book is a step in the right direction. As scientific discussion, it is largely inadequate and slanted. Evidence of this can also be found by counting the promotional quotes inside the book’s cover: all are from ministers, none are from scientists. I hope other scientists will follow Rana’s lead and develop more substantial books about the wonder of biochemistry in creation, while remaining open to all possible techniques by which the Divine Artist may have created.

Monday, August 11, 2008

Book Review: The Invention of Curried Sausage

How to describe this book? It's not a cookbook. It is history, but it's more about the end of World War II than curry or sausage. Here's the search terms from Amazon:

Key Phrases: equestrian badge, curried sausage, squirrel coat, Lena Brucker, Adolf Hitler

And yes, those are good search terms for the book. The story, told by Uwe Timm, is a surprising combination of these diverse elements. It opens a window on civilian life as Germany transitioned from wartime to post-wartime. I can quibble with the plot's depiction of marriage, or telling the truth, or a number of different things, but it's not really about that: it's about being in a country that's falling apart and what it takes to start to put things back together.

For all the war, and dark subject matter in general, this really is a surprisingly light book. The Holocaust is mentioned in a few particularly stirring pages but mostly separated from the story itself. It's also a fast read with plenty of white space, yet still it took me more than a week to complete. It was a surprise nominee for a 100 Best Books list, and while it probably isn't on my 100 Best Books list, I can understand it being at least on the 100 Good Books List.

Thursday, August 7, 2008

Music and Natural Theology

I've been waiting for the audio files for the Beyond Paley Natural Theology conference I attended in June to be posted, and it's getting close to two months and no results yet, so I thought I'd just post a few thoughts on what was my favorite talk there, by Jeremy Begbie titled "On the 'Naturalness' of Natural Theology: Learning from Rameau and Rosseau on Music." It sort of snuck up on me, because it was about comparing Rameau and Rosseau, and I didn't know that Rameau was one of the theorists who set up modern music, I just thought he was some random French philosopher. Once the comparison was made, it wasn't just a "compare and contrast" talk, but much of the talk focused on music and natural theology, and made fascinating points left and right about the relation. It makes sense, because music is so scientific at its heart, but I hadn't heard the two put together so well before.

One point Begbie made near the end: Objects must occupy locations, but different notes can occupy the same space, forming harmonies, yet remaining distinct and different. This brought to mind the Bose-Einstein condensate, in which if you get boson particles cold enough, they will collapse into an overlapping, big atom-like condensate. This had been demonstrated with rubidium: imagine overlapping rubidium atoms, like a chord! And the natural theology part of this is that this must be like the Trinity, or like the body of Christ in the church today.

That's just one sentence from the talk. If the talk is ever posted, it'll be here:

Tuesday, August 5, 2008

"Designing Proteins" Talk Online

So the ASA convention in Oregon kept me busy and away from my family all weekend. I got to present my research along with some of its theological implications. Met a lot of very interesting people from all over, all scientists and Christians. I may blog more about the goings-on of the weekend in a day or so, but for now I noticed the web implementation of the conference is very very fast, and the mp3 of my talk titled "Designing Proteins: The Creative Potential of Enthalpy and Entropy" is already up. If you'd like to listen in here it is:

Fast-forward past the first few minutes where they recorded the audio as I struggled to juggle laptops and VGA connections. I'm not sure how much sense the talk will make without the pictures ... or even with the pictures! The Q&A was fun too. (Sorry I was too nervous to remember to repeat the questions for the mike!) All talks are online, which is great because I can go back and listen to the talks I wasn't able to hear because often three talks are going on at once (or you're having a great conversation with someone over a meal and ... well all of the sudden the talks have been going on for half an hour already!).

Rest in Peace Aleksandr

Aleksandr Solzhenitsyn was as inspirational, then as annoying as any prophet can be. There's no way he was right on everything, but when he attacks you, you need to listen to him, even if you don't agree. And a small episode from his life has implications for historical first-century studies. This is from his obituary in the New York Times, via the Freakonomics blog:

At Ekibastuz, any writing would be seized as contraband. So he devised a method that enabled him to retain even long sections of prose. After seeing Lithuanian Catholic prisoners fashion rosaries out of beads made from chewed bread, he asked them to make a similar chain for him, but with more beads. In his hands, each bead came to represent a passage that he would repeat to himself until he could say it without hesitation. Only then would he move on to the next bead. He later wrote that by the end of his prison term, he had committed to memory 12,000 lines in this way.

[END of quote -- sorry, Blogger's block quote tool won't undo itself ... ]

I mention this because of the debates about oral tradition, and how accurate the gospels could be about something that had taken place decades before. Well, if some device was available to organize the stories in the people's minds, like the bread or beads, they could do a large amount even if they were brought up in the 20th century. In older times when you'd rely on this kind of memory more, I'll bet you could do away with the physical bread/bead reminder and just remember the stories. Not to mention, look at Mark's gospel: short stories a few sentences long, like beads on a string. Then the gospel writer would be putting the stories into a whole, but the stories could be accurate, down to the very words. So oral tradition could preserve Jesus' words accurately for a long time. It's not like a game of "Telephone" if the words are important to the people passing them on.