Friday, November 27, 2009

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.

Sunday, November 22, 2009

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!)

Monday, November 16, 2009

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

Thursday, November 12, 2009

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?

Tuesday, November 10, 2009

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 ...

Monday, November 9, 2009

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

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.

Thursday, November 5, 2009

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.