Thursday, June 28, 2012

Starry Starry Night, All Fall Down

Not only do you get to watch dominos fall, but you see the sheer amount of effort involved in setting it up. The 3-D effect of some of the swirls is a really nice touch:

Wednesday, June 27, 2012

New Protein Synthesis Video

This is a video of the steps in the assembly of the ribosome and the making of a protein, done with a certain undeniable style and exciting music. Plus it's only a minute long. What's not to like? (Protein Synthesis by Nuk Vikolic)

Protein Synthesis from Vuk Nikolic on Vimeo.

How Death Changed

I've watched a lot of operas and read a lot of Edgar Allan Poe (minor fact: my first publication was about him), so in my mental landscape there are a lot of deaths by tuberculosis. But of course, TB is not high on my list of worries for my kids. Ever wondered how these worries changed from 1900 to 2000? Here's a nice graph that spells it out by causes of death over time, edited by the Washington Post with original data from The New England Journal of Medicine. No wonder so many climactic arias involve TB.

For the more data-inclined, the NEJM has an interactive chart that shows how things changed decade by decade. (Notice the huge 1918 flu spike.) Can we project from this? Accidents may be going up, and the disease I first find that's increasing is Alzheimer's, which involves protein folding and is somewhat close to my current research. Also, chronic airways diseases, still going up. This chart contains the other point that cancer is actually going down, although barely, and heart disease has a steeper downward slope. There's lots more to find, and that interactive chart is a nice way to look at the data: I'd say have fun with the data, but that seems kind of weird when you're talking about causes of death.

Tuesday, June 26, 2012

Can You Tell What This Is?

This might LOOK like a brain, or perhaps a nicely parted head of hair, but it's not. To find out what it is, and for more amazing pictures, check out this link. I keep thinking of Moses and the Red Sea for some reason.

Monday, June 25, 2012

Anatomy and Physiology, LEGO Style

If I was an artist, I think I'd make something like this as my art. But I'm a biochemist, so I'll just post a link to pictures of how these sculptures were made. I especially like the endoskeleton makes sense in a LEGO-logic kind of way.

Waiting for the LEGO Radiology Facility now.

Saturday, June 23, 2012

Darwin is Not Dawkins

I just found this article by Denis Lamoureux in the latest issue of Perspectives on Science and Christian Faith, titled "Darwinian Theological Insights: Toward an Intellectually Fulfilled Christian Theism—Part I: Divine Creative Action and Intelligent Design in Nature."

It wins the triple crown: it makes a provocative point, it makes a useful point, and it does it with panache. Oh, and I think it's full-on right. I tried to come up with a one-sentence summary but instead I have three (a haiku?):

Charles Darwin was ambivalent about faith, he was not anti-faith.
Charles Darwin was an agnostic, not an atheist.
Charles Darwin was open to design, and Richard Dawkins' interpretation of Darwin is a cherry-picked portrait that ignores the ambivalence.

I also find it interesting that Lamoureux, in one sense the farthest thing from an Intelligent Design advocate, is insisting on using the word "design" to describe the good organization in nature. It's almost like Lamoureux is saying "This is a song ID Proponents stole from Charles Darwin. We're stealing it back."* I like that.

* A U2 reference. Google it with "Charles Manson" and "the Beatles" instead for the original context. (Guess I'm cherry picking?)

** Yes, three posts on a Saturday night. This is how I choose to use my Saturday nights. That reminds me of an old Bloom County comic that I won't bother making into a fourth post because that would be silly.

*** Lamoureux presented some of this in a talk at an ASA meeting with a similar title. Those itching to read part II might hunt that down in the meantime.

Colbert vs. Krauss

The reason why Stephen Colbert's TV persona works so well for so long is that sometimes he can go places others can't with it. Ironically, it takes the false personality to get closer to the truth. That's kind of a serious beginning for what is really a very funny clip. But those with ears to hear will notice in the final line a very serious and very old theological quotation (I associate it most strongly with John Scotus and technically it's a statement of apophatic theology). Pretty heady stuff, and like a lawyer in argument how he gets there is brilliant as well (makes my previous note on this blog about Krauss seem like, well, a quickly thrown together blog post):

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Book Review: Jerusalem

If you've wondered what it would be like to live in Jerusalem for a year, especially as an American father with young kids, this book will answer your questions better than text. As a graphic novel it can convey the different scenes with a few lines (conversion rate, 1 picture = 1000 words?). Delisle has a nice way of conveying the sense of a place with a minimum of detail, and I am fully convinced that I know what it would be like day in day out in that unique place. Not "holy" place -- Delisle is an amiable atheist and has only an academic interest in the myriad of sects and sectarians he encounters -- but he is more committed to journaling the experience than processing it for us, and it's what his eyes see that conveys the most. Although the result is somewhat superficial (and ahistoric!), I still feel like I've been on a few urban hikes through the area, and that itself is worth the price of admission. A few of the excursions stand out, especially his visit to the Samaritans and a series of contrasting tours he takes to the same place with ideologically opposite tour guides, and it might be nice to have those excerpted somewhere because this book is long, but I personally enjoyed every page.

Friday, June 22, 2012

Genetic Evidence for the First Temple?

Some Ethiopian genes look suspiciously like Israeli genes. And the shared genes appear to be 3000 years old. Just about the time a certain Queen of Sheba and her entourage visited a King Solomon, according to an ancient text or two. It's a small thing, but it's very interesting.

Does that mean that we can identify some of Solomon's genes? This is like some kind of weird mash-up of Raiders of the Lost Ark with GATTACA.

Thursday, June 21, 2012

Alien vs. Tron

The big question that most movies should set about to answer is, how can I make this experience worth 15 bucks (and 2.5 hours)? Movies that answer that question well and artfully are movies that I'm happy with. The biggest problem with Prometheus is that it set itself up to fail on this question by trying to make itself out to answer philosophical questions, bigger questions than a movie can answer. So the biggest problem with Prometheus is the ancient Greek problem of hubris. Funny how that works.

For me, this movie was worth it just to watch, and to explore a new world, and to find out some smidgens about how them nasty Aliens came to be. As such, it was well worth the 15 bucks. If only Ridley Scott and the writers hadn't made such a big fuss about how this wasn't really an Alien prequel, it was a separate movie, it was different and it answered big questions, etc. etc. etc. I think most negative reviews come from the expectations they set up for themselves. This movie isn't much more philosophical than any of the previous movies. It's about exploration, not philosophy. It may have some interesting things to think about in terms of human creation and mothers and pregnancy and things like that, but the other movies have the same level of depth.

In the end, I enjoyed Prometheus about as much and for about the same reasons as I enjoyed 2010's Tron: it looked really good and gave us some fascinating (and in the case of Prometheus, gooey and icky) passages to explore. Tron had its own aesthetic, Alien cribbed its from H.R. Giger, and I'm familiar enough with Giger's work that Prometheus didn't really look new to me. The science in both films combines a few interesting ideas with a bunch of ideas that are just not the way things work (bits in a computer having personality? in Tron; chemical facts such as rates of growth and the basic structure of DNA in Prometheus).

But even if it's more fiction than science, it still looks really cool. To me, that's worth 15 bucks. Just don't oversell it or certain critics will chain you to a rock and order an eagle to eat out your liver or something.

Monday, June 18, 2012

Pixar's 22 Rules

Pixar storyboard artist Emma Coats compiled a list of 22 story rules that have emerged from Pixar's success over the years in telling stories. I'm thinking compression: can these be summarized as just a few rules, or even (day I say) virtues? I'm thinking of the humility of putting the audience first, the fairness of having a character earn good things, the value of continuing to "show up" as a writer, and the thriftiness of keeping old ideas (coupled with the willingness to redraft and change them constantly). It reminds me about the songwriter process put forward by one of my favorite bands, The Choir, that a song should be shorter if possible and cut down rather than expanded out. The song is about the listener, not the band.

Here's the 22 Pixar rules (and here's a link back to the post that alerted me to them):

#1: You admire a character for trying more than for their successes.

#2: You gotta keep in mind what's interesting to you as an audience, not what's fun to do as a writer. They can be v. different.

#3: Trying for theme is important, but you won't see what the story is actually about til you're at the end of it. Now rewrite.

#4: Once upon a time there was ___. Every day, ___. One day ___. Because of that, ___. Because of that, ___. Until finally ___.

#5: Simplify. Focus. Combine characters. Hop over detours. You'll feel like you're losing valuable stuff but it sets you free.

#6: What is your character good at, comfortable with? Throw the polar opposite at them. Challenge them. How do they deal?

#7: Come up with your ending before you figure out your middle. Seriously. Endings are hard, get yours working up front.

#8: Finish your story, let go even if it's not perfect. In an ideal world you have both, but move on. Do better next time.

#9: When you're stuck, make a list of what WOULDN'T happen next. Lots of times the material to get you unstuck will show up.

#10: Pull apart the stories you like. What you like in them is a part of you; you've got to recognize it before you can use it.

#11: Putting it on paper lets you start fixing it. If it stays in your head, a perfect idea, you'll never share it with anyone.

#12: Discount the 1st thing that comes to mind. And the 2nd, 3rd, 4th, 5th – get the obvious out of the way. Surprise yourself.

#13: Give your characters opinions. Passive/malleable might seem likable to you as you write, but it's poison to the audience.

#14: Why must you tell THIS story? What's the belief burning within you that your story feeds off of? That's the heart of it.

#15: If you were your character, in this situation, how would you feel? Honesty lends credibility to unbelievable situations.

#16: What are the stakes? Give us reason to root for the character. What happens if they don't succeed? Stack the odds against.

#17: No work is ever wasted. If it's not working, let go and move on - it'll come back around to be useful later.

#18: You have to know yourself: the difference between doing your best & fussing. Story is testing, not refining.
#19: Coincidences to get characters into trouble are great; coincidences to get them out of it are cheating.

#20: Exercise: take the building blocks of a movie you dislike. How d'you rearrange them into what you DO like?

#21: You gotta identify with your situation/characters, can't just write ‘cool'. What would make YOU act that way?

#22: What's the essence of your story? Most economical telling of it? If you know that, you can build out from there.

Thursday, June 14, 2012

The Soup vs. The Miracle Mineral Solution

My friends with autistic children have it hard enough without having to deal with fake cures for autism. The most recent, and probably most egregious, treatment is called the Miracle Mineral Solution (MMS), although if there's any truth in advertising they should just call it what it is: bleach. Supposedly the bleach will cleanse the system from the toxins that cause autism.

There's something psychological going on if the idea is that autism is completely caused by the environment and can be scrubbed out with a caustic solution. It's like Lady MacBeth, rubbing her hands to remove the spot that isn't there. Autism is a complex interplay of environmental and genetic factors and it is tied up with the mysteries of brain function, which is the most protected part of the body against external chemical "toxins." It just doesn't make any sense to think you could wash it all out -- it would be like scrubbing your computer to fix the internal wiring!

But all that argument aside, my wife pointed out that the best argument against bleaching out the autism may have been presented on the most academic of all TV shows, The Soup starring Joel McHale. I never thought I'd be citing Jennifer Love Hewitt to cap off a scientific argument, but if it works, it works ... and the lady is right about this:

Saturday, June 9, 2012

Venus Refracting Sunlight

Here's a nice picture of refraction in a close-up of the recent transit of Venus. The thin, even ring of light around Venus is its thick atmosphere catching the sunlight and bending it so that the atmosphere is filled with light -- a halo for the planet of beauty.

Originally seen at the Bad Astronomy blog.

Friday, June 8, 2012

Erasing is What Costs Energy

My morning ritual now contains a new step: find the delete button. Overnight a few dozen emails collect, and no matter how often I try to unsubscribe (knowing even that can do more harm than good) or how much I try to reduce automatic emails, each year brings more emails waiting in the morning. I used to open each one before deleting but now it's fastest to just hit delete, delete, delete as I scan down the list of senders and subjects. Once I'm done I'm left with only three to five emails I actually want to open.

James Gleick mentions this phenomenon at the end of The Information concerning information overload, and even mentions a prescient scientist who saw this coming in the 60's. It's invitable and inexorable that information will expand, to the point that my primary email job is as much pruning as it is reading.

One of the things I learned about information theory earlier in the same book is that information has a cost but there's a surprising twist to it. The necessary cost is not in producing the information, but in erasing it. Rolf Landauer noted in 1961 that you can set up a system in a certain way so the information is recorded with no energetic cost (technically gain in heat outside the system). You can put bits in order like books on a shelf, and to a certain extent you can do that for free. But the necessary, unavoidable cost is taking the books off the shelf when you want to put new books there. Erasing the bits, or emptying the shelf, costs energy. So for this corner of information theory it's not that "time is money" so much as "erasing is money".

There's not an exact analogy here, but perhaps a metaphor, in that it's very hard to deliberately forget something. In trying to forget it, you of course remember it, and actually strengthen the memory. The strengthening goes all the way down to the neuron level, in that a neuron pathway that's used gets "thicker" and stronger. How do you not think about a white elephant? How do you weaken the "white elephant" synaptic pathway? One thing's for sure -- it's not by continuing to think about white elephants.

And pruning connections between neurons is as important as making them. One of the characteristics of autism is that not enough connections are pruned, too many connections are made and certain "circuits" in the brain are overloaded. Just this week I read about a study of the mouse brain that right before birth an amazing amount of pruning takes place, severing far more connections than are made. Brain development requires removing the wrong connections so that the right ones work right!

So what about when I want to forget something? Over time, this tangle of neurons in my head has been exposed to lots of crud, some my fault, some not. Even if it's entirely contained inside me, that burst of anger or of greed tilts the brain in that direction. Next time that burst comes more easily, and may even seem automatic, like something I can't help. Over time the brain skews toward what it experiences. It may be different in degree from an addiction, but it's not different in kind.

It's key to see every moment of life as a choice between the easy and the hard, the snap judgment and the "long obedience in the same direction." The very concept of free will and choice seems drowned out by all this information, but there is a delete button in the mind of turning away at the first sign of trouble. And it's not like an appetite for food or water -- the more you turn away and deny the urge the easier it is to do it the next time. Averaged over a long time, of course.

It's this delete button at the heart of thought that is very close to the Christian idea of forgiveness. Forgetting is not the same as forgiving -- but forgiving is a step toward forgetting. And the price, the energy, the hard thing is the erasing, the getting rid of the information, and there's so much information that getting rid of it is the major task of modern man. Taking out the trash and opening oneself to silence and being filled by light instead of darkness.

On the cross, Jesus erased our sins. I want to let that information come in -- but in order for it to saturate the brain I must first clean house and forgive. To the extent that I forgive, my bad stuff is erased and my sins are forgiven. "Forgive us our trespasses as we forgive those who trespass against us" in legal terms; "Forgive us our debts as we forgive our debtors" in economic terms.

So the Christian sees in the self-sacrifice of the lamb of God on the cross the action that will reverse all these tangled shortcomings and misdirected actions that we experience each day. That cost has been paid, but to fully participate in it requires the cost of personal erasure and a replication of that action in my own brain and my own actions. Each day there's more junk to delete, and I'm not talking about my inbox.

Agnus dei, qui tollis peccata mundi, miserere nobis.

Book Review: The Information: A History, A Theory, A Flood

James Gleick is one of my favorite science writers, and if I could figure out exactly why, I might become that much better of a writer myself. His books on Richard Feynman and Chaos Theory were what actually made me want to be a science writer in my early days of college. When I heard his most recent book was about information theory, I was a bit non-plussed. I wanted more of his writing about personalities like his small book on Newton, and it didn't sound like this would have much personality or history. It's information, after all! But Gleick kind of pulls it off. It helps that there is interesting, unknown history, especially with Charles Babbage and Claude Shannon, and that there's some depth to his subject, which Gleick is talented at drawing out details when others would gloss over it. I did listen to the audiobook version and I think my experience would have been better in print, because I missed visuals, and Gleick is definitely writing to be read more than to be heard. Ultimately Gleick's talent made the topic worth it, although I'm still wishing for even more personality.

Thursday, June 7, 2012

Book Review: Harvey Pekar's Cleveland

Sometimes you have to start from the end. I have heard all about Harvey Pekar the comic book writer (I think he prefers that term to graphic novelist) for years but I haven't been able to get past the apparent mundane nature of his subject (himself and his life, mostly) and the rough-edged, squishy feel of the associated artwork.

Pekar died recently and his last book, Cleveland, is a memoir that spans most of his life. I'm not sure why I got it from the library since I tried and failed to connect with his work before, but this last book is different. I was immediately brought in because from the first few pages it's clear that this book is as much about his hometown as it is about him. As his character walks around he narrates Cleveland's history and only later gets into his own life's details. It feels like an urban hike that I like to do (Boston's the best city for that, by the way), and it's a beautiful demonstration of the way the person is tied up in the place.

So I don't review every graphic novel I read here (sometimes it would take longer to write the review than to read the book) but I want to recommend this one. Now that I've started to see myself in Pekar, maybe I'll be able to finish his other more acclaimed books.