Epigenetic Enlightenment

May 19th, 2008

“Life’s experiences add molecular switches to the genes that control our brain activity,” is the subhead on an article in a recent issue of SciAm Mind. The article presents the new field known as epigenetics , which holds that experience can cause chemical changes that boost or depress the expression of certain genes.

This is a rich potential mechanism for describing interaction of nature and nurture in general, but in particular the progress of spiritual development associated with ongoing practices such as Zen meditation. Simply put, meditation practice could have chemical effects such as attaching methyl groups to genes, which quiets the gene by interfering with the ability of the RNA-based transcription mechanism. Or it could attach acetyl groups with the opposite effect, letting the genes express themselves more easily.

This is an intriguing supplement or alternative to other explanations of the long-term effects of meditation, such as neuroplasticity, but what is the gene, or genes, in question? Such a hypothesis will be a prerequisite for experimental design in this field.

Image of chromatin created by Nicolas Bouvier; courtesy of Genevieve Almouzni, Curie Institute, Paris, France.

Hofstadter and the Singularity

May 16th, 2008

I got a copy of Douglas Hofstadter’s “I Am a Strange Loop” (Amazon) for my birthday and spent the next month puzzling over why this inane book ever got written, other than to make a few bucks from aging technohippies with fond memories of Godel, Escher and Bach. It’s basically a random collection of unstructured jottings, boring personal stories, and contentless musings. Try as he might, Hofstadter never manages to convince us of the connection between Godel’s proof and some kind of loop that supposedly lies at the basis of our consciousness. Oddly, there’s almost no reference to any of the actual research in neuroscience or related fields which has started to cast light on the phenomenon of consciousness in recent years.

Hofstadter’s treatment of Zen in the book is emblematic of its problems. In a dialog between “Strange Loop #641”, a believer in the ideas of I Am a Strange Loop (such as they are), and “Strange Loop #642”, a doubter, he has them saying: Read the rest of this entry »

Music can cause your brain to grow

May 16th, 2008

Italian neuroscientists have that bombarding mice with easy listening music increases levels of brain-derived neurotropic factor ( ), in their hypothalmus specifically. However, levels of another neurotropic factor, NGF (nerve growth factor), declined. The findings suggest, according to the authors, that physiological effects of music, such as lowered blood pressure and heart rate or mood improvements, “might in part be mediated by modulation of neurotrophins.”

“First Dogen Book” now available in print

May 11th, 2008

I am pleased to announce the print availability of “First Dogen Book”, a brand new book containing extensively annotated translations of selected fascicles from Dogen’s Shobogenzo.

First Dogen Book is available for $19.95 from:

  • , the publisher

The fascicles included are:

  • Bendowa (Dialog on the Way of Commitment)
  • Genjo Koan (Truth Unfolding)
  • Uji (A Particular Hour)
  • Soshi Seirai I (Why the First Patriarch Came from the West)

Read the rest of this entry »

You know the sea nourishes life

May 9th, 2008

In the middle of Genjo Koan, Dogen introduces an analogy involving fish, birds, sea, and sky. This was actually the first bit of Dogen that I ever translated.

Swim as they may, fish find no end to the sea; fly as they may, birds find no end to the sky. Yet fish and bird still remain in the sea and sky as they have for ages…birds would perish instantly if they left the sky, fish would perish instantly if they left the sea.

This all seems rather understandable by Dogen’s standards. But just when we’re ready for some kind of insight or conclusion, Dogen launches into an opaque series of Chinese anagrams:


What do they mean?

Read the rest of this entry »

Numenware–the book

May 9th, 2008

2006 postings to Numenware are now available in book form for the low, low price of $19.95. What better belated Christmas present for your loved one or even yourself to read in the tub.

From the intro:

2006 was the year with the greatest density of neurotheological content on the blog, and these articles, taken as a whole, would I hope represent a meaningfully significant, if somewhat quirky, overview of the field.

Loyal readers of Numenware who read posts as they went up may have missed the discussion in the comments section, many of which are extremely informative. These comments have been included in the book, typos and all.

Buy Numenware 2006 from Lulu.com now . 140 pp., with an extensive (10 page) index. Digital version available for three bucks and change.

Why I Believe "Why We Believe" is Mush

May 6th, 2008

The word must be out about what Daddy’s interested in because under the tree for me at Christmas-time were two, count ’em, two books by Andrew Newberg, MD , namely “Why We Believe What We Believe” and “Why God Won’t Go Away”. Picked up the first one and started in on Chapter 1, “The Power of Belief”. The first story was about a guy for whom a cancer drug worked when he believed it would and didn’t when he didn’t. That seems a little off-topic–the book’s supposed to be about “Why We Believe”, not “What Belief Does”, but hey, let’s give Andy the benefit of the doubt. But then he undercuts his own case by quoting estimates that such spontaneous remissions occur only one in 3,000 or perhaps as few as 100,000 medical cases. And that’s even before you’ve eliminated spontaneous remissions not associated with “belief”. Why exactly are we supposed to be so concerned with something that might, or might not, be responsible for healing some infinitesimally tiny fraction of sick people?

Read the rest of this entry »

The Tale of Nathaniel the Toad

May 6th, 2008

Douglas Crockford is the oracle of Javascript and holds the right position on Javascript 2.0. He also writes the quirky Department of Style blog. Here’s today’s post:

Once upon a time there was a small toad named Nathaniel. Nathaniel was despised by everyone who knew him. Not because he was a toad, or because he pulled the wings and legs off of flies before he ate them, but because he could not be trusted.

One day at the forest tavern, where all the small forest creatures went nightly to get drunk, Nathaniel announced that he was never going to pay back the money he had borrowed from his little woodland friends. And he borrowed large sums of money from just about everyone.

So they killed him. And then they pulled his legs and arms off and ate him.

Representing branching sequences in XML

May 4th, 2008

Branching sequences are common in real life. For instance, a recipe can be represented as a sequence of steps, with branches corresponding to variations. Games of go or chess , of course, are the classic example of branching sequences, where branches handle the “could have/should have played there” comments. Branching sequences can even be used to handle linear text , with branches used for optional or alternate material.

If we have complete control over the programming environment we can implement branching sequences in any way we want, most of them quite obvious. But in today’s web-based world, there are good reasons to represent such structures using XML (for transformations, interoperability, or even storage in XML databases) and HTML (for display). What is the best way to do so?

Read the rest of this entry »

IEEE Special on the Singularity

May 4th, 2008

The magazine IEEE Spectrum is running a Special Report on the Singularity . Well worth glancing at.