Ambiance

Two Experiences with Science, A Week Apart

September 6, 2012 at 3:40 am (By Amba)

A week ago I visited friends at the beach. She is my best friend from high school, her husband is a mathematician and photographer.  She sat on the beach and read while he and I bounced in the waves and, back on terra firma, discussed a number of things.  Somehow—ah, I remember, it was in regard to the Flynn Effect, the slow but sure worldwide rise in IQ scores—I happened to bring up the limitations of current scientific theory and the soon-to-appear major book by the derided heretical scientist Rupert Sheldrake, who posits mind-like “morphogenetic fields” that are repositories of collective experience, governing form and behavior in nature. Sheldrake is vehemently ridiculed and virtually excommunicated because he suspects that something nonmaterial may be operating in nature. The current dogma—not too strong a word, given the emotional response to even tentative speculations otherwise—is that every phenomenon in biology, at least, can be explained by matter bumping into matter, chemicals locking onto receptors; thus, for example, the development of an embryo is directed by gradients of signaling molecules expressed by a timed sequence of genetic programs. No esoteric “fields” need be invoked to account for the differentiation and choreographed migration of cells into their destined somatic roles and places.

I didn’t get nearly that far into explaining who Sheldrake was or how he applied his theory to fields ranging from crystal formation in mineralogy to simultaneous discovery in science. I had barely begun when some cue, some keyword, alerted my friend’s sniffer to the sulfurous stench of heresy, and he began rather aggressively herding me back towards consensus. It reminded me of the compulsion of a border collie to herd guests into one corner of the living room, or the way an alarmed adult will too firmly grip a child’s arm to steer it away from the curb of a busy street.  I couldn’t escape the impression that I was being policed, for my own good and the common good; that every spark of dangerous nonsense must be pounced on and extinguished before it gets out of control and starts a forest fire.  Smokey the Science Bear.  It was very strange.

After I got home, my friend followed up with an e-mail offering, to my mind a bit patronizingly, to send me a book called The Demon-Haunted World, by Carl Sagan. I thanked him and said that I knew that book, and I was doing OK without it.

*        *       *

Tonight I am copyediting an article by an authority on molecular epigenetics, the fairly new, now exploding science of extragenomic modifications to DNA and its associated proteins that can modulate or silence gene expression in response to environmental stressors in lifelong, even heritable (and yet perhaps reversible), ways.  The article contains an astonishing statement that, a decade or less ago, would have been regarded as beyond the pale.

Until recently, it was believed that epigenetics stayed out of the genome—that it modified the expression of genes, but not the genetic code itself.  But now it turns out that methylation of DNA, one of the main epigenetic mechanisms, predisposes a cytosine base (C) to be deaminated and turn into thymine (T). Yep, a change in the actual genetic code. That can happen spontaneously—it would be one cause of what’s called a random point mutation, resulting in a single-nucleotide polymorphism—but it seems to happen at twice the usual rate in methylated regions. Not quite so random.

The author of the article is investigating the notion that “long noncoding RNAs” somehow play a guiding role in directing methyl groups to particular places on the genome in response to environmental factors.  And where do lncRNAs come from?  From the long stretches of what has, till now, sweetly been called “junk DNA”—”junk” because we don’t know what it’s doing. (Now they’re dubbing it “dark matter,” by analogy to the invisible majority-mass of galaxies, and finding that it seems to be a mass of switches that regulate the expression of the coding genes.)

What we have here, the author says, is “a mechanism by which epigenetic changes, guided by lncRNAs, could make permanent and heritable changes to the genome. . . . epigenetics, rather than random genetic point mutations, could provide the missing link between environmental pressure and resulting genetic variability.”

That’s the astonishing statement.  It’s rocked me because the one piece of neo-Darwinan dogma I’ve never been able to get my head around is that the mutations from which natural selection selects are entirely random.  I raised that question at the bottom of this AmbivaBlog post and in this one (where there is also an amusing warning for me) back in 2005, right around when the groundwork for the epigenetic revolution was being laid.  It was, on my part, a naïve, intuitive, boneheaded incomprehension that adaptation could be so unresponsive at root, could be shaped out of such dumb and blind materials.  What if genes could “perceive” the environment in some way, if the genetic changes that took place were somehow biased towards usefulness?  Wouldn’t it better account for the exquisite specificity of adaptation?  Scientists at the time patiently and patronizingly explained to me that the truths of science are often counterintuitive; the fact that they are so unbelievable to us is one of the ways we know they are true.

Meanwhile, the epigeneticists in their labs were working away.

P.S. I am not trying to prove the existence of God.  My contention is, just give it time, and science itself is going to blow what we’ve known as “science” out of the water—and religion, too.

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A Writer of a Certain Age

July 29, 2012 at 10:05 am (By Amba)

This quote came along at just the right moment.

Trees have commonly two growths in the year, a spring and a fall growth, the latter sometimes equaling the former, and you can see where the first was checked whether by cold or drouth, and wonder what there was in the summer to produce this check, this blight. So it is with man; most have a spring growth only, and never get over this first check to their youthful hopes, but plants of hardier constitution, or perchance planted in a more genial soil, speedily recover themselves, and, though they bear the scar or knot in remembrance of their disappointment, they push forward again and have a vigorous fall growth which is equivalent to a new spring. These two growths are now visible on the oak sprouts, the second already nearly equaling the first.

~ Henry David Thoreau, Journal (or “Blog Post”), July 14, 1852

Thoreau was 35 years old, the same “midlife” when Dante said he was lost in a dark wood.  I daresay we’ve pushed it back some.

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