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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36 Comments

  1. kngfish said,

    What always gets me is the speed of supposedly “random” genetic change. When I think “random”, I can easily see enormous numbers of trials, most of which fail long before the “useful” stage. Yet, at a sort of meta level genetic change does NOT seem to occur randomly, nor does “natural selection” appear to be a quick enough sorting out agent.

    We evolved the brains we have in like, what 300,000 years? Seems pretty quick for such a complex entity….

  2. Melinda said,

    Don’t know much about science books, but I do know about that “being herded towards consensus” feeling. Depending on how much sleep I’ve had the night before, my reaction is either:

    1. Be a heretic!

    2. Triangulate, fast!

    3. Change the subject.

  3. Charlie Martin said,

    It sort of depends on what you mean by “random”. There are a lot of constraints on what DNA can code — of 64 possible codons, only about 20 are meaningful. The others will simply cause protein synthesis to fail. This eliminates a lot of possible mutations.

    Beyond that, Steve Wolfram’s work with cellular automata showed that there are only a few “strings” that will generate complex outcomes for any particular starting state. The ones that don’t generate complex outcomes won’t lead to what we think of as life, either.

    As a result, I suspect it’s amenable to proof that DNA actually is very deterministic in what organisms it can code.

    Now, someone more theologically minded than I could probably make one hell of an argument from design out of that….

  4. amba12 said,

    I read something — I’ll have to retrace my steps — about the beaks of Galapagos finches, or some other family of birds with a lot of variation in beak shape adapted to different niches. It turned out that very small genetic (or epigenetic?) variations at a certain locus — molecular fine-tuning — would make big differences in the length, shape, thickness of the bill. This stuff will just blow your head right off your shoulders.

  5. kngfish said,

    I have a dumb question…how does this coding produce the results it does? Why does X generate, say, beak length or color? How? I just have no idea how these things work…

  6. amba12 said,

    I’ll find that again. I saw it a few years ago. It was one of those things that go through my head like an express train when I’m working and leaves an afterimage, without enough detail.

  7. mockturtle said,

    “junk DNA”—”junk” because we don’t know what it’s doing

    Yeah, like subatomic particles at one time.

    Now, someone more theologically minded than I could probably make one hell of an argument from design out of that….

    There are a LOT of very convincing scientific arguments for design if scientists would only get their brains out of their asses and put their prejudices aside long enough to seriously study them.

  8. amba12 said,

    OK, here is a summary of the beak work, and here is the entire original study. I Googled “genes for beak shape” and had this and more in about 10 seconds.

  9. wj said,

    What fascinates me is that the urge to uphold the current concensus is not limited to the field of study in question.

    I recall an incident when I was in college. Three of us were playing around with dowsing rods (in the hallway of the dorm, actually). And another student came by and informed us (tensely) that it was all scientifically impossible nonsense. Me: “Here we’ve got an engineer, a chemist, and a physicist, and we don’t see that it is impossible. And you, an English major, are telling us what is scientifically impossible??” To which he replied: “If that [dowsing] is true, my whole universe will collapse!” He was almost hysterical. I never did figure out why his universe was so fragile.

    Eventually, I came to a realization. There are some people (perhaps even a majority?) who simply have to have a world which is understood. They just can’t cope with having anything significant for which the answer is “We just don’t know.” I suspect that this is why medieval maps include some of the (to us) very odd things around the edges: they simply had to have something there — a blank space was not acceptable.

  10. karen said,

    I don’t mean to bring things back to cows in every single thread i comment on, but this seems relevant because now farmers can buy semen from Genomic tested bulls- they sell approx. a3X higher price tag and there is no proof in the pudding available- no daughters on the ground, no daughters milking, etc.

    The dairy(Holstein)industry is going goose poop over it all, except for those of us cautious and poorer folk that can’t drop the coin for the speculation w/out the Proofs(what we actually call the info on the daughters of any bull). Also, the speed of which generations of animals are developing is pretty outrageous, IMhumbleO. Heifers are ~flushed~(their fertilized eggs collected w/massive usage of hormones & precision timing)even before they calve out naturally– they aren’t even producing milk or maturing ~naturally~ through calvings. So, if all this genetic analysis proves not to be as accurate as expected/predicted- what are these gambling means to a lucrative end actually reaping? More like raping, if you ask me.

    We classified our cows today– cleaned them all up- washed tails and clipped udders and bellies(ever wonder where all those bitter little pieces of hair can work their way through?)(drive you batty!)- and we did pretty well. Some day, check out the Holstein World– to see how the big boys play the game. The info from the International Intrigue 2012 sale says 41 choices of flush averaged 23,751.22$. I’d pay that for a new car, perhaps.

  11. karen said,

    Sheldrake is a fave of real’s:0).

  12. realpc920 said,

    Sheldrake’s theories generally make sense, while the mainstream consensus about evolution is ridiculous. That’s why I like Sheldrake — because I like it when things make sense.

    The world IS demon-haunted, whether the materialists like it or not. They want to set themselves apart from the “ignorance and superstition” of earlier times. They want to think they are “enlightened” and superior. They want to separate themselves from the religious Right.

    The central argument of Dawkins and the materialists is that, given enough time, any impossible thing can happen. It’s similar to the multiple universe argument — anything at all is possible if there are an infinite number of universes.

    So they go to wild extremes of irrationality in order to support the illusion that they have de-mystified nature.

  13. wj said,

    karen, I don’t know about anybody else, but I really like the cow comments. Takes me back to my idyllic childhood on a farm. Keep ’em coming!

  14. realpc920 said,

    The book The Case of the Midwife Toad, by Arthur Koestler, is about a Lamarckian biologist who was ostracized and eventually driven to suicide. All because his research showed DNA could change in response to an animal’s needs.

    Do you want to know how Lamarckianism was “disproven” once and for all? A researcher cut the tails off of rats for several generations. But rats of each new generation still had tails. That was all it took to convince mainstream science that Darwinism was the only correct theory of evolution.

    We are an insane species, and we have created an insane civilization. Instead of believing that invisible gods and demons control the world, we thnk that WE control the world. We are above and outside of nature. It is dumb and we are smart, and we can make it do whatever we think we want.

    In the demon-haunted world, at least they recognized how small and helpless humanity really is.

  15. karen said,

    “In the demon-haunted world, at least they recognized how small and helpless humanity really is.”

    I totally agree and relate to this statement, real. And if i may, i will add that secularism and theology seem to be in a tug-o-war for the attention of our souls. I went to a funeral today- and even in such a setting as the Mass- the offertory hymn was ~Over the Rainbow~. Granted, the soloist was not Catholic, but it was a pretty odd song to hear for that particular timing. Just me.

    Since John died(B-in-L)i pray a lot, randomly. When i feel demons close-either a physical feeling, or a spiritual one, i say the St Micheal prayer. It’s not superstition- it’s a security. More blankie as opposed to rabbit’s foot. His 1st anniversary was Aug 29th. Did you know that’s the Feast day of St john the Baptist? I find that– comforting, but very unreal.
    ——————
    Heh- i knew if i poked real, she’d smile:0)… {waves}

    As for the cows- it’s so hard to separate myself from them!!! They end and i begin. Usually @their back ends-lol! Right now we have so many babies– 7 little girls all by the same sire- paternal sisters. My favourite is Finch- she’s from Flamingo- out of Flock. Finch is black, long-legged and long-necked. Her whole face is black– it’s beautiful. Actually- i find that to happen rarely, but we have about 5 animals w/no white on their faces.

  16. realpc920 said,

    I would not describe prayer as a blankie or a rabbit’s foot. Everyone prays, whether consciously or not. All of our thoughts, conscious and subconscious, are prayers.

    It doesn’t matter if you are religious or not, you are still made out of information and you are still a part of the universe which is made out of information.

    Consciousness, information, words, intelligence — aren’t these all really the same thing?

    Your thoughts — your prayers — define your place within the infinite information system. Our collectiver prayers define our species and our civilization.

    Your prayers determine how you resonate and what you resonate with. And that determines how you pray (how you think).

    Magic involves spells — words. And saying those words over potions (liquids). Remember the memory of water research? Oh by the way, one of the scientists who discovered HIV is now doing homeopathy research.

    It’s all words, it’s all prayers

  17. realpc920 said,

    And I meant to say — nothing is more powerful than prayer. So it is not just a security blanket.

  18. karen said,

    I can agree w/that- but, i feel when i consciously pray that particular prayer-it feels safe. It makes me feel safer- like security. Catholics get picked on a lot for the statues, icons, rosaries and repetitious prayers. They may appear to be like a rabbit’s foot to some, but not to me.

    I don’t believe in Magic, not the Harry Potter kind. ( I do believe in the destructive power of Satan and all his havoc seeking sects.) Yet, i loved Harry Potter and all the books and am re-reading them again for about the 6th time:0). I feel the allegorical resonance in those stories.
    I like the word ~resonance~. It’d be a great name for a … wait for it… COW.

  19. mockturtle said,

    WJ, your post about consensus was very insightful. I have found that, among doctors and scientists with whom I am acquainted, ‘intelligent design’ is not universally ridiculed nor is Darwinian evolution wholeheartedly endorsed. It is the journalists, teachers and social workers who most strongly defend Darwin.

    And, real, you’re spot on about man’s desire for control. Not that I think that the quest for knowledge is a bad thing. Not at all. Just that we need to admit we are not ‘the measure of all things’.

  20. amba12 said,

    I am savoring the notion of A Cow Named Resonance.

  21. realpc920 said,

    Karen, I think we all believe in magic, since that is how the universe works. Human beings ALWAYS beleived in magic, except for modern Christians and scientific atheists. Christians aren’t supposed to practice magic because somewhere in the New Testament it says not to. Jesus practiced magic, of course, and so did his disciples.

    Catholic priests sometimes perform exorcisms, which of course is magic. Catholicim is a mixture of ancient paganism and Christianity.

    Scientific atheists, especially James Randi (who is not a scientist, by the way), tell everyone that all magic is fake. Just because it CAN be faked, they think it is all always fake.

    Anyway, we do have an anti-magic culture. Fear of magic is very deep in our culture. Yes it is scary to think someone could ruin your life just by saying magic words. But not believing in magic won’t make it stop being real.

    This is a magic universe, created out of words.

    Just MY crazy opinion. But it only sounds crazy because it goes against our prevailing culture.

  22. Peter Hoh said,

    My contention is, just give it time, and science itself is going to blow what we’ve known as “science” out of the water

    Seems more than likely. This is how it’s played out in the past.

  23. karen said,

    We have a neighbour that just revamped his dairy barn and went from pipeline milking to a robot– a robotic milker! One is good up to about 60 cows. Anyway- the powers of progression and technology, eh? Plus, wwe have all that great wind power up on Lowell Mt, now.- 21 towers over 420 feet high. I guess my comment has more to do w/time.

    I don’t think all progress pays off int he end.

    As for magic= exorcism of evil spirits? I don’t believe that’s magic- i believe more in it being the power of good over evil, or the power of prayer. Words, yes. Words hurt or heal– in life as well as Faith. Ritual, tradition, prayer– is ancient.

    I’m not saying i don’t think magic exists- i am saying i don’t believe in it. My M-in-L goes to a psychic- that is a major no no for Catholics. Trust in the unfolding of the future is better than knowledge and control over it.

  24. mockturtle said,

    I agree with you, Karen. And when they shall say unto you, Seek unto them that have familiar spirits, and unto wizards that peep, and that mutter: should not a people seek unto their God? for the living to the dead? Isaiah 8:19 [I’ve always been amused by idea of peeping wizards, although I also take the verse seriously].

  25. realpc920 said,

    Catholicism assumes that magic is real, but you aren’t supposed to practice certain kinds of magic.

    But we really are not definiing “magic,” just assuming everyone knows what the word means. By my definition, praying is a kind of magic. Anything that tries to get spirits and gods to help us achieve our goals is magic, by my definition.

    And I consider all of religion to be magic. Religion started as magic and that’s what it still is.

    Shamans would go into a trance — which is similar to meditation — and communicate with spirits and gods. That is mysticism, and mystcism is the basis of all religion.

    A lot of what we now call religion really isn’t. Going to church once in a while and trying to be “nice” to people is not religion.

  26. Melinda said,

    Watching a classic movie about science vs. religion: “The Exorcist.”

    The real horror is that antediluvian medical equipment. I think they dug up stuff from the 40’s just to make it look scarier.

  27. karen said,

    I never saw that movie, Melinda.
    I saw Amityville Horror, though. Babysitting- alone.
    That was more a Good vs Evil movie, i think.

  28. Melinda said,

    Karen: Or a really bad housekeeping movie.

  29. karen said,

    If that were true, i wouldn’t have been so freaked out.
    Here’s one i can’t take credit for:
    “You could eat off my floors– there’s a 1000 things down there!”

  30. wj said,

    I don’t think all progress pays off int he end.

    karen, I think what you are trying to say is that not all change is progress. We can tell pretty immediately if something is changing. Whether it is a worthwhile change (i.e. progress) is harder to tell in most cases. Not least because even positive changes can have negative side effects — and we have to decide whether the gains outweigh the costs.

  31. karen said,

    Actually, regarding the wind tower issue- the people in the state of VT don’t get “to decide whether the gains outweigh the costs.” The only party allowed a ~vote~ on this construction that totally ruins the natural existence of our Lowell mountains are those that live in Lowell- and they all knew the payoff for a yes vote was- 500,000$/yr. HhhhmmmMMm- howtovote-howtovote… suckers. Wind power is supposed progress- it’s green and clean, eh?

    The rest of us were told to turn our heads to the right if the view was insulting to us.

    God only knows the repercussions of this ~green energy~ investment. I believe it will not be positive:0(. But, it’s a done deal- they are being set up as i type- well, during the daylight hrs- so, i have to accept this. But, i don’t like it.

  32. realpc920 said,

    “I am not trying to prove the existence of God.”

    No one expects anyone to prove the existence of God. But you can prove that materialism is nonsense.

  33. kngfish said,

    Karen, you’ve figured out that our whole economy is based on Robot Milkers! The question we have to ask is: Are you the Robot Milker or the Milkee?

  34. karen said,

    We joke around here that i’m my husband’s robot-
    i milk the cows for a lot less than 250G’s.
    Definitely not the milkee:0)!

  35. LouiseM said,

    The rest of us were told to turn our heads to the right if the view was insulting to us.
    I get the creeps driving through the wind farms on I65 in Indiana. With miles of , gigantic, pointed, moving blades atop poles on both sides of the highway, there is nowhere to turn one’s head to avoid seeing them. For me the view is more than insulting; it’s visually oppressive. I feel a sense of physical relief once we are through it. Maybe it’s the incongruity between the natural setting of the cornfields and the repetitive, uniform look and movement of the stark blades, (which appear mechanical and watch-like in the way they turn) that unsettles me. I consider these wind farms to be a blight on the landscape and cannot imagine having to daily live or work in such an area with no opportunity to avert one’s eyes or rest from the perpetual turning.

  36. TT Burnett said,

    A lot of people love their clockwork.

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