April 23, 2017

Something Wonderful: Molecular Visualizations of DNA

Credo in unum Deum, Patrem omnipoténtem, factorem cæli et terræ, visibílium ómnium et invisibílium.
["I believe in one God, the Father Almighty Maker of heaven and earth, and of all things visible and invisible."]-- Anne Barnhardt

God's Grandeur
by Gerard Manly Hopkins

The world is charged with the grandeur of God.
It will flame out, like shining from shook foil;
It gathers to a greatness, like the ooze of oil
Crushed. Why do men then now not reck his rod?
Generations have trod, have trod, have trod;
And all is seared with trade; bleared, smeared with toil;
And wears man's smudge and shares man's smell: the soil
Is bare now, nor can foot feel, being shod.

And for all this, nature is never spent;
There lives the dearest freshness deep down things;
And though the last lights off the black West went
Oh, morning, at the brown brink eastward, springs —
Because the Holy Ghost over the bent
World broods with warm breast and with ah! bright wings.

"There lives the dearest freshness deep down things"

At 2:21: "It spins the DNA as fast as a jet engine as it unwinds the double helix into two strands. One strand is copied continuously and can be seen spooling off to the right. Things are not so simple for the other strand, because it must be copied BACKWARDS."



Posted by gerardvanderleun at April 23, 2017 11:35 PM
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"It is impossible to speak in such a way that you cannot be misunderstood." -- Karl Popper N.B.: Comments are moderated and may not appear immediately. Comments that exceed the obscenity or stupidity limits will be either edited or expunged.

The more I learn of the universe, the more miraculous it all seems.

Posted by: pdwalker at August 26, 2012 9:23 AM

As daring as it feels to say I have a favorite poem, the truth is that this IS my favorite poem. It comes to mind constantly. Just today, as I walked the dogs through the woods, I wondered how there is always a wide-spread belief that we are suffering or about to suffer an environmental catastrophe of one sort or another. How can any sentient adult not have observed that, indeed, "there lives the dearest freshness deep-down things?"

Posted by: RigelDog at August 26, 2012 9:43 AM

This is the argument that should shut and nail the gob of Richard Dawkins and his ilk. But it won't. Sadly.

Posted by: Jewel at August 26, 2012 10:21 AM

Accident! Accident! Random chance, billions of years! Primordial soup, lightning, volcano dust! Panspermia! Best of all possible worlds! Multiple universes! HIGGS BOSON HIGGS BOSON I CANT HEAR YOU GOD STOP LOOKING AT ME NO ONES GONNA TELL ME WHAT TO DO IM FREE TO DO WHAT I WANT ANY OLD TIME IF YOU CANT POKE IT WITH A STICK IT AINT REAL O MIGHTY DARWIN SAVE ME BLAH BLAH BLAH BLAH

- The Scientific Community

Posted by: B Lewis at August 26, 2012 1:34 PM


Once again, people are inferring from the complexity of some physical process that God simply must exist. How could such complexity exist otherwise, without a Divine Cause to implement it?

*beats head against wall*

Gerard, Jewel, B., and the rest: I'm no atheist; I converted to Catholicism recently, after 30 years of being unchurched. I left the Episcopal Church because I was a young man to whom religion had become unimportant, and then the Episcopal Church left me by becoming revoltingly politically-correct.

What has me banging my cranium against the door-frame is Ann's argument (in effect) that the world's wonders are proof of God's existence. They are no such thing. God is not so foolish as to set the world up in that way. Our salvation lies not in being able to point to some worldly thing and use it as proof that God exists. Our salvation lies in our faith that God exists.

If His existence could somehow be proven, what room is there for faith? None. There would only be (given the perversity of human nature) the joyless, deadly certitude of always being watched, of always being judged, not only by God (Who would not want us to live in such fear of Him) but also by those who would profess to be His enforcers, and who would be all the more implacable for their unshakable belief in His existence (because, after all, it has been proven, yes?).

People will often point to the Second Law of Thermodynamics (layman's version: "The universe tends to disorder") and then to such complexity as the workings of our bodies, and say, "Aha! A violation of the Second Law! Only a divine being could cause such violations of the laws of physics to occur, therefore God must exist!".

Not so fast, folks. The Second Law, in the sense of things tending to disorder, applies with full force to isolated systems only.

And I suppose I should define my terms....

Thermodynamics is, at bottom, a study of how energy (heat, especially) moves from place to place, often changing form in the process.

Sometimes, the form becomes more useful, as in how the heat energy (not very useful) released by burning coal in a firebox heats water in a boiler to make steam, and the hot steam then drives some sort of engine to cause a shaft to turn, providing (very useful) mechanical energy to operate some piece of machinery.

Sometimes the form is less useful, as in the waste heat a steam engine must release to the environment. The Second Law requires that there be some waste-- it can't be helped.

In order to make sense of the process being analyzed, the thermodynamicist divides the universe into two parts-- the system, which is the part being studied, and the surroundings, which is the rest of the universe. The thermodynamicist examines not only what happens within the system, but also how it interacts with its surroundings. The steam engine in my example above not only has its workings which must be studied, but it also takes in fuel, air, and water from the surroundings and it releases ash, smoke, waste heat, waste water, and mechanical energy to the surroundings. The thermodynamicist must take all these things into account if he is to come up with a proper description of how a steam engine works.

An isolated system is one that does not interact in any way with its surroundings. Neither energy or matter enters or leaves the system. The only truly isolated system that we know of is the Universe itself, for (as far as we know) there is nothing outside of it.

A close approximation of an isolated system is a tightly-sealed Thermos bottle: hot coffee poured into it would (ideally) stay hot forever, thanks to the (ideally perfect) insulation, and the seal would prevent the coffee from leaking out or anything from leaking in. Thanks to the Second Law, very soon (a few months, maybe?) the coffee would begin to deteriorate, and in a few decades you would find that the contents, while still hot, would be undrinkable dreck.

A closed system is one that exchanges only energy with its surroundings. A common example of a closed system is a refrigerator-freezer: it takes in energy from its surroundings (through its electrical cord), and through its workings removes heat from its interior and rejects it to the surroundings by means of the coils on its back.

A freezer can also produce a local reduction in disorder, one example being the turning of (relatively disordered) water into (relatively ordered) ice, but only at the price of creating greater disorder in the surroundings. In plainer English, the freezer exports the disorder within it to its surroundings, and the process needed to export the internal disorder adds still more disorder to the surroundings. And so the Second Law (the universe tends to disorder) is obeyed.

An open system is one that exhanges both matter and energy with its surroundings. A steam engine (or a steam turbine) is an example of an open system, taking in matter and energy from its surroundings, changing their form, and rejecting them to the surroundings.

A steam engine, by itself, generates a lot of disorder, but the energy released by it can be used to cause reductions in disorder elsewhere, as in powering a freezer. But the Second Law is implacable-- the total amount of disorder in the Universe must increase as time passes.

Now that I've laid a whole bunch of terminology on your heads (or a pile of dreck at your feet, HI) I want to point out that the Second Law places no restrictions on where one places the boundary between the system and the surroundings. Certain placements are easier to deal with than others-- thermodynamics is, in some sense, and excerise in accounting-- but the placement is truly one of convenience.

If one takes the whole Earth as the system, and the rest of the Universe as the surroundings, then it's clear that the Earth is (approximately) a closed system. Its stock of matter is more or less fixed, but it does constantly receive fresh inputs of energy from the Sun. The fact of Earth being a closed system is sufficient condition for a local reduction in disorder.

Furthermore, local reductions in disorder occur more easily in open systems, which certain parts of the Earth could be considered to be-- again, depending on how one draws the boundaries.

Given the laws of physics and of thermodynamics, the emergence on Earth of physical or chemical complexity is not unlikely-- it is inevitable.

"But, but, but, Adams!", I hear you splutter, "Surely any complex molecule that somehow, by accident, came into existence was very soon destroyed by accident or sheer randomness!" Yes and no. Chance is a very powerful thing, the planet is a very big place, and the deeps of time (billions of years, folks) are beyond our ability to grasp. I'm sure that there were many times when candidate molecules for life almost survived, but got smashed back into the muck before they attained some critical condition that allowed them to protect and perpetuate themselves. But one molecule, somewhere, somehow, survived. It takes only one, you know, and it has to happen only once.

Or, to use another example......

Statistical thermodynamics points out something in a particular case that's hard to wrap one's mind around, but one can't argue with its conclusion. Specifically, imagine two sealed flasks, one containing air, and the other a vacuum, which are joined by a tube with a valve in it. If one opens the valve, the air in the one flask rushes into the flask with the vacuum, and the whole shebang is then filled with air (at reduced pressure, of course.) A layman will look at the arrangement and declare that the original state (one flask full of air, the other with a vacuum) will never occur spontaneously. Not so, says the statistical thermodynamicist-- it's very unlikely, yes, but the probability of it happening is not zero. The Universe would probably pass away before a vacuum would spontaneously appear in one of the flasks, but it will happen if you wait long enough.


I guess what I'm trying to say (now that I've either bored or insulted everyone here), is that to insist (either through a literal reading of the Book of Genesis, or by asserting intelligent design) on God taking a direct hand in causing this world to be as it is, is to be disrespectful to Him. God isn't Someone whom we can pull down to our level to understand, to confine to our pitiful understanding of how the world works or might work. If you want to assert that He is the Architect of the Universe, fine-- I won't argue with you. But He is so supremely competent that He has not built the Universe; rather, He has arranged things so that the Universe has built, and continues to build, itself.

That, ladies and gentlemen, is truly terrifying.

Hale Adams
Pikesville, People's Democratic Republic of Maryland

Posted by: Hale Adams at August 26, 2012 6:20 PM

For some reason the phrase "The body is the temple of God" comes to mind.

Posted by: Brett_McS at August 26, 2012 7:31 PM

Hale Adams: U MAD, BRO?

Posted by: B Lewis at August 26, 2012 9:41 PM

I had the same sense of awe when I first learned about DNA replication and viewed the animations of it. I was reading Bill Bryson's "A Short History of Nearly Everything," which summarizes the scientific knowledge of how we came into existence. Readers of this book who believe in God will see God's handiwork everywhere, but those who don't will see it as proof that God does NOT exist.

What I love about DNA replication is how the process 'evolved' from scratch. Start with a recipe of the primordial soup of amino acids, water, light, and billions of years of time. Wait for the right random interactions for the molecules to build amino chains (proteins), and these proteins in turn get more and more complex. Where all the action of replication occurs is inside the two molecules that build onto the 'half-strand'. They take floating amino acids and attach them to the strand. This attachment happens completely inside the support molecule - an anhydrous reaction... meaning no water molecules allowed! So the key to DNA evolution requires a process (really, a molecular bonding) that has simply astronomical odds of occurring randomly. I think Bryson calculates the odds. Believe in God and it's evidence of His existence. Don't believe in God and life itself the is proof that the odds won out.

Posted by: Monty at August 26, 2012 11:09 PM

It looks like intelligent design to me.

Posted by: mjazz at August 27, 2012 7:14 AM

Hale Adams, you should post your views at Uncommon Descent. I have to admit that the discussions there are beyond me. http://tinyurl.com/8sabt5e

Posted by: mjazz at August 27, 2012 7:57 AM

Imagine a future planetary exploration team is surveying the surface of Mars. During an excavation, they are astonished to discover what appears to be a computer chip embedded in the rock. Further investigation reveals the object to be a functional integrated circuit device.

"This is the most momentous discovery in the history of science, " says the team leader. "Finally, proof positive that an intelligent creature has existed on Mars at some point in the past. We are not alone!"

"Not so fast," says the chief scientist. "Just because we found a piece of silica that happens to be in the form of a computer chip doesn't necessarily imply that any extraterrestrial intelligence exists."

"It certainly does," says the team leader. "Micrographs show definitively that this is an integrated circuit chip. Since no human beings have ever been to Mars, and none of our probes have penetrated to this area, logic dictates that an extraterrestrial intelligence exists."

"Nope," says the scientist. "Extraordinary claims require extraordinary evidence. What evidence have you that this 'chip' was made my an intelligent being?"

The Team Leader is nonplussed. "I -- it's a circuit, Chief. A functional electronic circuit! The computer says it could be made to run like any IC chip. Integrated circuits don't just create themselves. Someone designed this!"

"That's an interesting statement of belief," replies the Chief Scientist, "But not a demonstrable fact." He examines his nails nonchalantly. "I can't accept your faith in some invisible sky person as a scientific theory, Team Leader. All I can know from what we have here is that we have found a functional circuit chip. Where it comes from, how it came to be -- all of this remains unknown."

"But somebody had to make it!" The Team Leader is incredulous. "It's obviously an artifact. Complex structures like computer chips don't just appear out of thin air!"

"Sure they do, Team Leader," says the Chief Scientist. "Biological cells. A single living cell is billions of times more complex than this chip we've found, and yet cells just 'appeared', without the aid of some fantastic 'designer' in the sky." He looks up from his nails. "Like a living cell, this chip merely appears to be the product of an intelligent designer. In fact, it's complexity is probably just the result of the random actions of wind, water, and radiation upon local geology over eons of time."

He stands, looks the Team Leader in the eye. "Just as we have learned that we need not invoke the supernatural to explain life, we need not posit a race of chip-designing Martians to explain this object. Like us, this chip was produced by the action of natural forces upon natural materials over billions of years of time. It, for lack of a better word, evolved into its present state." He points toward the airlock. "In fact, there are probably ancestors of this chip -- transitional forms -- buried in the rock beneath us right now."

"Sir!" cries a nearby technician. "We've finished the circuit analysis. The computer says this is a data storage chip -- and the data is readable!"

"What's it contain?" the Team Leader asks.

"A raster image sir," says the tech. "I'm calling it up now." On a nearby screen, an image appears: a creature utterly inhuman in form, but wearing what can only be the Martian equivalent of a clean-room suit. In one hand -- tentacle -- the creature holds a small box containing a duplicate of the found IC chip.

"Holy cow," says the Team Leader. "It's a photo. A photo of a Martian -- and he's holding the chip. I just won a freaking Nobel Prize!"

"Coincidence," scoffs the Chief Scientist. "Over billions of years, local radiation probably flipped the bits on that chip randomly into this configuration. It only appears to our pattern-sensitive brains to be a clear, color image of a blue-eyed extraterrestrial creature in a clean room suit holding in its appendage a copy of the so-called 'chip' we've found."

The tech and the Team Leader stare at the Chief Scientist open-mouthed.

"What?" asks the Chief Scientist. "It's Science 101: extraordinary claims require extraordinary evidence. I see no reason to believe in any Martians."

No one speaks for a handful of moments. "What," asks the Team Leader quietly, "would it take to make you believe?"

"Proof," responds the Chief Scientist primly. "I'm a scientist, Team Leader. If I can't poke it with a stick, it ain't real." The Chief Scientist grins ironically. "Call me Doubting Thomas. 'Except I shall see in his hands the print of the nails, and put my finger into the print of the nails, and thrust my hand into his side, I will not believe.'"

Posted by: B Lewis at August 27, 2012 8:31 AM

When I was a little kid in the 1950s, I remember the excitement when Watson and Crick described the “double-helix” of DNA. In a biology class in the 1960s, I watched through a microscope as a cell divided, and we did the table of inherited characteristics described first by Mendel. It seemed incredible to me that I could be in a normal high school class and be watching something as though it were a commonplace that so many people had wondered about over time. I had read about the 1660s development of the microscope, by Leeuwenhoek, who first described the microscopic “little creatures” he had discovered. A contemporary of his (and of Isaac Newton) was Robert Hooke, and I had actually been privileged to hold in my hands an original copy of Hooke’s “Micrographia”, with its magnificent drawings of the first microscopic details of what Hooke had seen. He was the one who coined the name “cell”.

These men were giants! I wondered then what Leeuwnhoek or Newton or Hooke or Darwin or Mendel would have said if I could have brought them forward in time to look through my humble classroom microscope at the cell of the “little creature” as it divided. I imagined telling them what we had learned about heredity and how it worked. I was so exhilarated that I got goosebumps on my arms, and I very clearly remember looking at them and knowing that the mechanism that gave me those goosebumps was contained within every cell of my body, being duplicated countless times just so that the proper cells on my arms would react like that when I was overwhelmed.

Since that time I have read of the work of those who have gone deeper and deeper into the biological phenomena, and now, watching videos like that one above, still getting goosebumps as I had so long ago, I know that there is no way that anyone could even begin to describe the mechanism of genetic materials to those historic figures. Somewhere during the last half-century we crossed a threshold into scientific realms of such nuanced complexity that the experts of today would have little common vocabulary in word or tool or image to quickly communicate what is happening. We see farther, and more deeply, because our tools—including mathematics—have given us super abilities of a worth far beyond those of any movie superhero.

What a gift the Internet is! And Mr. Van der Leun, thank you for posting so many wonderful things. Your site is a treasure trove!

By the way, the biological mechanism in the video above reminds me of the artwork of a woman named Bathsheba Grossman, who does both sculpture and subsurface laser etching in crystals of subjects from mathematics, science, and technology. If the video thrills you, so will her work. (She can be found at www.bathsheba.com. I don’t know how to make it a link.)

Please check out her artwork—it also is truly “Something Wonderful”!

Posted by: Minta Marie Morze at August 27, 2012 8:52 PM

Anyone who makes a comment about Richard Dawkins should at least have read his book, The Selfish Gene.

Your lack of imagination is what makes you think that something this miraculous could only be the work of God.

People, you have got to READ! Just because you can't think of something doesn't mean it doesn't have an explanation. And if you haven't taken the time to actually understand evolution, DNA, or replication - for instance - then how do you think you can really understand it?

It's taken scientists many years and much hard work to arrive at the knowledge we have today, knowledge that is responsible for you being alive, if you've ever taken any medications.

Seriously, read, and stop posting things that make you sound like morons.

Posted by: satanfornoreason at February 6, 2013 8:27 AM

Dunno, but life and nano technology seem to be different flavors of the same ice cream...like French vanilla and, say, Vanilla Bean Ice creams. ...and they seem to be tending towards convergence. And if you are wondering, I'm a Chemical Engineer by training and a Presbyterian by faith.

Posted by: Kalashnikat at April 24, 2017 6:21 AM

From Psalm 139:

13 For you created my inmost being;
you knit me together in my mother’s womb.

14 I praise you because I am fearfully and wonderfully made;
your works are wonderful, I know that full well.

15 My frame was not hidden from you when I was made in the secret place,
when I was woven together in the depths of the earth.

16 Your eyes saw my unformed body;
all the days ordained for me were written in your book before one of them came to be.

17 How precious to me are your thoughts, O God!
How vast is the sum of them!

Posted by: ahem at April 24, 2017 6:28 AM

Right on, Adams. Right on.

What's the building block of all nature? The elementary particle Conundrum. Rightists cannot accept this. As the author once said, [their] God Is Too Small.

The ultimate failure of the saved-by-works faithists* is their intellectual cudgel. Apparently G-d, being mute and impotent, needs Man to espouse with great force His Message.

A G-d vast enough** to make a Universe is certainly vast enough to confound Man and remain forever the stuff of our greatest mystics. And even that formulation is daft when you think it through: They, at least, had the sense not to evangelize with the great force of religious mediocrity.

*Something changed when saved-by-faith became a challenge, and therefore saved-by-the-work of one's mighty faith.

**Even the label 'vast' is sufficient to prove one knows nothing of G-d. How exactly do you quantify the infinite?

Posted by: Ten at April 24, 2017 8:53 AM

Incidentally, as facile as BLewis's story is, it makes no case for G-d (outside a slightly smug emotion). That case lies elsewhere, outside the Universe, obviously, and in the stuff of Mind.

'Science' made a bad move when it threw out philosophy. Being the giants they are, rightists then capitulated by fighting it back, all on its own terms.

This led to nonsense like the Creator kicking off the big bang. But bangism is a crap creation myth; a dumb theory Science hasn't had the sense to see for what it is.

Likewise the religiously-wielded Laws of Nature every time they make any exception to their simple-minded Uniformitarianism impossible just by rote assertion, a fallacy they're used for endlessly.

Need an exception to the purported 'laws' of thermodynamics? The Universe is itself one: Until you consider the Pre-state State, you have nothing. Rightists consider only the post-state state, the one left them by the generous Scientists who confound them both with bullshit.

Both camps are locked in a pointless dance with one another.

The Universe is two things simultaneously. Vast enough to not even be slightly considerable from the inside, and miniscule enough that even at its ferocious clip light takes some fourteen billion years to transit from one edge to the opposite.

Imagine if it took you fourteen billion years to navigate a nine inch plate of beans. And does that creating G-d not see the physical universe as little more? That's how you 'define' G-d, no? By It's size?

The thing isn't size or complexity. It's the utter violation of Void (and purported thermodynamic 'laws') that mere existence entails. Figure THAT one out, Scientists. And Believers.

Posted by: Ten at April 24, 2017 9:17 AM

I have a secret. My secret is that I play an online game every day. It's not a role-playing game, but one that virtually creates a reality somewhat different than the one we live in.

One day several months ago, the thought occurred to me, "Wouldn't it be cool if the characters in the game could become sentient and experience real human-like emotions?" My very next thought was, "Wow, if I could do that then I would be just like G-d."

Then I began meditating on this thought, "What if my reality is just like those characters in a game being played by beings in another dimension?"

The thought came to me, "If humans can create an entire alternate universe in cyberspace where otherworldly creatures are programmed into existence, then why couldn't G-d create us in our dimension/universe?"

My next thought was, "Wow, this entire generation can be judged by G-d on judgement day by a stupid computer game." For if man can create entire worlds, creatures and sentient beings in cyberspace, there is no question that a higher order G-d could have created US.

Further, if we can code whatever the heck we want into our virtual world, then so can He. He could even code bones into stones for dinosaurs that never existed at all. The Coder could have left all sorts of unexplained writings and objects behind to test our faith in Him.

Only a few weeks after I had these thoughts I saw the article where Elon Musk was offering a reward to anyone who could hack the Matrix in which we lived. As someone who routinely prays to the Great Coder and his Son, I thought about requesting Musk's reward. Unfortunately, my faith is just too weak for me to hack the Matrix (i.e. God's creation) at will. I can only point to the many inexplicable blessings in my life that seem to come from Faith in the Great Coder.

And so, I'm left with commenting on American Digest. Who knows, maybe I was even prompted by the Great Coder in the Sky to type these words? He might have even coded them into the Matrix Himself while I was asleep in bed this night?

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