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Saturday, March 25, 2017



Finch on San Cristobal

Finch on Isla Espanola
The finches didn't really make an impression on Darwin. He didn't, at first, notice that the finches in his collection were different from each other until long after he left the Galapagos. When the realization finally came to him, his notes were inadequate for matching each sample to its island. It raises the question, "What are you uniquely qualified for and prepared to discover?"

Mitchell: So, uh... so, how go the repairs?
Lee: Well, the main engines are gone, unless we can find some way to re-energize them.
Mitchell: You better check the starboard impulse packs. Those points have about decayed to lead.
Lee: Oh, yeah, sure, Mitch.
Mitchell: I'm not joking, Lee! You activate those packs, and you'll blow the whole impulse deck.
Lee: I'll, uh, get on it right away. I just wanted to stop by and make sure you were OK. See you later.

Helmsman Gary Mitchell (Gary Lockwood) and ship's psychiatrist Dr. Elizabeth Dehner (Sally Kellerman) evolving.  Picture by Paramount Television

Mitchell: He's a fool.
Dr. Dehner: A fool?
Mitchell: He'd seen those points, and he hadn't noticed their condition.
Dr. Dehner: How do you know?
Mitchell: The image of what he'd seen was still in his mind.

Star Trek, "Where No Man Has Gone Before.
-Paramount Television
Maybe it's best to think of seeing as an interactive event. We see things, maybe every day. But then one day we look again and something finally clicks and we say, "Oh! Now I see!" or "Eureka!"

Education, experience, and familiarity all contribute to the process of seeing, which results in a gaze that can be more discriminating and more encompassing.

Suppose a photo editor needs pictures of World Foods Market on Barbur Blvd. and there are two available photographers, Scott and Monkey-cam. Some background knowledge of the photographers might figure into the editor's decision about who should be assigned, depending on what the goals are for a given article.

Or say the editor needs pictures of Long Island in the middle of Willapa Bay.

Or say the editor needs pictures of 3 species tacos for an unbiased article about the best tacos in the world.

In each case, the photographer's background and life experience greatly factor into what gets noticed. I guess my point is, the hard time I did at the oligonucleotide factory changed the way I see.

Evolution of a painter

In 1994, I started working as a technician in the synthesis department of a small company that made oligonucleotides, or single-stranded DNA. There I learned that machines (reminiscent of multi-flavored Big Gulp machines) could dispense the 4 different bases (phosphoramidites dAdenosine, dCytidine, dGuanosine and Thymidine) and string them together into specific chains (or sequences) per customer request.

A bank of synthesis units
Section of an oligonucleotide — single stranded DNA
The machines don't do as good a job of making oligonucleotides as nature does. Each time a coupling happens, there are failures which, if the sequence is long, have to be removed later during a purification process.

Oligonucleotides being injected into an HPLC purification column
When that process is complete and the amidite chains are dried for shipment, the material looks something like this:

Visually represented here is enough single stranded material to fulfill a 50 nanomole order. If this particular sequence is 21 mers long (21 bases, for instance, 5'-ACT-GGC-ATA-GGA-AAA-TAT-GAT-3') then a leading manufacturer of oligonucleotides could sell you (as of this writing) an unpurified version for something like 8 - 13 dollars.

Once the customer gets their material, they may utilize it as a primer, where it enables DNA polymerase (a complicated DNA zipper) to get a running start at massively amplifying a desired DNA sequence.

A vague depiction of DNA polymerase assembling DNA according to a single-stranded template
(DNA polymerase not pictured)

The key trick is that, single stranded DNA, uncoiled and open, acts as a template that allow accurate reproduction by DNA polymerase. The polymerase reads the template, finds the complementary base (an A for a T, or a C for a G) and 'zips' them together making long double stranded molecules (or DNA proper).

This is the basis for the iconic double helix, (imagine twisting the ends of this 'ladder') a quaternary code able to store the data necessary for growing ever evolving life-forms.

This code is passed down to us from our parents, and the way it works is how a mixture of our parent's physical characteristics ultimately find expression in us.

Really long stretches of DNA are genes. Collections of genes comprise Chromosomes. Collections of chromosomes in a cell define the organism of which that cell is a part, and all the genetic information in a cell is called the genome. The human genome was not sequenced until 2001, seven years after I started working at the oligonucleotide factory.

The amazing thing we know now is that,

"...the DNA code is invariant across all living creatures, while the individual genes themselves vary...a truly astounding fact, which shows more clearly than anything else that all living creatures are descended from a single ancestor...the whole gene/protein system for running the same in all animals, plants, fungi, bacteria, archaea and viruses. What varies is what is written in the code, not the code itself. And when we look comparatively at what is written in the code — the actual genetic sequences in all these different creatures — we find the same kind of hierarchical tree of resemblance."
                         - The Greatest Show on Earth, Richard Dawkins.

Now the tree of life is informed by molecular biology. I am told it closely correlates to and sometimes corrects older charts that were based on Linnaean taxonomy. (See Tree of Life Web Project: (

Yet in 1837, Darwin, was formulating his theory, and sketching in his notebook, certain that there was a mechanism for heredity, but never knowing what it was.


The Popular Science Monthly, Volume 57 p. 87, reproduction of frontispiece from Darwin, Charles (1890), Journal of researches into the natural history and geology of the various countries visited by H.M.S. Beagle etc. (First Murray illustrated edition), London: John Murray (The Voyage of the Beagle).

For an amazing depiction of life aboard a British Navy ship, see Master and Commander: The Far Side of the World. Bonus: They visit the Galapagos.


The Nemo III

Floor plans compared

First stop: North be continued

If you need to catch up with Part 1:

PART THREE: The Book of Nature is now available:

Tuesday, March 14, 2017



A blue-footed booby. This picture is inexplicably composed to exclude the signature bright blue feet.

By then, I had already watched boobies ham-footedly seducing each other with incongruous bright blue feet, disappointed pirouetting sea lions with my graceless, spastic snorkeling — unable to join in their joyous dance — and seen the fork-tailed silhouettes of magnificent frigate birds gliding beneath a near full-moon. That evening, we (me and eleven other travelers) sat in the common area of a 75 foot catamaran being introduced to the crew. 

Crew of the Nemo III with our guide Veronica acting as translator

Through our guides, the crew asked us, "Why did you come to the Galapagos?"

Up until that point, I'm not sure that I had ever put my reasons into words — and as I stuttered and paused too long looking for the right ones, I began to realize that it wasn't just for exotic 3 species tacos, it was because I wanted to articulate a story of discovery and revelation — to flesh out an account of a scientist deciphering the underlying truths of our existence in the universe. But I felt like an evangelical missionary who hadn't and couldn't read Greek or Hebrew texts — or a witness at a trial who hadn't actually seen the crime.

My short answer was, that while there are some who journey to Jerusalem, and some to Mecca, I was on that boat, 600 miles off the coast of Ecuador, because I wanted to see the peculiar islands that jarred something in Darwin's mind — something that years later shaped his thinking in regards to the origin of species. I wanted to affirm Darwin's observations. I wanted to feel the blind hands of nature shaping life as if by design

Early mariners noted the Galapagos would often disappear into the mist caused by the cold Humboldt current spilling into the tropics earning them some references as the Enchanted Islands.

As Darth Vader said, "... let me... look on you with my *own* eyes."

So there I was on a naturalistic pilgrimage, not to retrace the stations of the cross or purchase relics, but to follow in the metaphorical wake of H.M.S. Beagle to study the ripples left by its passage through history.

As David Byrne said, "Well...How did I get here?


The Elephant of Surprise spots my Dad.

I was away at Bible College one year, learning to present sermons via Pastor Jim Cook's patented 3-point-outline method. All the while, unbeknownst to anybody, the Elephant of Surprise trampled roughshod through the ranks of my family.

Later, as the recipient of increasingly ominous news, I found myself surrounded by people who optimistically saw God as active in their daily lives, helping them to prepare for tests, providing money for them just when it was needed, and (in some fashion that was never explicitly clear) helping them with their life decisions. Often, daily existence was viewed as just another day of spiritual warfare, in which we young Christians were encouraged to gird up our loins ( and enter the secular fray wielding the sword of the Spirit — His word (or as narrowly defined by my conservative college, the Bible (hence the likely etymology of the term Bible beaters)). Kind hearted people (some of them strangers) prayed for and otherwise cared for me and my family, so much so that it was hard to tell if it was God working, or just kind hearted friends and strangers. It turns out there are all kinds of Christians and they all have slightly different versions of what they think God is like, and what they think God wants us to do. 

Left to right, top to bottom: 1. Traditional kind of oily Jesus. 2. Rugged Jesus. 3. Pretty good singer Jesus, but kind of bitchy. 4.Whitest Jesus ever. 5. White haired man in sky. 6. Scientificly ethnic Jesus. 7. God as a Lion. 8. God as a cheating wrestler (Still loses to Jacob). 9. Ganesh. 10. Burning bush. 11. Popular idol in 2017. 12. Elephant of Surprise.

But you never really "see" God, unless he looks like the people of faith who feed the hungry, heal the sick, and welcome the stranger. In fact, that's my big take-away from my year among the Baptists. If God works in the world, he uses human hands. Well... I say that's the big take-away, but there was also this joke. Why don't Baptists typically have sex while standing up? Because they're afraid it might lead to dancing.

"But Scott!" you exclaim, "Why are you bringing this up at the beginning of your Galapagos story?

Well, because there's another elephant in this story — the elephant in the room. It's the elephant that pits Bible believers against science — creationists against those who, through science, are learning how life evolved on earth. This year's political climate is accelerating the already extreme polarization between liberals and conservatives. Much is being done to cast doubt on our institutions of learning. Agencies that have marshaled our best technologies to examine the earth and the life upon it are being muzzled and defunded. Some of this (certainly not all of it) is happening because sincere people of faith believe they must stand up for God. It doesn't escape me that my whole-hearted excitement regarding what's being learned about evolution will be seen as heretical and threatening by some of my conservative friends. For them, I'd like to propose a temporary suspension of disbelief.

Consider this allegorical aid. Imagine a potter sitting before a potter's wheel (Personally, I like to imagine Demi Moore).

From the motion picture, Ghost: Paramount Pictures

Now imagine Demi Moore is the theory of evolution. Imagine she is shaping an animal (pot) through natural selection. Keep in mind that Demi Moore is blind, but you can see that even so, she has successfully shaped many different animals on the shelf behind her.

Now, in terms of science, that's all the further I have to go. But for the sake of my conservative friends, lets introduce Patrick Swayze.

From the motion picture, Ghost: Paramount Pictures

In this picture, we'll imagine that Patrick Swayze is God. Demi Moore is still doing all the work, but let's say she works for Patrick. As far as science is concerned, Patrick is invisible. He (so far) can't be measured, and his activity in the world, so far as we can see, looks an awful lot like Demi's work. Since we can't rule out Patrick, and if it helps you to see him helping in some way, say making the raw materials (Universe, earth, clay) or making Demi in the first place (but not so much guiding her hands), then lets do that until I finish my story.


Bronze pour with: Professor (Vicky R.), Hooker (Mike E.), Guy you can't see (Probably Brian H.), and me driving the crucible.

Our ad-hoc furnace roared like...well, the blower that forced burning gas around the now radiating crucible like a tornado. It sounded something like a jet engine, and as the air above the furnace shimmered and rippled, I imagined the tightly-focused spinning conflagration we engineered was causing the ground to vibrate. We armored ourselves with leather and asbestos garments to protect our skin from the searing heat and to, perhaps, fend off molten projectiles should the liquid metal contact water hidden in improperly heated ingot-molds. Driving the crucible to the waiting molds, bearing the weight of the bronze, feeling the sweat dripping down my forehead, watching the metal flow like lava — it is at this moment that I feel like Prometheus stealing fire from the Gods.

When the crucible is empty, when we who have toiled have commenced eating meat and cheese from great paper platters and drinking cold beers enriched (or diluted?) by tomato juice, the bronze filled molds will still be steaming in the sand, cooling, becoming a new thing. By doing this, I have become a brother to men who worked in foundries over four thousand years ago, sharing elemental secrets that have shaped today's technology and which I now use to give shape to my ideas and emotions.

TOP: Bronze scraps from ancient Greece (on display in the archeological museum in Athens)
BOTTOM: Bronze scraps on the floor from one of my bronze pours and why when I saw the display in Athens, I felt connected to history like never before.

Investing wax piece in ceramic shell, an alternative to plaster.

This is a gift of science. I don't know who the first person was to figure out how to make a crucible. But somebody tried, failed, and tried again. It took insightful observations and repeated experiments. Doubtless, limbs and lives were lost along the way. And now we stand atop a hard-won pile of all the knowledge collected before us. We can do this because the universe though often inscrutable, is also reasonably consistent for objects longer than the Planck length.


When it comes to telling biographical stories, the most salient aspect seems to be that you can't really do a very definitive job unless you start from the end. At the entrance to a fork, a trivial decision based on a whim or intuition may result in finding the job of your dreams on one hand, or death by a rabid beaver who severs your carotid artery on the other. Sometimes, it isn't really a matter of even making a decision.

One year, when I was 14, I was sent to spend part of a summer on a wheat farm in Kansas with my Great Uncle Carl and Aunt Alvina. 

My long suffering Aunt Alvina and Uncle Carl being patient while 14 year old scott tries to pose them like that American Gothic painiting

In one of the outbuildings, there was an old workbench, and tacked to a low lying rafter were rows of rabbit ears. I inquired about the unexpected decorations and learned that during various years and seasons, rabbits, doing what rabbits do, earned themselves a bounty. Enterprising youth, I also learned, could make money in exchange for rabbit ears. This inspired in me a certain Elmer Fuddish compulsion to shoot a rabbit, and it was not long before Uncle Carl set me up with an old .22 rifle.

My dreams of making money soon evaporated as I began to realize that shooting the wiry jack rabbits was  no easy task. The rabbits were well camouflaged in the straw colored fields, and I only ever saw them if I spooked them by walking too close. When they were startled, they'd leap into action like those antelope on T.V. trying to evade cheetahs. They knew how to zig-zag.  Try as I might, my errant bullets did little but kick up tiny fountains of dust in the rich Kansas top soil, or pinged off stone fence-posts and ricocheted off old farm-machinery so that technically, I was more dangerous to myself than I was to the rabbits. It became obvious that my expenditure in ammunition was going to exceed any foreseeable bounty-income. Soon it simply became a challenge to see if it would be possible for me to shoot a rabbit at all.

Then, one evening it happened. The rabbit took off. It started zigging to the left. I anticipated it's zag to the right, got a good lead on it, pulled the trigger. I watched in amazement, then horror as the rabbit ran at top speed into the path of my bullet. In an airborne instant, the heavy impact of the bullet shattered the graceful rhythm of its stride. It fell from the sky in uncoordinated, sloppy summersaults, like a rag doll — like a race car flipping end for end.

I walked out to my kill. I looked down at my victim with conflicting emotions. I was excited and proud that I had finally achieved my goal, but I was also surprised by the finality of my act, the taking of life. I reached down to claim my trophy. I picked it up by the back legs and headed back to the homestead. The body was limp, but still warm, and as I walked, some last firing of synapses caused those back legs to kick and spasm as if resurrected and angry. It frightened me and I dropped it like a hot potato.

When that rabbit was running, it was beautiful. It had been shaped by its environment over endless millennia to evade its predators. Now it lay in the dirt growing cold — a bloody bag of organs and meat.

 Uncle Carl added the rabbit's ears to the collection with a tack and we looked at them for a silent moment. I looked to Uncle Carl for a clue about how I should be feeling. He didn't give me any clues.

Ol' Blue, the truck in which I learned to drive.

There once was a guy named Steve C. He was a foreman for a construction company — a company that I worked for as an employee of a painting sub-contractor. One year, Steve built a laboratory for a biotech company. He was a handy guy to have around since he was both intelligent and resourceful. As he worked at finishing the building, the client began moving biotech equipment into the new facility, and Steve found he was able to help with setting up the production line and evidently demonstrated an aptitude that won him a new job as the new production manager for the biotech company.

Soon the new biotech company began to grow and Steve found he needed to hire more people to run the machines. He began hiring his close friends from the construction industry. This made sense, because they were people he knew he could work with. However, they all had similar interests, the greatest of which was a common appreciation for hunting. When hunting season rolled around, Steve suddenly realized his mistake. Everyone wanted to go hunting which would leave the production line understaffed. What they needed was another worker who didn't hunt.

That's how I became a laboratory technician.

To be continued...

Part 2 is now available at:

The Narrative Image NAVIGATION AID

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