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Wednesday, April 5, 2017


“These people have learned not from books, but in the fields, in the wood, on the river bank. Their teachers have been the birds themselves, when they sang to them, the sun when it left a glow of crimson behind it at setting, the very trees, and wild herbs.”
  Anton Chekhov, “A Day in the Country”

“We are tossed about by external causes in many ways, and like waves driven by contrary winds, we waver and are unconscious of the issue and our fate.' We think we are most ourselves when we are most passionate, whereas it is then we are most passive, caught in some ancestral torrent of impulse or feeling, and swept on to a precipitate reaction which meets only part of the situation because without thought only part of a situation can be perceived.”
 ― Will Durant, The Story of Philosophy

“Thanks, Scott, for your comments. I am grateful.
Very simply, we can encounter God without even reading the Bible. Aquinas says if you want to know something about God, then begin with creation.


I'm having trouble finding attribution info for the Pee Wee picture - likely Warner Pictures
Who’s that sexy thang I see over there?
That’s me, standin’ in the mirror…
…If I was you, I’d want to be me too.
—Meghan Trainor

Elvis picture from very cool poster at

‘Cause I’m a model, you know what I mean
And I do my little turn on the catwalk
Yeah, on the catwalk
On the catwalk, yeah
I shake my little tush on the catwalk
Right Said Fred

Portland to Charlotte, to Miami, to Quito and finally to Baltra Island in the Galapagos archipelago (600 miles off the coast of Ecuador) - Map illustration derived from Google Earth
The Ecuadorian flight attendants were uncannily identical in appearance — from their red hats (faintly reminiscent of Hot Dog on a Stick Uniforms) to their tight bun hairdos to their matching lipstick — so that I was unsure whether I had slid into an alternate universe of 60’s stewardesses or a future populated by identical clones. In either case, they performed their jobs with military efficiency and no sooner had the plane landed, then all the doors were thrown open and we passengers spilled down the closest set of ramp- stairs to the sun baked tarmac.

Though I am handicapped by a severe case of monolingualism, the airport personnel were experienced enough, and our cruise guides attentive enough that I merely needed the skills of a cow to be herded to the transfer buses. Languid iguanas watched our little tourist parade with their impassive sidewise gaze, a gaze that because it only half meets our own, manages to seem indifferent…but probably really is indifferent. 

All the buses followed a curvy, dusty road down to what appeared to be the only destination on Baltra, a dock on the side of a small bay, where we were all deposited — a giant bolus of privileged humanity — into a staging area then sifted and spread onto our prospective boats.

While the fleet of excursion vessels prepared to disperse among the different islands, the passengers of the Nemo III were baptized into the equatorial waters of the bay through voluntary self-dunkings as we strove to demonstrate our capacities to regain entry into the kayaks we would soon be using (provided we mastered this skill). For me it perfectly accentuated the idea that I was suddenly immersed into a new environment.

Darwin spent 1 month in the Galapagos (Sept. 17th – Oct. 17th), though only 24 days actually spent on just 4 of the islands. Ultimately, I would set foot on 5 different islands and 4 islets over the course of 7 days, only two of which I’d have in common with Darwin. I mention this because when I figured it out, I was surprised at how little time he spent there on a voyage that lasted almost 5 years. Clearly, the ideas that were eventually triggered by observations in the Galapagos occurred only in the context of the rest of his observations on the South American Continent and other island chains spanning the globe — not to mention his academic training. I imagine he had to know very well how things were 'KNOWN' to be, in order to recognize the subtle importance of say, tortoises customized for each island.

The Galapagos Islands are volcanos that arise from the activity of a stationary hotspot underneath the Nazca tectonic plate. As the Nazca plate inches eastward over the hotspot on its way to subverting South America (causing frequent earthquakes in Ecuador) the resulting chain of islands poking above the ocean can be seen as a trace of the plate’s motion over geologic time, the islands to the West being the youngest and the Easternmost the oldest and most weathered. This idea of tectonic plates — drifting and colliding continental jigsaw pieces — would have been of keen interest to Darwin, who was looking for ways to explain why he was finding seashells embedded thousands of feet high in the South American mountains.

Not wasting any time, our nimble 75 foot catamaran sliced its way to North Seymour which would serve as my introduction to what the islands had to offer. “North Seymour — the island where you will ‘see more’” said Veronica the guide, seemingly embarrassed  before she even started saying it, but determined to share the dubious homophone regardless.

Our arrival at North Seymour was much like approaching a bird-shit stained jetty. I didn’t know if this was going to be a big island or a little island (I did research ahead of time, but my variable memory of 13 major islands with their alternate names didn’t include this one) and I didn’t really know enough to have a preference. In retrospect, I can imagine that this little flat shelf was a remnant of a Santa Cruz lava flow in a long past distant epoch. 

Long before we arrived I could see distinctive birds circling over the island vultures…or perhaps pterodactyls.

The crew took us to shore in what, by common consent, was referred to as a ‘panga’…but having grown up with Jacques Cousteau specials, I thought it resembled a ‘Zodiac’ (and began to wish I had a Steve Zissou style red watch-cap instead of my camouflaged boonie hat).

Nocturnal gull

Andres, our other guide (besides Veronica) soon explained that the circling birds were frigate birds. There were two kinds of frigate birds. Great frigate birds and Magnificent frigate birds. When Andres said it, it sounded like Mag-KNEE-fee-cent frigate birds, which to my mind, sounded somehow more spectacular. Turns out, these birds make a living by stealing from other birds which explains why they patrol the territory from high in the sky like opportunistic drones looking for a vulnerable target.  Andres explained how to distinguish magnificent frigate birds from great frigate birds (something about an ‘M’ on their chests?), but as I was often some distance away frantically searching my backpack for the wrong lens to use during our guide’s comprehensive explanations, I missed this subtle point.

A male frigate bird with red inflated I'm-ready-to-have-sex display

Like a peacock's ridiculous tail, this football sized red balloon shows how bad-assed its owner is since it can still perform all its alpha-bird functions while heavily disadvantaged.

Probably not a male frigate bird

The frigate bird's nest is not very elaborate.

The male frigate bird blows up his throat pouch display which essentially screams, "Pay attention to me! Pay attention to me!" Eventually he will stage a big production with his wings which will unfortunately remind me of Chinese Opera.

At this point, unexpectedly thrown (well, not entirely unexpectedly thrown) into a real life nature documentary, I began to imagine I could hear David Attenborough’s voice commenting about everything I happened to look at.  High above me, a dozen fork- tailed birds wheeled in a haphazard gyre while my audio hallucination whispered  “…frigate birds spend —months — continuously airborne at sea.” in that hushed way he has that makes it feel like you’re conspiring together not to have the T.V. animals over-hear.

Ecuadorians have come to treasure their Galapagos Islands and have grown serious about protecting them and the island’s unique species. To visit the islands, you need to be accompanied by a certified guide, stay on designated trails, refrain from bringing food, and keep a prescribed distance from the animals no matter how they try to interact with you.

Historically, the animals of the Galapagos (even many of the birds) exhibit no fear of humans. It’s as if they are consciously ignoring you. But when it comes to the sea lions, it seems they not only understand they are immune from human disturbance, they like to rub that fact in your face — how else to explain their propensity to nap in the middle of the designated trails? Because of this behavior, and others, it is easy for me to feel kinship with these fellow mammals who have abandoned life on land.

Sea lions are kind of perfect role models if you want to take a lazy vacation. But from what I’ve seen, they share my short-sightedness with regard to career goals.

In the distance, I noted Daphne Major’s abrupt shoreline and appreciated all the more the story of Peter and Rosemary Grant’s research as chronicled in The Beak of the Finch — a book I’d been reading previous to my trip — an amazing account that gives insight into the incredible discipline required to see evolution happen in real time ( 
In their unique island laboratory, they’ve been continuously studying generations of finches for 40 years.

August falls into the Galapagos’ garĂșa season, cooler weather marked by mist and clouds that shroud the highlands. The guides explained that the Humboldt current (cold water circulating up from the Antarctic) moderates the temperature here to the upper, middle seventies (Fahrenheit) while also infusing the water with a wealth of plankton and krill. Otherwise, there isn’t much precipitation, and the lower landscapes where the clouds cannot reach remain arid and appear desert-like. 

The shrub-like trees that grow here remind me of the krummholz back home that vie for existence at the upper limits of the timberline. Krummholz is the German word that means twisted wood and should never be used in the sentence, “I want to kiss you so please wipe that cheese away from your krummholz.”

Cacti will (unbeknownst to me at this point) greet us in many different forms as we hop from island to island, but for now, this one tempts the local land iguanas with fleshy pads of refreshment…almost out of reach.

(Yes I know. This iguana is not actually eating cactus. But at the evening photo review, it became evident that others had caught it in the act of propping itself on its hind legs to grasp at the lowest hanging cactus pads)

When I shared these pictures at the evening picture review, my serendipitous travel cohorts accused me of being a typical guy — focused primarily on butts and boobies (booby jokes never get old…right? I mean right?).

As I watched the booby set about laying out a poop nest, various questions occurred to me:
Is this a booby dream home?
Do prospective mates find this sexy?
How does one compare this to other poop nests (texture, smell, distance expelled, or symmetrical dispersal)?
Is there a booby vocational college that teaches poop-nests 101 — and if not, what the hell?
How many meals does this represent?
Is there an equivalent human behavior (for instance, in a material culture, do we tend to surround ourselves with a lot of shit?)
Is that anus blue?
…and did you just catch yourself looking?

By strictly evolutionary standards, I’m an abject failure. As an animal standing amidst all my cousin animals, I wonder if my failure is due to succumbing to bad instincts, or overruling good instincts with untested ideologies (free will, individuality, golden rules) springing from an experimental brain. Would I be happier if, in my late teens, I was seized by an overpowering urge to make a poop-nest?

Is my genetic makeup such that I would have better thrived as a Viking, utilizing my bulk to wield a broad-sword or battle axe —“… to crush my enemies, see them driven before me…” — only to be (upon return from raiding parties) forever confounded by smaller, quicker-thinking lawyers and accountants?

A well adjusted blue-footed booby making a living, diving recklessly into the ocean for fish among the rocks and surf.

Boobies doing what comes naturally.

To be continued...

see also:

Galapagos Pilgrimage Part 1

Galapagos Pilgrimage Part 2

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 Barber 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:


Just a reminder:

All text and images appearing here are protected by copyright (unless otherwise noted), s.d. 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016 and 2017.