GALAPAGOS PILGRIMAGE - PART TWO

SEEING THINGS

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 life...is 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: (http://tolweb.org/tree/)

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.

1835

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.
http://www.rogerebert.com/reviews/master-and-commander-the-far-side-of-the-world-2003

2016

The Nemo III

Floor plans compared

First stop: North Seymour...to be continued

If you need to catch up with Part 1: https://thenarrativeimage.blogspot.com/2017/03/galapagos-pilgrimage-part-one.html

PART THREE: The Book of Nature is now available:
https://thenarrativeimage.blogspot.com/2017/04/galapagos-pilgrimage-part-three-book-of.html

My "Personal Relationship" with Smith & Bybee Lakes

Paint a man’s house and he’ll have a nice painted house for about four years.

But teach a man to paint and he’ll be able to make his canoe look like a fish.

-Old Chinese Proverb-

“So…” devil’s-advocate-Scott leads off, “…how do you have a personal relationship with a wetland area?”

“Well…” I reply, “…it isn’t quite as complicated as having an imaginary dialogue with yourself, or believing in an invisible living God who was executed (briefly) in a political dispute with first century Romans…but…I guess what I’m really describing is a certain familiarity with a physical area developed over time.”

“I see,” says devil’s-advocate-Scott (hereafter simply Rational Scott or R.S.), “you’re simply anthropomorphizing the wetland area.”

“I wish you wouldn’t be so dismissive.” I say, sensitive to the smug tones accenting Rational Scott’s immediate conclusion. I continue, “This metaphorical framework for relating to an ‘area’ as an organism may not be entirely unfounded – that is, it may lead to knowledge and understanding – I mean, it’s not out of the question…entirely?” The certitude with which I began my speech slowly dwindled away under Rational Scott’s scrutiny, his eyes laughing beneath comically furrowed brows. Sadly, what I hoped would be a statement finishes as a confidence-less question.

At this point, a wise man would probably just drop it…but it’s me after all, so I keep on talking.

Chris preparing to perform a magic trick – he’s going to make that beer disappear.

I guess you could say it all started when Chris stood up in his canoe to take a piss and tipped over into the water. This made him considerably less enamored with the canoe, and he ended up trading it for my Atari Jaguar, Sega Genesis, and 80 dollars cash. Those particular game consoles date the transaction to approximately 1995.

That’s about how long I’ve known Smith and Bybee Lakes.

That’s a pretty long relationship for me.

Metro’s kayak launch path – almost wholly underwater.

Over the years, I’ve become familiar with their many moods…and come to understand how they are affected by the seasons. For instance, right now, they’re burning the candle at both ends during these longest days of the year, and putting up with a serious water retention issue.

There’s a nature trail that loops around a short peninsula that juts in-between Smith Lake and Bybee Lake. This observation structure on the east (Smith) side of the peninsula is up to its handrail in water.

…and the path leading to it is also submerged.

When the region's winter supply of water is still tied up in the mountain snowpack, the trail looks more like this.

But this spring, melting snow and endless rain have resulted in a path that looks like this.

The bird-blind on the west (Bybee) side of the peninsula is also standing in water.

Comparison shot

Invasive species continually vie for dominance in an eco-system beset by the challenges of being in proximity to vast numbers of people. Despite weeks of flooding, purple loosestrife manages to keep its head above water.

Last year, some channels were completely clogged with it.

And other plant species worked at converting all the water to biomass.

As the importance of wetlands has become understood – its capacity for filtering and cleaning water, its contributions toward flood control and its ability to support diverse wildlife – Metro has made enlightened efforts to impose the seasonal variation of water levels on the area through the installation of a water control structure. While not a perfect science, they do their best to mimic the natural rhythms of seasonal wetlands.

This piece of ‘designed’ wood brings me the message that the water control structure is currently not exercising much control.

The water control structure is completely submerged on my 06-25-11 visit.

Water was already rushing into the lake from the Columbia slough as early as

04-02-11

In August of 2009, water levels were considerably lower.

One of the characters I met at Bybee Lake.

He used to tell better stories in his younger days, when he still had limbs for gesticulating.

Another invasive species – the yellow flag Iris.

These things may look delicate and fragile but are every bit as resilient as those broomsticks in The Sorcerer’s Apprentice.

The Force is strong with this one.

I think this is beautiful.

But I don’t know why I think it’s beautiful.

I used to wonder if maybe preferences for landscapes (lakescapes?) were written into our genetic code somehow – perhaps some instinct that leads us to environments rich with life. I tried to research it a little, but the general consensus is that, given our origins, we’d likely be attracted to landscapes that resemble Africa’s savannahs.

But then again, we have the capacity to supplement our ‘instincts’ with the memory of our experiences (plus those memories available to us from our cultures) and we can play the ‘what if’ game, like, what if I had a fishing pole, or what if there are deer trapped on that peninsula or …remember that last time I caught a big catfish…wasn’t it on blue water as smooth as this where startled carp slapped the bottom of the boat, just like they’re doing now?

The sun presses against the back of my neck with almost tangible fingers, intent on tanning my hide – that is, intent on converting it to leather. I paddle in-between the wading trees and float in the cool air beneath the forest canopy. Here where the trees respire, I feel as if I partake in the breath of life.

Volumes of air move purposefully across temperature and pressure gradients as the sun withdraws its face.

I look for the ribbon that marks my route through the trees to the shore.