Wednesday, August 14, 2019

Pageant of Evolution (2), geological rearranging.

Here's my second Pageant of Evolution column, of course as I've said before I never finish projects I simply meet deadlines.  So it is that the version I'm sharing has gone through some more edits since the one that appeared at the Four Corners Free Press.  I'll be following this post with more highlighted video lectures by real sciences who will supply real substance behind this enthusiast's overview of Earth's magnificent Evolution.

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Last month’s Four Corners Free Press column left off with Earth looking like a snowball roughly seven hundred million years ago.  In fact, there were a number of snowball epochs in Earth’s past, though most didn’t actually have glaciers growing all the way to the equator.  For this column those specifics make little difference since my point is mainly to introduce folks to the marvelous dynamics of Earth’s Evolution.  More exacting details are easy to find on the internet.

Monday, August 12, 2019

Diary August 11, 2019 - Defeated? What's it mean?

I received the following comment in response to my "Diary July 31, 2019" which was an introduction of sorts to why I've dedicated this month to Earth's Pageant of Evolution.  Since it's clear that “Defeat” is something we rationalists will be forced to deal with more and more, I’ve decided to offer this challenging response as a stand alone post.  

Thanks, it's nice to know some can relate to what I'm trying to write about. 

"Defeated" is such an ugly word.  How about righteously pissed off, heartbreakingly disappointed, fatalistic resignation as I watch the tipping points sneak past an apathetic willfully ignorant public thanks to ruthlessly dishonest propaganda media empires.  Sure, I’ve felt profound defeats that have floored me, but if you're alive you can’t stay on the floor for long.

You know in our own life's delicate dance we're required to be 'Present' to something - what will it be?  I can't watch Trump news, too much 'crazy making' going on, the normalization of their unAmerican dysfunctionality and their hideous disconnect from physical reality is too much.  Add to that continued Democratic Party ineptness, massive voter indifference, and it's simply horrifying for me to keep watching since it's beyond my ability to do anything about - when so few actually care or are aware.  All that's left for me is to continue striving to better enunciate rational fundamental principles and to continue living my life with dignity best I can.

My inner spirit is alive and well - supported by appreciation for down to Earth reality along with my place in the flow of Evolution, (rather than dependence on self-delusion and angry insecurity).  I've lived a life that the young me would be as proud of as the old me is.  No horror can take that away.  Besides, I'm aware that I'm a passionate empathetic guy and I learned long ago getting my heart kicked in and torn up now and then, is part of living an engaged life, then we get up, dust off and cowboy up.  

Saturday, August 10, 2019

Michael Russell - what a scientist sounds like - Emergence, serpentinization engine, electron exchange

If you enjoyed Robert Hazen and Jack Szostak, then you’ll want to add Michael Russell since his talks compliments what Dr. Szostak was explaining.  Of course, what you get out of these lectures is proportional to how well you already know the topic.  That said, any intelligent curious person can still get plenty of fascinating insights and better appreciation for the complexities scientists have come to understand by listening and then doing a little side research for themselves.  It's not like the fundamentals themselves are that difficult, it is the details that get impossibly complex and difficult to grasp.

The key is an honest curiosity to become aware of the world we live within.

With that I present another another couple lectures about the physics of Life’s folds within folds of cumulative harmonic complexity flowing down the cascade of time, one day at a time, one second at a time.  Before getting to my next essay.

Michael Russell: On the Emergence of Life Through "Negative" Entropy Trapping
MoleCluesTV,  Published on Mar 26, 2014

Dr Michael Russel's lecture at the Molecular Frontiers Symposium at the Royal Swedish Academy of Sciences in Stockholm, Sweden, May 2011. The topic of the symposium was "Origin of Life and Molecular Evolution". Check our YouTube channel for more exciting science videos! For more information, visit

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Origin of life through convection and serpentinization - Michael Russell (SETI Talks)

The alkaline hydrothermal theory for the emergence of life holds that the endergonic (thermodynamically uphill) reactions vital for life's origin and continued existence require free energy converters (nano-engines) fuelled by various disequilibria. The first two primary engines were i) a carbon fixation engine to generate the organic building blocks of life by reaction between hydrothermal CH4 and H2 with the CO2 and NO in atmosphere and ocean, ii) a proton pyrophosphatase engine exploiting the natural pH gradient between alkaline hydrothermal solution and acidulous ocean to drive biosynthesis by condensations of these same building blocks.

To this end there occurred on the early Earth and other such rocky bodies, inorganic prebiotic molecules that would have been precipitated at the interface between a submarine alkaline hydrothermal solution and the metal-bearing acidulous ocean.

Dr. Russell will show how these metals, especially iron, occurred as readymade nano-scale sulfides and oxides with the same structures and valences as the active centers of those biotic metalloenzymes shown to be present in the Last Universal Common Ancestor of all life.


Interest: The emergence of life and of oxygenic photosynthesis
Michael Russell | NASA Jet Propulsion Laboratory

The discovery of fossil hydrothermal chimneys in Ireland got us interested in the emergence of life, particularly in a hydrothermal source of energy and substrate.
1. We suggest that basic to life’s emergence was the formation of mineral compartments across which steep redox, pH, ionic and temperature gradients were poised. The pH gradient acting across the inorganic membrane (acid outside, alkaline inside) constituted a natural protonmotive force, and the redox gradient could augment this force by chemiosmosis. The energy focused across the barrier in this way is commensurate with that required by all life. Also the compartments solve the “concentration problem”.
2. The theory predicted the discovery of off-ridge alkaline hydrothermal springs of moderate temperature by Kelley et al. (2001, 2005).
3. As expected, these springs contain significant (i.e., 15 mmol/litre) H2, which could reduce the CO2 concentrated in the first oceans on this and other comparable planets. This process evolved from a geochemical feedback system to an autogenic metabolism.
4. We are impressed by the structural similarity between greigite (a Ni-Fe-sulfide) and the active centres of various essential proteins that must have existed within the first microbes (e.g., CODH/ACS & ferredoxins). Theoretically it is possible for moieties of this mineral structure to be sequestered by short achiral peptides and the whole to act as the first electron transfer agents, hydrogenases and synthetases.
5. Echoing early workers such as Fuchs, Wood and Edwards, it seems that metals and metal sulfides were first to do the biochemical work of CO2 fixation, and that the acetyl-coenzyme-A pathway developed first in an alkaline hydrothermal mound – a mound that acted as a flow reactor and affinity column. The generation of acetate and methane during serpentinization may be speeded up in the mound and eventually “quickened” through the onset of life at the same site. The different outcomes of reduction, to acetate- or methane-generating metabolists, may have gelled genetically to produce representatives of the two prokaryotic domains, viz., the acetogenic bacteria and the methanoarchaea
6. The continued coupling between life and convection may also explain the onset of oxygenic photosynthesis. A feature of this model is that a Ca-Mn-oxide entity in littoral manganiferous sediments obducted to the photic zone, was co-opted as the Oxygen-Evolving Complex by PS2 in the cyanobacterial ancestor. If so, it would appear that both chemosynthesis and oxygenic photosynthesis emerged within the confines of mineral constituents (Ni-Fe sulfides and Ca-Mn oxides respectively) — constituents that were then co-opted as catalysts by their prokaryotic hosts.
7. Experiments are underway to test the idea that a Hadean hydrothermal mound would act as a flow-through chemical reactor and affinity column to produce organic molecules from CO2 and H2.

Our chemical Eden
Tim Requarth  |  January 11, 2016

To figure out the origin of life might take a conceptual shift towards seeing it as a pattern of molecular energy

Mike Russell found his moment of inspiration on a warm spring evening in Glasgow in 1983, when his 11-year-old son broke a new toy. The toy in question was a chemical garden, a small plastic tank in which stalagmite-like tendrils grew out of seed crystals placed in a mineral solution. Although the tendrils appeared solid from the outside, when shattered they revealed their true nature: each one was actually a network of hollow tubes, like bundles of tiny cocktail straws.
At the time, Russell, a geologist, was struggling to understand an unusual rock he had recently found. It, too, was solid on the outside but inside was full of hollow tubes, their thin walls riddled with microscopic compartments. It dawned on him then that this rock …
… What seemed obvious to Russell was that his hypothetical chemical gardens could solve one of the deepest riddles of life’s origin: the energy problem. Then as now, many leading theories of life’s origins had their roots in Charles Darwin’s speculation of a ‘warm little pond’, in which inanimate matter, energised by heat, sunlight or lightning, formed complex molecules that eventually began reproducing themselves. For decades, most origin-of-life research has focused on how such self-replicating chemistry could have arisen. They largely brushed aside the other key question, how the first living things obtained the energy to grow, reproduce and evolve to greater complexity. 
But in Russell’s mind, the origin of life and the source of the energy it needed were a single issue, the two parts inextricably intertwined. …

New Study Outlines 'Water World' Theory of Life's Origins

Whitney Clavin, News Media Contact
Jet Propulsion Laboratory, Pasadena, Calif.
April 15, 2014  

Life took root more than four billion years ago on our nascent Earth, a wetter and harsher place than now, bathed in sizzling ultraviolet rays. What started out as simple cells ultimately transformed into slime molds, frogs, elephants, humans and the rest of our planet's living kingdoms. How did it all begin?
A new study from researchers at NASA's Jet Propulsion Laboratory in Pasadena, Calif., and the Icy Worlds team at NASA's Astrobiology Institute, based at NASA's Ames Research Center in Moffett Field, Calif., describes how electrical energy naturally produced at the sea floor might have given rise to life. While the scientists had already proposed this hypothesis -- called "submarine alkaline hydrothermal emergence of life" -- the new report assembles decades of field, laboratory and theoretical research into a grand, unified picture.
According to the findings, which also can be thought of as the "water world" theory, …


New theory for origin of life

Mineral cells might have incubated first living things.
Nature | John Whitfield

Published online 4 December 2002 | Nature | doi:10.1038/news021202-2

Life on Earth may have begun in rocks on the ocean floor. More than 4 billion years ago, tiny cavities in minerals may have served as the first cells, two biologists are proposing1. Other researchers argue that the idea leaves many questions unanswered.
The key to the new theory is iron sulphide. Hot springs deposit a honeycomb of this mineral on the ocean floor, with pockets a few hundredths of a millimetre across. This would have been the ideal place for life to get going, say William Martin, of Heinrich-Heine University in Dusseldorf, Germany, and Michael Russell of the Scottish Universities Environmental Research Centre in Glasgow, UK. …


Then there aways seems to be a bit more… ever more folds within folds of cumulative harmonic complexity flowing down the cascade of time, for the receptive and perceptive.

The Manganese-calcium oxide cluster of Photosystem II
and its assimilation by the Cyanobacteria
Alumnus, Department of Chemistry
Florida State University, Tallahassee, FL, USA
June 2006


Wednesday, August 7, 2019

Jack Szostak - what a scientist sounds like - Origins, geochemistry to biochemistry.

Whereas Robert Hazen went after the origins problem from a mineralogist's perspective, Professor of chemistry and chemical biology, the 2009 Nobel Prize laureate Jack Szostak goes at it from his expertise, the biologist’s perspective.  
Both have found that they needed to combine their expertise and to reach out to other branches of science in order to constructively tackle the problem of understanding the transition from geochemistry to biochemistry and then to full blown life as we know it.
He is another excellent public speaker so his talks are a joy to listen to.  Here I share a collection of seven informative videos of his talks along with some bio information.

Jack Szostak: The Early Earth and the Origins of Cellular Life

MoleCluesTVPublished on May 16, 2019  (32:11 min.)

Lecture by Dr Jack Szostak, 2009 Nobel laureate in Physiology or Medicine, at the Molecular Frontiers Symposium "Planet Earth: A Scientific Journey", at Stockholm University May 9-10, 2019.

The Szostak Lab

Sunday, August 4, 2019

Robert Hazen - what a scientist sounds like - Origins, mineral evolution

In order to get a change of scenery I spent the summer of 2006 working north of Boulder and living in a Teepee.  My transportation was mainly my bike and Longmont was a better destination than crowded Boulder.  It also sported a very nice library with a big non-fiction audio book collection, which was very exciting considering I’d long run out of decent nonfictions at my home town fiction loving library.  Browsing through their rows of “The Great Courses” series, I spied something new "Origins of Life."

Origins of Life
Professor Robert M. Hazen, Ph.D.
George Mason University
The Great - course 1515

With a title like that, I couldn’t say no.  It turned out to deliver one astounding surprise after another, along with a few revelations to boot.  I needed to listened a second time before returning, despite its 12 hour length.  Since then I've made a point of listening to pretty near every YouTube lecture featuring him and there are many. 

I also liked that this new understanding also vindicates my own reflexive disgust at having read some serious scientists assume that for the first few billions of years nothing happened on Earth.  It seemed a ridiculous notion to me and so it was.  Just like junk DNA, or wasted brain matter, nonsense - it was simply that we hadn’t learned enough to know what it was doing yet.  Seems that conceit and short sightedness has been a predominate feature in human thinking going way back.

The beauty of science is that truth and honesty and evidence is valued - authoritative facts win in the end.  This is because scientists belong to a community of dedicated, competitive, informed, skeptical individuals who buy into the basic premise that: We Need Each Other To Keep Ourselves Honest.  
Also they work under a set of rules, that puts honest observation at the top of the list, because constructively learning about our planet, along with her ways and means, is the goal.  A place where geophysical facts rule over personal opinion and preferences. 
According to Neal deGrasse Tyson this is how science operates:
(1) Question authority. No idea is true just because someone says so, including me. 
(2) Think for yourself. Question yourself. Don't believe anything just because you want to. Believing something doesn't make it so. 
(3) Test ideas by the evidence gained from observation and experiment. If a favorite idea fails a well-designed test, it's wrong. Get over it. 
(4) Follow the evidence wherever it leads. If you have no evidence, reserve judgment. 
And perhaps the most important rule of all...
(5) Remember: you could be wrong. Even the best scientists have been wrong about some things. Newton, Einstein, and every other great scientist in history -- they all made mistakes. Of course they did. They were human. 
Science is a way to keep from fooling ourselves, and each other.
{Mistakes are learning opportunities !}

Friday, August 2, 2019

Pageant of Evolution (1), the warm up.

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A couple month's ago I was feeling guilty for not submitted anything to the Four Corners Free Press in a while.  Also I'd been all involved in that filthy downer job of sorting through Jim Steele's "What's Natural?" deceptions and I needed something positive.

So, with days to go before deadline, I decided to write about the Pageant of Evolution.  I cheated by rewriting the evolution pitch off this blog.  I though it would be a cinch since I think about Evolution a lot anyways.

During those days (and since) I tapped into a wonderful vain of scientific lectures on YouTube regarding latest findings in "origins" research, as well as the Evolution process in general to help refresh my memory and to get my creative juices flowing.

Instead I wound up chagrined and annoyed by how out of date I'd allowed myself to get.  But as they say, the project is never finished you only meet deadlines.  So even as I was summiting this column, I knew I had to give it another shot.  I'm sharing this Pageant of Evolution #1 because I want to explore my own learning process and the development, dare I say evolution, of my understanding.  Sharing the agony of defeat, along with the joy of victory and constructive learning.

Besides being chagrined, I was thinking of times I'd referred to myself as a student of climate science and now feeling mighty silly about that conceit.  I may be a genuine "Student of Life" but I'm no scholar, no "Student" - I come to realize, to appreciate, that I'm a self-taught  "Enthusiast," a lover, a poet, Earth and life are a stage and experiencing it is my game - with science being my clearest path to better understanding my observations.

A real student of science possesses a discipline, a focus and sticktoitiveness I can't muster.  I'm like a happy puppy dog were every new scent is a fascinating adventure.  Though at 64, a creakier puppy for sure, oh but what a collection of experiences and learning.

Wednesday, July 31, 2019

Diary July 31, 2019

This past winter and spring I spent a good deal of time dissecting Jim Steele’s malicious game of deliberate deception in his Pacifica Tribune’s “What’s Natural?’ column and it was taking its toll.

On the one hand, I like the work of studying others’ writings - investigating and searching out new information, double checking my own assertions and recollections, learning, relearning and taking the time to examine, recognize and expose the ‘mechanics of deception’ in action.  In that way it’s my classroom and a positive exercise.

On the other hand, it’s profoundly depressing coming face to face with these real life intellectual zombies that never ever seem to change.  They pompously cry for debate, yet try having a serious constructive dialogue with them.  First comes the attitudes of superiority, then the dismissal, then avoidance, then insults and derision, then they run and hide, but never an adult discussion.  

And no one seems to care much!  Free pass for all.  So they get away with it, over and over like a spreading pathogen, and no one seems capable of doing anything about it.

Ask questions, make challenges, explain the simple and well understood science of Earth’s climate.  Write and rewrite, present evidence, teach, reason, strive till you're blue.  Yet not a word is heard, not a lesson is absorbed.   Absolutely nothing gets incorporated into their understanding.  Utter hopelessness.

Contrarian arguments today are exactly the same as they were ten, twenty and more years ago.  It’s like the immortal words of Homer Simpson: “No Marge, I didn’t learn a thing.”