Atom Smith

February 4, 2015 “Darwinian evolution is a law of physics, not just an organizing principle of biology - an inevitable result of how information is organized in complex systems.  If so, life was inevitable, not a fluke.”  Manfred Eigen - Nobel Laureate

“No person has been more responsible for more drastic modifications of the average person’s world view than Charles Darwin.”  Ernst Mayr - renowned 20th C. bologist

“Darwin founded a new branch of the philosophy of science.  He introduced historicity.”


  • E. Mayr

“A Christianity of miracles or one of natural truth?” - Matthew Arnold( 1822-1888)

Darwinism: Time, chance and contingency at work - no God required

Darwinism: Nothing is pre-determined as a final cause.  Life is NOT working toward a known end,

“Mid-Victorian evangelicals were the proper heirs of the Reformation and 17th century Puritan divines.”

“The Evangelical emphasis on an imaginative and emotional experience of Christ made this form of Protestantism a religious equivalent and stimulus of English Romanticism.  It made belief a living factor in people’s lives, not a dour or restrictive force.  The fact is , it provided an emotional, imaginative form of belief that endowed adherents with a sense of their own identities.”

“Darwinism dissolves Victorian Christian typology.”

- George Landow - Brown University

Christian contempt for the temporal world slowly dissolved over the course of the Victorian era.

Mid-Victorian zeitgeist, the philosophical underpinning, the idea-air being breathed by  Victorians contained molecules of Smith, Lyell, Malthus, Bentham, Carlyle, Arnold and Lamarck along with a turbulent broth of residual Puritan Christianity.  From this air Darwin precipitated his notion of evolution.

There are four key parts of Darwin’s theory:

  1. Non-constancy of species - i.e. species evolve over time ( an outrageous noton in early-mid  Victorian era)
  2. Evolution begets branching of organisms, descent from common ancestor of all species.
  3. Gradualism - The gradual, accumulated effects of daily events observable in real time over vast amounts of time - tens, hundreds of millions of years.
  4. Natural selection upon individuals of a species as the primary mechanism of change in organisms.

Four men formed the molten core of the Victorian zeitgeist, all of particular significance to Darwin:  Adam Smith, Charles Lyell and Thomas Malthus and Jeremy Bentham.

General notions floating in Mid-Victorian air included the idea of civilization working inexorably  toward progress, man’s conquest of and dominance over nature and Man’s preeminent position at the top of the animal hierarchy.  There was a bourgeois-upper class awareness of unprecedented transition - of change - of evolution in the air.  All of society was evolving very rapidly toward a better condition ( it couldn’t get no worse !).  The pressure against “Steady-State” Evangelical Christianity of the day became immense.

Adam Smith (1723-1790)  In his iconic tome “The Wealth of Nations”  Smith makes the following observations: People are motivated by self-interest.  People work harder for personal gain.  All groups interacting and competing with one another produce the best goods at the cheapest price.  Creativity emerges as people strive to meet the needs of a supply and demand economy.  Darwin expanded these ideas to the realm of all organisms forming the core of his theory.

Charles Lyell (1797-1875) “The present is the key to the past.” - foremost Victorian geologist, brought to light the vastness of geological time with forces working continuously on Earth and the effects of  time to transform small change into very large effects: “Uniformitarianism”  Darwin used this idea to explain the effects of eons on the relatedness of all living things. The extension of processes seen in present time back through to their origin, their gradual change, their evolution.

Thomas Malthus ( 1766-1834) “An Essay On the Principle of Population”

“The increase of population is limited by the means of subsistance.”  “The actual population is kept equal to the means of subsistence by misery and vice.”

Malthus  illuminated the effects of large populations on their members as they compete for scarce resources.  Darwin noted that this pressure has the effect of selecting for the fittest.

Jeremy Bentham (1748-1832)

“People will lean toward that which is beneficial in the long term.”

“Individual rational decision making would promote greater happiness-felicific calculus.”

“Law without a legislator”

“Greatest happiness for the greatest number is the foundation of moral legislation.”

“Self interest - pleasure over pain”

Darwin’s paradigm-shifting book:  On The Origin of Species, published in 1861, was saturated with the ideas percolating through his Victorian zeit.  Adam Smith for the notion of  groups left to ther own devices, Charles  Lyell,  for the immensity of geological-evolutionary  time and the gradualism and uniformity of change, for Thomas Malthus on the pressure of individuals in a population on one another as they compete for food, shelter, sex, prestige - the stuff of life. Jeremy Bentham - the advantage of being left alone.

For Darwin the central battle for life on Earth was played out by individual members of different species.  The individual human, tiger, rose bush, microorganism was the causal agent of evolution, the center of the action, the nexus.  150 years later Stephen Jay Gould proposed that the nexus was at the next level up the taxonomic ladder- the species,  Richard Dawkins asserts it is a level lower than that preferred by Darwin- the gene.

Perhaps the causal level is at the atom.  At the carbon, hydrogen and or oxygen atoms in the base pairs composing  RNA and DNA molecules.  It is the atom which, if left to its own devices, will evolve toward function,  toward survivability.  “Decisions” made by atoms in bond formation during metabolism or replication are the crux of evolution.  Atoms struggle for dominance.  Atoms thrive or starve.  Atoms change launching an act of symbiosis or competition that proves useful and gets locked into the sustem or proves of no use or destructive and gets rejected.  “The Invisible Hand” made visible today by Non-contact Atomic Force Microscopy among many other methods of seeing at the atomic scale.

“Thoughts escape the brain and enter the environment bya coding process that converts them from a neural form into rhythmic,mechanical displacements of soft tissue ( mouth movement or fingers on a keyboard or pen on paper)” - Paul King -computational neuroscientist -  MIT

JB questions:

  1. When does a parasite become a symbiont?  A.  when its presence is obvious it remains a parasite, when it blends well and its effect is primarily positive,  it is a symbiont.
  2. Are “good” bacteria always “good” ?  Do “good” bacteria ever go bad - turn against their host?
  3. Do numbers of bacterial individuals effect goodness or badness?  Does one’s immune system keep numbers in check throughout the host organism’s life?  say “good” unit 500 million then bad at greater than this number - you become ill.  Phagocytes gone ineffective.
  4. Can “bad” microorganisms be tamed to do good work.
  5. Do antibiotics kill all bacteria in my gut or just some of them?
  6. What antibiotics have the worst ill effects on human digestion?
  7. Do bacteria affect glandular activity? Protein synthesis?  Hormone synthesis?
  8. Do all of the antibiotics given to American cattle wreck their digestive process?
  9. Are atomic constituents of a protein molecule motivated by self interest or cooperation?  How about “motivation” of nucleic acids?
  10. Do people work harder for personal gain than they would if whipped by a slavemaster?
  11. Do cell nucleii have slavemaster molecules that drive the other cell components?
  12. Does the cytoplasm have a slavemaster or a choir director?  A timekeeper, a boss organelle?
  13. Are gold and or silver human micronutrients?
  14. What would Adam Smith’s “government regulation” be in a cell?
  15. What represents the ‘central government’ in a cell?
  16. Is the ‘central government’ composed of neurons?  are they nearby?  Are they at the brain?
  17. If so, are these neurons chiefly electrically activated or chemically activated?
  18. Are there any neurons that carry only chemical signals and no electrical signals?
  19. Is there a fine network of nano-dendrites that reach every cell in the body?
  20. Do the liver, kidney, gall bladder, adrenal gland, pancreas,spleen, heart, lungs have neurons?
  21. Do each of these organs / glands have a specific assigned zone in the brain separate from all others for organ coordination and regulation?

“All groups interacting and competing with one another produce the best and cheapest goods.” - Adam Smith

  1.  Do cells in a single organ or organ system compete with one another in any way, for nutrients or space or a role in organ function?
  2.  Do kidney cells compete with heart cells under any circumstances?
  3.  If starving of any nutrient what is the hierarchy of service among organ systems?
  4.  Does the brain eat first or last?
  5.  Is there inter-organ cannibalism in any instance?
  6.  Is there a gland or a protein that functions as the director of cannibal dining order of service.  Is it first come-first served?  Is there any evidence of altruism at this level?

“Creativity emerges as people strive to meet the needs of a supply and demand economy.” - Adam Smith

  1.  does genetic mutation, symbiosis, parasitism emerge as cell parts or entire cells strive t meet the needs of supply and demand?
  2.  There are thousands of different proteins in a cell.  How are needs assessed and by what organelle or metabolic process / structure?
  3.  what is “need” at a cell?  mitochondria need oxygen.  Cells need to expel CO2 and other waste.
  4.  what is cell waste?  Is any of it a nutrient for other cells or metabolic systems?
  5.  Is all cell waste ejected from cell by the same process?  If not, how many different methods of “taking out the trash”

“When one group organizes to dominate a market it is beneficial to the entity but does little of no good for society.” - Adam Smith

  1.  Does existence imply dominaton?  Is there a positive amount of “unionism” or “corporate behavior”  at the cell?
  2.  Cancer cells form a corporation and expand to dominate their market.
  3.  How are cell corporations regulated?  How are cell unions held in check?  Is there a ‘correct’ amount of cancer?
  4.  Do all mammals possess cancer cells or cancer causing mechanisms at all times with cancer only manifest when system is compromised?  Is there any system other than the immune system involved in fighting cancer?
  5.  Do we “get” cancer or catch cancer?  does cancer emerge from our life-long microbiota?

RNA dominates its market - especially when locked up in the form of DNA in the chromosome, mitochondria and spirochetes ( sperm tails).

  1.  what is the function of uracil?
  2.  why does RNA have uracil and DNA doesn’t have it?
  3.  Might uracil provide a dynamic imbalance - a drive toward action in RNA whereas DNA with its A-T, G-C just sits and waits to be courted, counted, copied, coerced, manhandled, abused, violated, raped, chopped, channeled, routed, modified, tacked onto.
  4.  How did golgi apparatus evolve?  What was its precursor form?
  5.  Might golgi precursors remain among the living as free microorganisms?
  6.  If so, are they hidden in a deep ocean trench or all around us in the soil, our water, our bodies?  Might we each have free / maneuverable / assignable as well as locked up golgi apparatus?
  7.  What is the earliest bacteria, archaea, protista with the golgi  or pre-golgi apparatus?

In the spirit of Atom Smith let’s review some devices for looking at atoms at work:

  1. Atomic probe - grain boundaries
  2. 3DAP - scaning probe microscope
  3. Atomic Force microscope
  4. Scanning-tunneling microscope: measures changes in electric current between top and sample
  5. Magnetic force microscope - tip senses change in the magnetic structure of the surface at the atomic level.  Microscope tip can be used to snag individual atoms and move them around.

JB Experiment:

  1. Find bacteria that withstand sub-freezing temp.
  2. Freeze them
  3. Shift carbon atom at thymine at single base pair in a hox-type gene that codes for membrane continuity i.e. plasmid hydrophobic/phylic.
  4. See what happens
  5. Does membrane fail to form?
  6. Do lipid tails lose hydrophobic tendencies?

When walking through a grove of trees, most of what one sees is the remains of events from many years ago.  One sees only the residue of biological process.  Like looking at a distant galaxy whose light left millions of years ago.  Most of the important stuff that is happening now in the grove is at an invisible scale.  there is intense action but it is microscopic or smaller for the most part.

cutting down a tree is like a supernova explosion in terms of organism causality.  The event is a big one, it is visible, its effects cascade all the way down the hierarchy of causal agents creating a big phase shift.  The tree changes from being fed to being food.

Cutting the tree was an external cause for tree’s demise.  Demise could have resulted from a deadly mutated gene, a bacterial infection, a viral attack or insect infestation.  Is there anything smaller than a virus that can kill a tree or a human?

Daily life as we see it in our temporal world is like seeing cities from 30,000 feet in an airliner.  general structures only, no indication of human movement or our physical existence, let alone myriad dramatic human interactions occurring day and night.

To Investigate: ( from BRUKER slide shows):

  1. Self-assembling cartwheel proteins at centriole dimerization: adhesion-topography correlation
  2. Multiparametric correlation NS Matlab toolbox

Bruker instruments:

  1. Atomic force microscopy
  2. Fluorescence
  3. Tribiology
  4. Stylus Profilometry
  5. Nano-indentation


“Modulus mapping across individual br monomers

  1.  Lipid bilayer formation
  2. Langmuir-bloggett deposition
  3. Tip functionalization protocol - biotin labelled antibody
  4. Common binding chemistries
  5. Molecular recognition mapping
  6. PF-QNM of mammalian cells - the role of mechanical forces in disease
  7. Stem cell migration
  8. Spleen, Gall Bladder, Lymphocyte
  9. BRUKER - Gunther Laukien - NMR expert
  10. See: Bruker optics, bio-spin

JBQ:  Are lymphocytes descended from ancient bacterial symbionts?

Just as Charles Darwin swam in a Victorian sea, we swim in a Postmodern sea that allows / encourages / forces  ideas such as Eldredge-Gould’s Punctuated Equilibrium and Lynn Margulis’ Symbiotic evolution.  We live in different air - the power and nature of this air transcends science and art - it determines what science and what art gets done and how it is received.  It is what we believe; It is how we believe, how we know, what we are able to know.  We now live in an age of nonlinearity, the inversion or dispersion of hierarchies, uncertainty is for certain, change is relentless, seeing from multiple simultaneous viewpoints is derigeur.  Odd as it may seem, we still see a great deal of victorian style Modernism in our thinking-feeling-knowing i.e. rigid hierarchy and linearity.

By studying the “water” Darwin swam in,  we can be more attentive to the restrictions of our water - our zeit.  To realize that we swim in water at all is a major step toward a deeper truth.  Examine all that you take for granted, it requires 150 years for a social paradigm to fully shift from one nexus to that following.  The Postmodern epoch began with a bang ( or a sinking) in 1912.  It is now well underway but still shared with the core of The Descended Grid of Modernism.  Be kind to those harboring the historic worldview - it has much value.  We will have to just all get along in our now deeply multivalent world that is simultaneously Modern and Postmodern.

Darwin had his blacksmith.  We shall have our atom smith, she who works with a scanning-tunneling microscope to move the building blocks of matter.

  • 2/4/15  4:57pm