Taxonomic Gearbox

February 13, 2015 People divide reality into categories,  hierarchies based on origin in time, relations in space, levels of complexity, etc. Carl Linnaeus (1707-1778), Iconic-pioneering-paradigm shifting Swedish taxonomist- botanist- zoologist, developed a system for classifying living things,  by their observable physical characteristics,  in a nested hierarchy that has evolved from his 18th century  “Linnean Taxonomy”  to our current “Scientific Classification”  It is an evolving system incorporating new information revealed by genetic studies.

A single organism is currently a member of at least nine  different levels of this Scientific Classification:  Using the dog as an example, starting at the broadest category that also happens to include the organisms eukaryotic bacteria, slime and molds - Eukaryota: organisms with a nucleus in every cell.









Species……..Canis lupus

Subspecies….Canis lupis familiaris

Note: In the Linnaean - Scientific  system currently in use,  the first of the two names of the organism is always capitalized, the second of the two is always lower case and the latin name is ALWAYS in italics - Canis lupis, Homo sapiens

Most people associate Charles Darwin with the Victorian Zeitgeist solvent,  that Monkeys and humans are very similar - note the following quote from a 1747 letter:

“It does not please you that I’ve placed man among the anthropomorpha, perhaps because of the term human form but man learns to know himself.  Let us not quibble over words.  It will be the same to me whatever name we apply.  but I seek from you and from the whole world a generic difference between man and simian that follows from the principles of natural history.

I absolutely know of none.  If only someone might tell me a single one!  If I would have called man a simian or vice versa I would have brought together all the theologians against me.  Perhaps I ought to have by virtue of the law of discipline.”              - Carl Linnaeus-1747 in a letter to critic Johann Gemlin

A human comprises quarks, atoms, nucleotides, amino acids, molecules, cells, organs, organ systems, a body and mind, each with a definite boundary (or not), a family, a social group, a community, a city, a county, state, nation, a continent, a hemisphere, the Earth, the Solar System, Milky Way, our nebular cluster, our Universe, each one, a level of the taxonomic hierarchy, all equally important.

Linnaean system stops at the organism level on the lower end and at the upper end with single cell organisms. A bit confusing when imagined as a ladder.  A ladder with the same stuff at the top and the bottom is perplexing.  It might be more clear  to use a ring or a mobius strip as the heuristic rather than a ladder for the  taxonomy of living things as we arrive full circle with small stuff at each end or, if a circle,  the starting point.  We need names for the lower as well as the higher levels so that we may discuss them in evolutionary terms.  It is tedious and confusing these days as each scientist  uses his or her own peculiar array of terms for the taxonomic levels of causality and the associated components within each organism.

Taxonomic Symmetry - Top and bottom - “The Blake Addenda”

I propose the following names for levels descending from the Species  down the taxonomic ladder to  the Radus and up the ladder from the Domain to the Radus.  I have added ten levels to the bottom and the same ten new levels to the top of the ladder. The new terms  represent the same things at each of the two ends-symmetry.

Genus…….as known

Species… known

(continuing down the taxonomic ladder) ( and up beyond the Domain)

  1. Orgum….. organs in a single body
  2. Cellum…...cells within a single organ, cells throughout an organism not  protists
  3. Cromum... organelles,chromosomes (as physical entity w/ DNA, histones etc) golgi structures, endoplasmic reticulum rough and smooth, ribosomes, etc, etc-not proteins
  4. Protum….. DNA molecule,  all proteins, peptides, polypeptides, lipids, etc
  5. Genum…..individual genes (as parts of DNA affecting one another) and immediate intermediaries within process of protein synthesis and cell metabolism
  6. Parum…....base pairs in position at DNA
  7. Tidum…... nucleotides not at DNA molecule - free-floating
  8. Unitum….single atoms composing a molecule or free floating
  9. Nucum…..particles that exist within the atomic nucleus: quarks, mesons, pi-mesons, leptons, gluons, bosons, etc.
  10. Wavum..…..particle or wave of radiation @ electromagnetic spectrum that enter the nucleus during lifetime of an atom

A mutagenic cosmic ray that launches a new species could strike at any level of the taxonomic hierarchy  from a free-floating quark to any component at any level of an organism.  A quark direct strike would have a different effect than a strike that first hits a carbon atom then a quark or nucleotide-carbon atom-quark or human skin, organ, cell nucleus, chromosome, nucleotide, carbon atom and then quark.  So we must have a name for each level of causation or confusion reigns.  The cosmic ray intervention might occur in a symbiont or parasite having evolutionary effects on the subject organism - there are many many pathways to mutation-evolution.

Without new categories added to scientific taxonomy, it is a chore to discuss the causal effects of one level of living ( organic, pre-organic) matter on another.  One has only  a yeasty broth of confusion with every theorist using his or her own batch of terms-that must be defined and clarified and specified and customized anew in every single book on an important evolutionary subject. Scientific hog-slop is the result.  This is seen at its muddiest when reading hundreds upon hundreds of pages of Stephen Jay Gould trying to make a case for his bold swerve away from Neo-Darwinian dogma up to species level evolutionary causality in his towering tome “The Structure Of Evolutionary Theory”  and even more so in the convoluted intensities of Richard Dawkins in his book “The Selfish Gene”.  both men have fascinating insight into levels of evolutionary causation  that becomes confusing for lack of simple taxonomic  terminology.

Going back in evolutionary-Lyellian  time one proceeds from large animals to smaller animals to microscopic organisms to anaerobic bacteria in primordial soup to pelagic amino acids to a world of only  molecules of sulphur, hydrogen, methane to dust particles orbiting the sun in bands like Saturn’s rings over 5 billion years ago

Note an interesting correlation moving UP the taxonomic ladder to more inclusive groups of animals and plants classified by their  visible structures:  the larger, more inclusive taxon, gradually  includes  SMALLER things.  At the highest current Linnean level, that of  the Domain are the single cell organisms ( eukaryotes, prokaryotes and archaea)   Now!  using The Blake Addenda, continue UP the taxonomic ladder.  Note that categories expand their scope, their coverage of invisible Earthly stuff  as smaller things with far earlier origins come into view.

Domestic dogs evolved half a million years ago

Rats evolved 100 million years ago,

Sponges 500 MYA

Free floating amino acids arrived 4 billion years ago

Atomic molecules coalesce of Earth from orbiting dust 5 BYA

Quarks emege from The Big Bang 13.5 BYA

So, you see, we need twenty new taxonomic levels ( 10 at the top and 10 at the bottom) in order to describe /discuss the evolutionary interrelations between all  levels.  Stephen Jay Gould and Richard Dawkins made careers out of adding a single taxonomic level apiece modernizing The Theory of Evolution.  Dawkins’ gene-centric theory and Gould’s  species-centric.  With these two notable scientists duking it out in the captain’s tower,  it’s not difficult to extend their powerful but convoluted arguments to the whole shebang throughout and at BOTH ends of the taxonomic ladder - to the bottom, wherever that might lurk,  as well as the top,  as we seek levels more inclusive than those traditionally mentioned. Currently, the taxon most inclusive of all organisms is the Domain.  I propose ten levels up the Linnean ladder beyond the Domain and these are the very same ten levels below the Species and Individuals level.

As one can see, the stuff from the very highest realm of my proposed extended ladder is all around us.  It is the stuff we are all made of, quarks and all,  We live in a world of primordial stuff,  as has been noted by others.

Neither linnaeus nor Darwin knew of things smaller than a single cell.  Now that we have tools for studying subatomic particles there is no reason not to admit the evolutionary causal effects of ALL realms of the Taxonomy on one another as well as their equality.  Gould, Dawkins and Kimura have made tight cases for extending evolutionary causality to those beyond the  Neo- Darwinian level of the individual but until now, we did not have a taxonomic lingo for such discussion.

In deference to Japanese scientist Motoo Kimura- Neural Theory of Molecular Evolution - 1968 let’s call the group containing Chromum, Protum, Genum and Parum -all together as  Kimurum when discussing these levels as one.  Kimurum is non-Darwinian in its causality so strict Darwinism must be restricted to the activity of organisms in their temporal environment, ecosystems at real world scale.  Darwinian details of evolutionary causality don’t hold up well under either Dawkins or Gould’s theories and dissolve altogether at the Kimurum sub-gene levels.

There are trillions of events per second at the quark level, billions at the atomic level, thousands at the nucleotide level, hundreds at the cell level, dozens at the organ level

several at the organism level.  One a day at the species level, one a month at the genus level, one a year at the phylum level, one per millenium at the Kingdom level.

These zones of causality are all interrelated, each with its immediate neighbors and each with all others in a boggling network of effect.  The neural network of the human brain is a micro-model of this all-cosmic realm and style of information-swapping  All levels are linked to one another just as the gears in a gearbox.  Think of the action of the quarks on orbiting electrons as a gear the diameter of a pea meshed with a gear the diameter of the Earth.  the pea is revolving at hyper speed, the Earth is crawling.

The gearbox of organic causality.  Effects up and down the amended taxonomic ladder.  Small things creating big changes.  small events adding up over time for big effects.  Small drive large - large drive small - intermediate drive both ways up and down.  Events within a cell effect one billion atoms in that cell and also the organ system in which it acts thus the body, the family, the society, the race and the biosphere.  The Butterfly Effect.  There are no small moves.

At the top end of this taxonomic system the protists are free-floating, towards the bottom end most protists live within animals and plants in symbiosis of one degree or another from mitochondria to food digesting bacteria in the gut.  Imagining the entire history of evolution as a large, wide cylinder, larger animals form a thin film on the outside of a vast tub of microorganisms that in turn sits in a large pond of microorganisms.  Sub-atomic particles are the end units at the lowest rung, hidden inside each organism.  Sub-atomic particles are ALSO the end units at the TOP beyond the Kingdom and Domain floating free in the earth, the ocean, the air and beyond in their new categories: Tidum, Unitum, Nucum and Wavum.


  1. What is the message of this top / bottom taxonomic symmetry?
  2. At what levels of this hierarchy does life happen?
  3. Is it really an hierarchy or some other system of organization that defies hierarchical order?  Perhaps a mobius
  4. Are large animals in the middle of a ladder?
  5. Are large animals a zone in a ring or a band on a mobius strip?
  6. Are large animals just another node in a global 3-D network?
  7. The heuristic of a taxonomic ladder has large flaws.
  8. Are there really no “levels” at all - just one large entity - Gaia?
  9. At what point in evolutionary time did the population of bacteria reach its maximum?
  10. Was bacterial overcrowding the reason large animals evolved - to carry bacteria into previously unfriendly territory
  11.  It would be interesting to classify all living things with DNA only - nothing more and see what shakes out.
  12.  We know that solar and cosmic radiation causes genetic mutation, is there internal radiation coming up from the sub-atomic particles that causes genetic mutation?  Internal vs external radiation or re-radiation from deep within  cell nuclear components
  13.  A UV ray from sunlight strikes an electron then a quark in a carbon atom, can this ray ricochet in various ways for a variety of effects on the DNA
  14.  Is there a language of re-radiation - UV-1, UV-2, UV-3, Gamma-1, Gamma-2, Gamma-3, each with its own likelihood of causing a mutation?
  15. Mutagenic-speciation initiating radiation arrives from within or without the individual i.e. evolutionary mutation’s causal agents might come from lower interior levels acting up the ladder of causation
  16. Thus radiation initiates gene mutation - Kimuran random variation from outside and inside, up and down the taxonomic ladder
  17. Even with internal causation of mutation from atomic level, all causation is ultimately external from sunlight or other cosmic radiation or even from a laboratory energy source.  Thus Dawkins’ and Gould’s notion of two adjacent interacting levels, those of bookkeepers and causal agents, works as we find adjacent pairs all the way down to the lowest level of the taxonomic ladder.
  18. The primary mutator is the gamma ray, the secondary mutator is the atom, the tertiary mutator is the disturbed nucleotide and on up the ladder to the species and clade
  19. One gamma ray may not be sufficient to launch a new species but a billion gamma rays might do the job-
  20. Investigate  cumulative effects of radiation, thresholds of tolerance, rates of genetic repair.
  21. Cancer cells exceed the rate of repair or avoid repair.  Once cancer cells form a colony they have their own identity and are not seen as “different” thus left to their own devices.
  22. Search for “identity-destroying agents - try Stochastic Resonance techniques in order to “harmonize”  with the disease-causing agent thus diffusing it.

Question re: Epigenetics:

  1.  If an atom can be modified  by radiation from sunlight or changed by an electron that has been dislodged from an adjacent atom,  that was in turn struck by an external ray, could not this subject atom be changed by an electrical or chemical signal from a neuron?  If so, then one’s own mind can be the source for permanent, heritable, evolutionary effects in the genome.  See: “The Ugly Gene” essay in this series - essay #1.
  1.  If the electrical signal passing through a synapse can excite orbiting electrons of the carbon atom in a thymine molecule initiating a “random” mutation i.e. change at the base-pair level, could not an emotion easily initiate a gene mutation?  i.e. an acceleration of random events that would increase chances of a stochastic cluster of neuronal events resulting in a gene mutation - a heritable trait?  The initial synaptic signal launching this signal might be a burn from a fire or a burn from romantic rejection. or perhaps the  pleasure of love won.
  1.  Rather than the Linnean model of classification by observable structure perhaps a taxonomic system that uses the principle of first appearance during evolutionary history would be more precise and so,  more useful.
  1.  If Richard Dawkins makes a widely read case for the gene as the key actor in speciation then the gene ought to have its own designation in the system of scientific classification.  If the gene is in play as the most important level, as asserted by Dawkins,  the floodgates open and  we go down through all levels to the chromatin, its atomic constituents and the sub-atomic building blocks of the hydrogen atom. After all, it is the atom that takes the hit from the UV photon.
  1.  To say the gene is the most important level and the center of the evolutionary show, of speciation is like saying the man died because he was shot in the brain - so far so good ( except for the man) but what part of the brain was hit? It was the GA-22 region of the audio cortex.  Can he still hear? Yes, but not as many frequencies as before the wound.  What part of the basilar membrane was damaged? and so on you get it.  Names for all levels of cause and effect ease discussion and guide experiment, examination, treatment.
  1.  Using “The Blake Addenda” to the current system of scientific classification let’s look at the realm of the Nucum ( that which is within the atomic nucleus).  The Higgs particle is to the carbon atom, whose nucleus is its playground,  as a human is to the Milky Way galaxy.  It is the interrupted Higgs particle that launches the “Butterfly” chain of causality resulting in a mutated gene.
  1.  The amount of random “Kimuran neural modifications in a single gene is ten to the 20th power.  The Higgs particles in a gene provide a lot of opportunity for evolutionary selection at ALL higher taxonomic levels.  If the Higgs is the “God” particle then “God” did / does create our world via sunlight and other cosmic radiation.
  1.  Random speculation ( from old reading notes in this set)  apropos of another subject altogether: Methanogenic archaea causing prehistoric methane explosions that proved to be saltational catastrophes at a time when 99% of organic matter was free-floating.  there is a theory of Bermuda Triangle disasters being caused by colossal methane gas bubbles.  Bolide impact strikes a trapped methane bubble causing bacterial disintegration-recombination 4 BYA.
  1.  The difference between an insect and a human is cosmetic compared to the difference between a guanine molecule and a carbon atom or the difference between an electron and a proton or a proton and a gluon or a gluon and a Higgs Boson.
  1.  The diversity of animal and plant life is a vast exercise in product packaging, candy wrappers for the Gaian Snickers bar that must sell itself in myriad environments, on, above, below the Earth and its oceans.  DNA to Arctic Ice “You don’t like Mastodons?  Try these Polar Bears, seals and Inuits.”
  1.  Fact: Eukaryotes ( things whose cells have nuclei such as ALL plants and animals) represent a tiny minority of the numbers of living things ( not biomass-just numbers).
  1.  Fact:  there are ten times more microbes than cells in the human body but due to size their biomass is about equal.
  1.  first prokaryotes - 3.5 to 4.5 billion years ago
  2.  First eukaryotes - 1.6 to 2.1 billion years ago
  3.  Normal human cells have 23 pairs of chromosomes for a total of 46 except for the sperm and egg ( gametes) that have half as many
  4.  Are all synapses at neurons?
  5.  Can a liver cell have a synapse?  An adrenal cell?