D. J. Scott
[Last Update: June 28th, 2018]


D. J. Scott
Karen Hogan & Allen Olson
“Truth & Reason”
6 June 2018


This is the paper that got me into trouble at The Evergreen State College. I wrote the paper in response to many inaccurate statements that my instructor had made during the course of our class that betrayed her inappropriately out-of-date knowledge on the subject of evolutionary biology. Until I wrote this, she'd been teaching what was once the majority opinion in the field; an opinion that has since become incredibly controversial and is no longer considered appropriate by the majority of biologists. My instructor, in response, back-peddled and accused me of arguing against a "straw-man" version of what she'd been teaching (when in reality this "straw-man" of evolutionary theory was exactly what she'd taught in class). This led to me reporting my instructor to The Evergreen State College's academic deans' office for Misappropriation of Federal Funds.


My response to Karen Hogan's criticism of this paper. Click here

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“From Progressive Evolution to Opportunistic Evolution”

Copyright © 2017-2018 by Dustin Jon Scott
[Last Update: June 6th, 2018]


Formerly in the field of biology there seemed to be consensus that the morphological complexity of organisms tends overwhelmingly to increase in evolution (McShea, 1991). Though a great deal of theoretical inquiry (including computer simulations in recent decades) has focused on the question of how complexity increases with evolutionary time, empirical evidence, as garnered from the fossil record, from genetic studies, from ecology, from phylogenic analyses, and from numerous other biological sciences, has failed to demonstrate whether complexity tends to increase at all, and in fact seems to demonstrate the opposite pattern: Evolution tends to prefer simplicity over complexity.

Part I


Evolutionary scientists from the last decade of the 19th until around the mid-20th century commonly believed that evolution leads unidirectionally toward increasing complexity, in spite of a complete lack of empirical evidence in support of this view (McShea, 1991).

In the latter half of the 20th century, however, this began to change.

Part I.a.


Each generation of creatures is forged by those that were able to breed in the last, and in any generation individuals vary in fitness (Lucretius, 50 B.C.E.). This is plainly obvious for anyone to see; the artificial selection that humans have been practicing for millennia depends on it (Lucretius, 50 B.C.E.), this selfsame process occurred without the aid of humans during the “Tellurian age” (Lucretius, 50 B.C.E.), transforming the Earth over and over again (Lucretius, 50 B.C.E.), and the appearance of humans are a big part of the reason why the current wave (of artificially-selected domestic creatures and the few remaining wild species) replaced the last (Lucretius, 50 B.C.E.). Yet, strangely, people at various points in history have sought to mystify evolution, adding vaguely spiritual layers of meaning, often to bolster the human ego in a quasi-religious manner that places humans as the apex of some grand evolutionary process that drives things to become more complex over time (the implication here being that humans, a relatively "new" species, are the most complex form of life).

The belief that evolution leads purposefully toward greater complexity was held by John-Baptiste Lamarck, who believed that there was both a complexifying force and an adaptive force driving evolution. Most historical treatments of Lamarckianism focus on how Darwinism overturned Lamarck’s “acquired characteristic” model of the adaptive force, but neglect his complexifying force.

The term “orthogenesis” was first coined by Wilhelm Haacke (1893), and popularized by Theodor Eimer in (1898).

For a time this postulated internal drive toward evermore complicated organisms was suggested as an alternative to natural selection as the driving force behind evolution.

Proposed “internalist” (orthogenic) mechanisms for increasing complexity, according to McShea (1991), include:

1. Invisible fluids — Lamarck (1809) believed in the spontaneous generation of living things and that lineages tend to increase in complexity over time due to invisible fluids that lay ever-present in the environment but somehow become trapped inside organisms, modifying the cellular tissues through which they move, opening passages, forming canals, and finally creating new and different organs, enhancing complexity over time. Lamarck believed the effect of the environment, on the other hand, was mainly that of retarding this process of “complexification”. (Future theories of evolution would resurrect this idea of a “complexifying” force at odds with a simplifying environmental force, as it would later become apparent that natural selection, which eventually replaced Lamarck's “adaptice force”, tends to simplify and streamline organisms over time, while the “complexifying force” seems to be most prevalant during times of low selective pressure, suggesting that increasing complexity may be a thermodynamic process related to the accumulation of entropy when selective pressure is low enough to permit it; more on this later).

2. Instability of the homogeneous — Spencer (1890, in McShea, 1991) claimed that dynamic systems become less homogeneous and more concentrated as they evolve, referring to this as “The Law of Evolution” (note that here he was not referring to biological evolution, but to directional change in dynamic systems in general). In this conception, any perturbation to a homogeneous system leads to instability and re-organization of parts, resulting in complexity. Since life on Earth is in a constantly perturbed state (always metabolizing, respiring, &c.), it tends to become more complex over time.

3. Repetition and differentiation of parts — Cope (1871, in McShea, 1991) suggests that evolution occurs by acceleration of ontogenies (an idea first put forth by Haeckel) resulting in the repetition of existing parts which can then be differentiated, producing complexity.

4. The path of least resistance — Saunders & Ho (1976, 1981, in McShea 1991) posit that component additions are easier to achieve in development than deletions are because once evolved, components tend to be integrated into developmental pathways, making them difficult to remove (which we now know to be entirely wrong, see Maughan &al, 2007). According to Saunders & Ho, “[t]his asymmetry would be slight but sufficient to drive an evolutionary trend in complexity,” (McShea, 1991).

5. Complexity from entropy — In one version of this hypothesis, dynamic systems far from thermodynamic equilibrium may spontaneously develop complex structures and will tend to become more complex as those systems grow and age (Salthe 1985; Wicken 1987; in McShea, 1991). In another version, accumulation of entropy leads to morphological complexity, leading a configurational disorder that would typically be very harmful to a living organism, and increasing biological complexity is mainly a matter of increasing the fatal threshold (presumably via natural selection) for this configurational disorder.

Part I.b.

“Blind“ Orthogenesis

It would be flattering to the scientific community to say that because natural selection could be observed to be the driving force behind evolutionary change in at least some cases (I’m sure we’re all familiar with the canonical textbook examples of industrial melanism, DDT-resistant insects, and antiobiotic-resistant bacteria), and could easily be inferred or deduced in others, orthogenesis obsolesced resultantly in accord with Occam’s razor. Unfortunately, this is not the case. The reality is that Ernst Mayr politically assassinated the term in the journal Nature in 1948 by stating that it implied "some supernatural force" (Ruse, 1996).

Whatever the reason, we defaulted back to the almost identical idea that life becomes more complex over time, not necessarily because of some mystical force that literally impels living things to become more complex over time, but because of a quasi-mystical principle that more complex things are inherently more fit and thus favored by natural selection. This was essentially an atheistic form of orthogenesis, and was the version of evolutionary theory championed by Darwin and Huxley.

While this “blind” or “naturalistic” form of orthogenesis may seem little different from the other, "purposed" variety of orthogenesis (that is to say, orthogenesis proper) from a modern perspective, one must understand that 20th century scientists were suffering from a mass delusion that complex multicellular lifeforms made up the bulk of life on Earth, regarded bacteria as little more than "germs", were unaware of the Archaea and artificially smashed them together with the bacteria into a kingdom called the “monera” while giving one Archaeal phylum, the Eukarya, four other kingdoms, then the highest taxonomic division of life, regarded the bacteria as “simple” and “primitive” without bothering to qualify or clarify the sort of complexity being spoken of or in regard to which qualities being compared, assumed without evidence that the earliest organisms should have been the simplest, that of course the modern organisms most distantly related to us bear the greatest resemblance to these primitive ancestors, did not typically regard the fossil record as containing anything of great interest until the Cambrian explosion about half a billion years ago, believed that there was a “great chain of being”-like evolutionary “March of Progress” toward ever-greater complexity, culminating in Earth's present biodiversity and Her youngest of species, such as our own, perched therefore at the end as the penultimate of complexity, a truth which expresses itself in that feature which at a cursory glance at Earth's biodiversity would at first seem to make humans most unique among animals: our grotesquely over-inflated brain. So married were they to this essentially orthogenetic narrative, that most scientists never thought to question it, arguing instead over why it seemed complexity had been increasing over time.

Proposed “externalist” mechanisms for increasing complexity, according to McShea (1991), include:

1. Selection for complexity — Rensch (1960) argues that the addition of parts permits more division of parts (occasional Drosophila mutants borne with legs growing where their antennae should be seem might be seen as aluding to something like this having occurred during the evolution of insects, however it must be remembered that modern insects and arachnids have fewer limbs and body segments than the more basal arthropods of yester-era), which makes more complex organisms more efficient, and this superior efficiency grants more complex creatures a selective advantage over simpler, less efficient organisms. Bonner (1988) expands on this by claiming that natural selection not only favors efficiency and therefore complexity, but also large size, which in turn may demand greater efficiency, which would also demand greater complexity.

2. Selection for other features — it may be that complexity increases passively as a side-effect of selection for other features, for example large size, which would generally necessitate a larger number of cells and hence create more opportunity for further differentiation of cell types.

3. Niche partititioning — Waddington (1969) suggests a system whereby increasing organismal diversity results in more complex ecological niches, which require greater organismal complexity to fill, which in turn creates more organismal diversity, and more complex niches, &c., in a sort of positive complexity feedback loop.

It must've seemed from their point of view that this “blind” or “naturalistic” orthogenesis could not have been more conceptually an opposite theory of evolution than orthogenesis proper. The version of the narrative invoking natural selection as an explanation during this time differed from orthogenetic theory merely in using as its mechenism a quasi-mystical principle that more complex organisms are inherently more fit and are therefore to be favored by natural selection, but to the average 20th century scientist, these two nigh-identic narratives were as different as night and day. Consider as an analogy how when the heliocentric model of the Solar system was first proposed, it must've seemed the polar opposite of geocentrism, yet compared to our modern point-of-view, a conception of the Universe placing a single star, our Sun, at the center of the known Universe, would seem little different from geocentrism; in both the case of heliocentrism and "blind" orthogenesis, scientists at the time were incapable of understanding how not-the-opposite of geocentrism and orthogenesis respectively their ideas really were, because the science simply hadn't evolved that far yet.

All of this is not to say that there were not during this time period skeptics of the idea that complexity had been gradually increasing over evolutionary time.

Though natural selection persists today as the most likely explanation for the majority of evolutionary change, the “blind” orthogenesis model of phylogeny that natural selection was intended as a mechanism for has since been discarded.

Part I.c.

Irreducible Complexity

Natural selection doesn't typically favor complexity, although occasionally complexity manages to arise nonetheless (Ayala, 2007).

While the term “irreducible complexity” generally refers to the creationist / theistic evolutionist hypothesis that certain biological systems could not logically have developed incrementally by means of natural selection as such would have required orthogenesis-like guided co-evolution of diverse, formerly independent components, an idea championed by the notorious Michael Behe (1996), there existed in the recent past an eerily similar notion in the scientific community: The idea that there is a certain “minimum” or “irreducible” complexity for life on Earth, that life started at the simplest, most irreducible level, and thus has become on average more complex over time not because evolution necessarily favors complexity, but simply because there is a limit to how simple things can become which means that any increase in the range of complexity of life on Earth would also necessarily raise the average complexity level. This concept was sound according to its own internal logic, but was based on 2 premises that were merely assumed rather than evidenced: [1] The idea that life on Earth has, on average, become more complex over time (McShea, 1991); and [2] the idea that once life had formed, nothing could evolve to become simpler than this “baseline” or “starting point” complexity.

Proposed “undirected” mechanisms for increasing complexity, according to McShea (1991), include:

1. Random walk — One possibility proposed by Fischer (1986) is that most evolutionary lineages could, due to sheer luck, just happen to wander in the direction of increasing complexity for no real reason at all.

2. Diffusion — Building upon this, Fischer proposes another possibility: If each evolutionary lineage follows its own random walk, and lineages tend to decrease in complexity as often as decrease, but there is a “complexity floor”, then the mean complexity for all lineages should climb upward over time. This is similar to Maynard Smith’s (1970) suggestion that if the first organisms had to be simple, then later organisms had “nowhere to go but up”.

3. The ratchet — Stebbins (1969) proposes that adaptive radiations resulting from the invasion of new habitats could cause major evolutionary jumps in complexity, not due to an intrisic drive toward complexity, but is contingent on pre-existing conditions such as promising morphological specializations. This lays the foundation for future jumps in complexity, resulting in the upper limit for complexity for life on Earth constantly ratcheting slowly upward.

Part I.d.

Back to Basics

Evolution is defined merely as a change in allele frequencies in a population over time. Evolution is most resoundingly not defined as an increase in complexity over time, and there's a damned good reason for that: If it were, it would’ve had to’ve been tossed out by now for lack of evidence.

Although as recently as 15-20 years ago, one could see statements that complexity has “obviously” increased over time (e.g., Carroll, 2001), this was already the viewpoint of a sad minority, obstinently digging their heels into the sand and proclaiming defiantly their refusal to go whithersoever the evidence lead, clinging instead to their eukaryocentric delusions of evolution leading inevitably to evermore complex forms of multicellularity, and their anthropocentric desire to situate humans, a relatively new species, at the end of a very long evolutionary march of progress. This was religion, not science. A position of faith utterly devoid of empirical support.

The idea of evolution driving toward ever-greater complexity is absurd on the face of it, when one considers that those who held this view also regarded the organisms who reproduce the fastest and have therefore experienced the greatest number of generations and hence have evolved the most since our common ancestor as the simplest and most primitive, whereas the organisms they regarded as the most complex (such has humans) tended to be reproductively lethargic and have therefore evolved far less since our common ancestor. That it took so long for the biological community at large to realize this should cause us all to hang our heads in shame for belonging to a species capable of such backward, delusional thinking.

“Since Nature banned with horror their increase,
And powerless were they to reach unto
The coveted flower of fair maturity,
Or to find aliment, or to intertwine
In works of Venus. For we see there must
Concur in life conditions manifold,
If life is ever by begetting life
To forge the generations one by one:
First, foods must be; and, next, a path whereby
The seeds of impregnation in the frame
May ooze, released from the members all;
Last, the possession of those instruments
Whereby the male with female can unite,
The one with other in mutual ravishments.”
Lucretius, 50 B.C.E.

Natural selection cares nought for increasing complexity, but for survival and reproduction, as Lucretius evermore eloquently proclaimed in his poem, On the Nature of Things, more than two millennia ago. Often times, if not most of the time, it seems natural selection tends to simplify and streamline rather than to “complexify”. It tends to be the simpler systems, not the more complex ones, which are more efficient, as our bacterial brethren prove with their rapid reproductive rates and enviable adaptability (although part of what allows them to reproduce so fast, in addition to their simple morphology, is a doubly complex (compared to eukaryotes) system of transcription and translation at the heart of an incredibly advanced cellular metabolism). Complexity tends to arise when selective pressure is low, and may even represent an accumulation of entropy that would more likely’ve been trimmed away in a scenario with higher selective pressure in which efficiency would be more vital. This may help to explain why we see explosions in morphological/anatomical complexity immediately after mass extinction events, when we would expect selective pressure to be lowest.

While we can say with a high degree of certainty that there now exist on the Earth organisms far more morphologically complex than any that lived a billion years ago, and while it seems probable, though it is far from certain in light of recent theories regarding primal eukaryogenesis, that there were on Earth a billion years ago creatures more complex than anything that existed two billion years thither, which were, in turn, presumably, at least according to traditional and now it seems very possibly incorrect views regarding eukaryogenesis and abiogenesis, more complex than the first living things, it is not clear that this has been the overall evolutionary trend or that the cases of increasing complexity we've seen aren't actually the exception rather than the rule for evolution. Our perception that life has, on the whole, become more complex over time is now seen as possibly being the result of a sampling bias. It is now commonly believed that there has overall been no significant net-increase in the complexity of life on Earth, commonly understood that there is no particular reason to think that changes in allele frequencies over time would necessarily result in a gradual, unidirectional increase in complexity over time, commonly known that there are many examples of natural selection preferring to streamline and simplify than to keep unnecessarily complicated or to complicate further (especially being that complexity is evolutionarily costly), and commonly reasoned that in any case (whether there has been an overall net-increase, and overall net-decrease, or no significant overall change in the complexity of life on Earth), evolution (which is defined as a change in allele frequencies in a population over time) remains the only viable explanation for Earth's current biodiversity.

Much of this change in evolutionary thought has already filtered down into the popular culture. In the 2001 sci-fi comedy Evolution, for example, an ill-conceived attempt to use napalm to destroy an alien threat that reproduces and therefore evolves much faster in the presence of heat energy produces a gigantic amoeba-like organism, causing one character to remark, "That's evolution?!" to which another replies, "The 'simplest' organisms are often the most fit," which was a refreshingly accurate scientific observation in a major Hollywood production. Similarly, the articles Making Life Simple (Morton, 1999) and Evolution myths: Natural selection leads to ever greater complexity (Le Page, 2008) at New Scientist, as well as the Wikipedia article on the Evolution of biological complexity (Wikipedia, 2018) all reflect that evolution is no-longer seen as a unidirectional process that leads intrinsically to evermore morphologically complicated forms. That evolution is opportunistic and has no inherent preference for complexity is now so well-understood that to call it "academic" would be an understatement; that natural selection often favors simplicity and that organisms can vary not only in degree of complexity but in type (i.e., genomic complexity, morphological complexity, metabolic complexity, &c.), is now largely regarded as simply a matter of common sense.

Part II

Part II.a.


While orthogenesis might seem relatively easy to debunk from a modern point of view, it was not so when the only alternative being offered was a version of evolutionary theory that, like orthogenesis, posited that complexity should increase over time.

Could we have proven orthogenesis wrong with any late 19th century to mid-20th century knowledge? As it turns out, yes, we easily could have! In “The Origin of Species”, Darwin conjectures that when natural selection doesn’t work (i.e., when selective pressure is extremely low), organisms will remain unchanged for long periods of time (Seravin, 2001).

Organisms appear to change over time.
Natural Selection
Evolution is the result of natural selection.
Observations / Experiments
Discovery of the Coelacanth, a type of lobe-finned fish (the group of fishes to which we tetrapods belong), the Tuatara, and observations of ancient, modern-looking representatives of today’s groups (such as crocodilians).
Calculations / Armchair Stuff
If natural selection rather than orthogenesis is the explanation for evolution, then we might find some creatures in that have apparently evaded the forces of selection and have remained largely unchanged over long periods of time.
There exist some “living fossils” — creatures who’ve remained unchanged over long periods of time.
There should exist some “living fossils” — creatures who’ve remained unchanged over long periods of time.
Figure 1 — a comparison of observed evolution with the theory of natural selection of inherited traits.

Part II.b.

“Blind” Orthogenesis

Since this conception of evolution for the most part made all of the same predictions as the alternative model of evolutionary theory was making at the time, orthogenesis could not be officially “debunked” (aside from the aforementioned “living fossils”) without also shedding doubt as to whether evolution truly proceeded as we had always envisioned. It therefore took multiple examples of reduction (evolutionary processes that tend to reduce complexity over time, such as phenotypic loss, neoteny, and parasitism) for biologists to realize that evolution is not necessarily about organisms becoming more complex over time.

Parasitic organisms such as Plasmodia and mycoplasmas are reductionist lifeforms that have dispensed with a number of traits that parasitism has made obsolete in their lineages (Sirand-Pugnet &al., 2007).

Phenotypic loss describes morphological simplification and streamlining over time (Maughan &al, 2007). Modern sharks have for the most part adopted a generic “shark shape” that while now familiar is a much simplified version of the morphologically diverse and often intricately morphologically complex group from which they evolved. Consider for example ancient sharks like the 420 MYO Mongolepis, 390-320 MYO Stethacanthus, the 365 MYO Cladoselache, the 360 MYO Falcatus, the 350 MYO Edestus, the 270 MYO Helicoprion, the 259-66 MYO Hybodus, the 200 MYO Xenacanthus, or the 120-70 MYO Scapanorhuynchus. Modern cephalopods also show evidence of simplification and phenotypic loss compared to ancient cephalopods, many of whom had incredibly elaborate shell designs. Similarly, slugs evolved from snails, not the other way around. Modern jellies have likewise been much simplified compared to the ancestral group out of which they evolved.

Diversity of Biological Complexity
Living things vary widely in morphological and genomic complexity.
“Blind” Orthogenesis
Morphological complexity arises due to an externalist mechanism such as natural selection.
Observations / Experiments
Phenotypic loss (Maughan &al, 2007). “Simple” modern sharks from “complex” fossil sharks. “Simple” modern cephalopods from “complex” fossil cephalopods. “Simple” modern jellies from “complex” fossil jellies. Slugs from snails.
Calculations / Armchair Stuff
If natural selection invariably favors complexity and is the primary mechanism for evolutionary change, then organisms should (almost?) never evolve to become simpler or more streamlined over time.
Many successful lineages appear to be simplified versions of the groups out of which they evolved. Numerous lineages of unicellular organisms appear to have evolved from multicellular organisms.
There should be no known cases of modern organisms appearing to be simplified or streamlined versions of the fossil groups out of which they evolved.
Figure 2 —

Although natural selection certainly works as an explanation of evolutionary change over time, there are enough instances of reduction (far too many to create a comprehensive list here) that we either needed to re-evaluate whether natural selection tends to favor complexity, or we needed to re-examine whether many of the evolutionary changes documented in the fossil record were due primarily to natural selection or possibly due primarily to some other force, such as a thermodynamic entropy-driven model for increasing complexity, or possibly some form of genetic drift in low-selective-pressure situations (“constructive neutral evolution”), or whether many of what had previously been viewed as clear-cut increases in complexity were in fact, and perhaps to some counterintuitively, due to reductive processes. Though this issue is far from settled as of the year 2018 C.E., it currently appears as though both of these alternatives to “blind” orthogenesis have found a great deal of support in the past few decades, and are far from mutually exclusive.

Part II.c.

Irreducible Complexity

Whether or not this “irreducible complexity” model of evolution is more correct than the previous orthogenesis and orthogenesis-like version of evolution via natural selection can be tested by comparing predictions with the distribution of complexity among the biota.

Figure 3 — a comparison of what we would expect to see occurring over evolutionary time assuming either a passive or active evolutionary trend toward increasing complexity. (Original image by Tim Vickers, public domain)
Figure 4 — a depiction of what we would expect to see occurring over evolutionary time assuming an active evolutionary trend toward increasing complexity. Complex organisms should become more plentiful as complexity level increases, while the minimum complexity level is constantly shorn upward due to being out-competed by other organisms.
Diversity of Biological Complexity
Living things vary widely in morphological and genomic complexity, from single-celled forms to filaments to biofilms to aggregates to “complex” multicellular life.
Active Trend
There has been an active trend toward increasing complexity since the origin of life on Earth, either due to “internalist” mechanisms (i.e., orthogenesis) or “externalist” mechanisms (i.e., “blind” orthogenesis).
Observations / Experiments
Observations and statistical extrapolations based on genetic diversity of samples by Oren, 2004; Schloss & Handelsman, 2004; Sweetlove, 2014; and Whitman &al., 1998, among many others over the last two centuries or so.
Calculations / Armchair Stuff
If the has been an “active” trend toward complexity, then we should not only see the maximum complexity level increasing over time, but also the average and minimum complexity levels as simpler lifeforms are continually replaced by more complex ones.
107 to 109 extant prokaryotes (Oren, 2004; Schloss & Handelsman, 2004), compared to 8.7·106 &plusmin; 1.3·106 extant eukaryotes (Sweetlove, 2014). Prokaryotic cells make up the majority of cells and by far the majority of individual organisms found in nature (Whitman &al., 1998).
Complex multicellular organisms should by now vastly outnumber “simple” multicellular organisms, which should in-turn vastly outnumber unicellular organisms.
Figure 5 — a comparison of the observed diversity of biological complexity with the idea of an active trend (such as being driven by an orthogenic force, or favored by natural selection) toward increasing complexity.

It’s also possible that there‘s been a passive trend toward increasing complexity (Carroll, 2001).

Figure 6 — a depiction of what we would expect to see occurring over evolutionary time assuming a passive evolutionary trend toward increasing complexity. Here, the maximum complexity level keeps climbing upward, but is represented by an ever-diminishing percentage of the total number of living things.
Diversity of Biological Complexity
Living things vary widely in morphological and genomic complexity, from single-celled forms to filaments to biofilms to aggregates to “complex” multicellular life.
Passive Trend
There may have been a passive trend toward increasing complexity over the history of life on Earth (Carroll, 2001).
Observations / Experiments
Observations and statistical extrapolations based on genetic diversity of samples by Oren, 2004; Schloss & Handelsman, 2004; Sweetlove, 2014; and Whitman &al., 1998, among many others over the last two centuries or so.
Calculations / Armchair Stuff
A passive trend toward complexity would have complexity increasing in ever-smaller percentages of living things as a side-effect of an increasing range of diversity, with “simple” organisms always representing the majority.
107 to 109 extant prokaryotes (Oren, 2004; Schloss & Handelsman, 2004), compared to 8.7·106 &plusmin; 1.3·106 extant eukaryotes (Sweetlove, 2014). Prokaryotic cells make up the majority of cells and by far the majority of individual organisms found in nature (Whitman &al., 1998).
Prokaryotes should outnumber eukaryotes by a substantial amount, both in terms of the number of known species and in terms of total biomass, at any given time in Earth’s history, while the upper limit for complexity increases among a continuously diminishing minority.
Figure 7 — a comparison of observed evolutionary change with what we would expect to see occurring over evolutionary time if there were a passive trend toward increasing complexity.

Part II.c-1.

Consideration of Viruses, Organelles, and Other "Pseudobiota"

Viruses, organisms so simple that there is some debate over whether they should qualify as living things, are the dominant biological entities on this planet (Koonin & Wolf, 2012).

There are three main hypotheses for the viral origins:

1. Virus-first hypothesis — viruses could have evolved from complex molecules of protein and nucleic acid before cells first appeared on earth (Villarreal, 2005) and had a profound influence on the evolution of these first cells (Nasir &al., 2012). This idea has been criticized for contradicting the definition of the word “virus”, which implies requiring a host cell for replication (if viruses came first then there were no host cells). Nevertheless, it is possible that small, virus-like replicons which were not yet parasites are the direct ancestors of at least some modern viruses.

2. Reduction hypothesis — viruses could be reduced from prokaryotic organisms such as the Rickettsia (whence our mitochondria also derive) or Rickettsia-like endoparasites (Nasir &al., 2012; Koonin & Wolf, 2012).

3. Escape hypothesis — viruses may have begun as segments of their host genomes (Nasir &al., 2012; Koonin & Wolf, 2012), and one may suspect perhaps even from bacterial and archaeal plasmids, such as for example Rickettsial plasmids.

Contemporary virologists hypothesize that no single one of these hypotheses is “the” definitive explanation for the evolution of viruses, but perhaps that a combination of all three occurred, resulting in a polyphyletic grouping (Nasir &al., 2012; Koonin & Wolf, 2012; Forterre, 2014).

Since viruses lack the ability to reproduce on their own, it is fair at least to strongly suspect that they are simpler than the first self-replicating organisms would have been. This creates a problem for the notion that life began at or near the simplest, most irreducible level of complexity possible.

If we assume a baseline complexity level roughly comparable to modern prokaryotes (there are reasons for thinking the first living things may have been either more or less complex than modern prokaryotes; discussed later), then determining whether our perception of life on Earth as having generally evolved in the direction of higher complexity is an example of selection bias due to our eukaryocentrism, or whether the idea of a quasi-mystical "drive toward complexity" has merit, is simply a matter of comparing the number of times complex multicellularity has evolved, minus the number of reversions to unicellularity, compared to the number of times viruses, prokaryote-derived organelles like mitochondria and chloroplasts, and other "quasi-biota" or "pseudobiota" have evolved.

Eukaryotic-Bacterial Lipid Similarity
Biological entities vary widely in morphological and genomic complexity, from viruses to organelles to cells, from single-celled forms to filaments to biofilms to aggregates to “complex” multicellular life.
Irreducible Complexity
The first living things represent the "baseline" complexity for life on Earth, and any increases in the range of complexity of living things since the origin of life has resulted therefore in an increase in the average level of complexity.
Observations / Experiments
Numerous observations over the past two centuries has yielded an impre
Calculations / Armchair Stuff
Any increases in the range of complexity of living things since the origin of life has resulted therefore in an increase in the average level of complexity, and organisms should never evolve to become simpler than the first lifeforms would have been.
N1 independent evolutions of multicellularity.
N2 independent reversions to unicellularity.
N3 independent evolutions of viruses.
N4 independent evolutions of organelles.
Independent evolutions of multicellularity should greatly outnumber reversions to unicellularity, while viruses and organelles should not be expected to exist.
Figure 8 — a comparison of observed evolutionary change with what we would expect to see occurring over evolutionary time if the irreducible complexity model were true.

Numbers for this analysis were difficult to come by. However, consider the following:

N1: Multicellularity has evolved at least 46 times in eukaryotes (Grosberg & Strathmann, 2007): At least once (perhaps twice) in animals, three times in fungi, and repeatedly in Chloroplastids (algae and land plants).

N2: a cursory search through the literature did not immediately reveal any estimates regarding the total known or estimated number of reversions to unicellularity, however some examples include Saccharomyces and many other related yeasts in the Saccharomycotina (Medina &al, 2003), Cryptococcus albidus and related species (Medina &al, 2003), yeasts in the Taphrinomycotina (Medina &al, 2003), Schizosaccharomyces sp. (Medina &al, 2003), and Pneumocystis carinii (Medina &al, 2003). While yeasts have long been regarded as secondarily unicellular (Whittaker, 1969), they belong to the phyla Ascomycota (sac fungi) and Basidiomycota (mushrooms, puffballs, stinkhorns, bracket fungi, other polypores, chanterelles, boletes, jelly fungi, earth stars, smuts, rusts, bunts, mirror yeasts, and the aforementioned human pathogenic yeast Cryptococcus) within subkingdom Dikarya (“higher” fungi), which means the grouping is informal and polyphyletic; the yeasts taxonomically and cladistically nest within otherwise “complex” multicellular taxa and therefore most likely represent several independent reversions to unicellularity. That this is generally the preferred assumption to the idea of yeasts being more primitive and their various multicellular relatives as more derived has as much to do with genome size as it does with Occam’s razor: positing large-scale reduction in numerous independent lineages requires fewer unproved or unprovable assumptions than imagining large-scale convergent evolution toward multicellularity in a variety of lineages, many of which end up coincidentally or through some unseen lateral gene transfer end up sharing genes related to multicellularity. That reduction is the evolutionarily easier explanation here is very telling about whether we should expect in general for evolution to tend toward greater complexity. In contrast to these multiple reversions to unicellularity,

N3: Viruses are now generally assumed to be a polyphyletic group that has evolved from the eukarya and prokarya both through reduction and segregation (Nasir &al., 2012; Koonin & Wolf, 2012), as well as from ancestors that were co-evolving with the first cells. While we’ve yet to definitively work out exactly how many times viruses have evolved from cellular lifeforms, the number of independent evolutions here is likely immense.

N4: The only organelles known for certain to have evolved from prokaryotes are plastids and mitochondria, however a variety of other organelles, such as ribosomes and prokaryotic plasmids (which are not true organelles but share many features in common with them), may have also begun their evolutionary lineages as cellular organisms.

So while it appears as though reversions to unicellularity from multicellularity are relatively common, that a likely huge number of viruses have evolved from prokaryotic and eukaryotic organisms through both segregation and reduction, and that at least two and possibly a great deal more organelles evolved from prokaryotes, and that plasmids may have evolved from prokaryotes multiples different times, meaning that it is relatively obvious that what authors have in the past called “regressive” evolution is actually far more common than orthogenesis-like “progressive” evolution, lack of exact numbers here makes it impossible, at the present moment, to quantify exactly by what proportion “regressive” evolution seems to be preferred.

Another approach to this problem might be to measure the evolutionary success of these strategies not in terms of how many times “regressive” or “progressive” evolution has taken place with regard to unicellularity and multicellularity, but the relative success of the different strategies. For this we would still assume the same roughly prokaryote-equivalent “baseline” complexity (again, the first living things and/or Last Universal Common Ancestor may have been either more or less anatomically complex than modern prokaryotes, and there are good reasons for supporting either scenario), we would merely have to compare the number of multicellular organisms, unicellular organism, and “pseudobiota”.

Thus, failure to acknowledge the pseudobiota is in this context a fallacy of a limited sample. While some might object to the consideration of the pseudobiota with regard to the question of complexity on the grounds that viruses fail to fulfill all the criteria for being considered "alive" and thus are not examples of “life”, to maintain that there is a certain “minimum” or “irreducible” complexity that living things never fall below while regarding any biological entity which evolves below this invisible line of irreducible complexity as "not alive", is fallacious reasoning; it is a tautology designed to justify selection bias, or in other words: Refusal to acknowledge the pseudobiota is in this context a No-True-Scotsman argument.

Part II.c-2.

Uncertain Baseline Complexity

Primal Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life (Egel, 2011)

Eukaryotic-Bacterial Lipid Similarity
Eukaryotes and Bacteria have a similar lipid composition unshared by the Archaea.
NuCom Hypothesis
The Eukaryotes and Bacteria share a common nucleated ancestor, and the Bacteria have since become enucleated in an example of reduction.
Observations / Experiments
Nuclear compartments have been observed in the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) phyla (Staley, 2013).
Calculations / Armchair Stuff
If the NuCom hypothesis is correct, then some Bacteria might still possess nuclear compartments (Staley, 2013).
Eukaryotes and Bacteria probably share a common, nucleated ancestor (Staley, 2013).
If the NuCom hypothesis is correct, then some Bacteria might still possess nuclear compartments (Staley, 2013).
Figure 9 — a comparison of observed evolutionary change with Staley’s The Nuclear Compartment Commonality Hypothesis (2013)

Note that if the Eukarya are as deeply nested within the Archaea as currently appears to be the case (Eme &al, 2017), then one of the consequences of the NuCom hypothesis being true is that a number of independent lineages leading to all extant non-eukaryotic Archaea must've shed their nuclear compartments independently of one another, so that while eukaryogenesis only occured once, and much earlier than traditionally hypothesized, "prokaryogenesis" has occured many times over, which is consistent with phenotypic loss being evolutionarily easier than the addition of new and complex traits.

This, however, only gets us as far back as the Last Universal Common Ancestor (LUCA), the common ancestor of the Eukarya/Archaea and the Bacteria. Even if the evolutionary trend has been toward greater simplicity rather than toward greater complexity since the LUCA, what of the First Universal Common Ancestor (FUCA), or first lifeforms? Wouldn’t a proto-eukaryotic LUCA still be far more complex than the very earliest lifeforms? Not necessarily! If we define the first living things as the first biological entities made up of nucleic acids housed in a lipid bilayer, then the Primal Eukaryogenesis hypothesis (Egel, 2011) suggests the first living things may have been more complex than

Part II.d.

Moving Forward

The relevant question now is why past generations of scientists wrongly inferred an overall, over-arching, largest-possible-scale evolutionary trend toward ever-increasing complexity since the origin of life, despite a complete lack of evidence.

Reasons suggested by McShea (1991) for all of this “gestalt” include:

1. Humans are essentially psychic — “One [possibility] is that complexity does increase, and that we unconsciously compute complexity between earlier and later organisms with some innate, cognitive algorithm, or even perceive differences directly, in ways that we simply cannot yet articulate. If so, then our only project is to discover how to say what we already know,” (McShea, 1991). This is probably the least likely of all scenarios, however it appears to be the assumption that the majority of scientists during the late 19th and early-to-mid 20th were operating under.

2. Properties other than complexity are causing the gestalt — as McShea writes, “Comparing a cat with a clam, for example, many will get a vague impression that ‘something more’ is going on in the cat.” McShea then goes onto question whether this “something more” is actually greater complexity, or other qualities like greater intelligence, greater mobility, or simply greater similarity to humans. McShea then reminds that complexity has to do with number of different kinds of parts and the irregularity of their arrangement. McShea points out that since cats and clams are so anatomically different from one another, comparing their parts is not straight-forward, and that if cats strike us as seeming to have more parts, it could simply be that they are, on average, larger creatures and much more closely related to us, making their parts easier for us to identify (both in being easier for us to see and in being more familiar to us). “Possibly, as one reviewer suggested, organisms simply look more and more different from modern ones as we scan further and further back in time; if the moderns are assumed to be very complex, then less familiar might be mistaken for less complex. The human perspective, like any other, has its biases.” (McShea, 1991)

3. Hyperbole of unrepresentative samples — it’s also possible that the few clear-cut cases of increasing complexity (such as the rise of multicellularity) so dominate our perception of evolution that we wrongly generalize such cases to long-term trends. This especially might be skewing our perception of how evolution works because such leaps forward in anatomical complexity might not be due to “day-to-day” evolutionary forces like genetic drift or natural selection, but due instead to exceptional, out-of-context events like meteor strikes (for example, mitochondrial acquisition could never have happened without bacteria, who might not even be native to Earth (Scott, 2018)!). Those who held to the belief that complexity tends to increase over time were thus living in the exceptions.

4. Projection of technological trends — just as it is popularly imagined that the evolution of tool-manufacturing has instilled in our minds the false “common sense” notion that all useful things require a creator, the trend in technology toward increasing complexity of devices may be causing us to read a similar trend into the history of life on Earth. These “common sense” notions, or “obvious truths” may simply be the part of our brain that knows how to recognize a human-created artifact trying to find such patterns even where none exist (not wholly unlike a religious person thinking he or she has seen the face of the Virgin Mary in a piece of toast).

5. Conflation of complexity with progress — also have a tendency to read progress into evolution as we connect progress with complexity. McShea (1991) points out that more complex organisms, like more complex machines, are commonly imagined to have progressive qualities such as sophistication and /or efficiency. McShea posits that these assumptions form a sort of reciprocal reinforcement, “to comfortably maintain (without close examination) pet notions of progressive evolution and complexity increase,” (1991).

While there is still much to learn about the subject of evolution, understanding our own biases, our own anthropocentrisms, and most importantly, understanding how ludicrously, hopelessly skewed our disgustingly human perception of life on Earth was during the 20th century, appears now more than ever to be integral to the future of evolutionary science. Whereas in the 19th and 20th centuries our scientists seemed to think that the anthropocentric lenses through which they viewed the world were more-or-less accurate, we now know that evolution isn’t some deity that had a special motive in creating us, nor does evolution seem to greatly favor what we think of as “complex” organisms (those that are more similar to ourselves). In fact, we complex multicellular Eukaryotes seem to be nobbut a thin layer of skin congealed atop the primordial soup; an evolutionary side-effect of microbial evolution.

That we consider ourselves to be so special, proves just how very un-special we are.


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