The Elements of Evolution – Conservation


Evolution is continually propelled by the past, always modifying its own context and creating the conditions for new steps. This dependence on the past makes the process highly constrained by history. ~ English botanist Enrico Coen

Well over 3 BYA the global community of viruses had homogenized extant prokaryotes on a regime of DNA as the stable library for protein production, with RNA acting as librarian: the intermediate interpreter of DNA sequences. Genetic code used 20 amino acids, with ribosomes acting as protein factories via RNA construal.

Primordial prokaryotes had the machinery for metabolism and self-reproduction honed. Enzyme exploitation via cofactors was well in hand. Life was good.

Of the 548 metabolic enzymes found in E. coli bacteria, 50% are in all life forms. Only 13% are bacteria specific.

Deep Homology

Dissimilar organs, such as the distinctive eyes of mollusks, insects, and vertebrates, were long thought to have evolved independently. Instead, the genotypes which shape disparate bodies and regulate development are ancient and highly conserved.

Structural genes vary little among species. Such long-held genic bases are termed toolkit genes. Those which control embryonic development comprise the evo-devo gene toolkit. Deep homology is the appreciation that growth and differentiation processes are governed by mechanisms that are selfsame (homologous) and deeply conserved across much of life.

Cell-cycle oscillation, while remarkably uniform in the end, does not come by that harmony on its own. ~ American molecular biologist Ned Wingreen

Energy waves define and synchronize living systems. Such vital energetic harmony (lengyre) is the only way that life sustains itself. These waves take matterist form via calcium ion channels, which are universally employed by all life forms for a vast array of functions, from embryonic development to all sorts of cell signaling, include brain activity.

Cell divisions across an embryo occur in rapid synchrony – like clockwork – starting within minutes of fertilization.  ~ American molecular biologist Scott McIsaac et al

During germination embryonic cells skirt chaotic breakdown only through perfectly timed energy wave induced synchronization.

Genetic similarity is both structural and functional. The same DNA from vastly different organisms can be exchanged, such as between bacteria and mice, and still work.

Humans and baker’s yeast last shared an ancestor a billion years ago. Despite this evolutionary gulf, 47% of the genes in these 2 species are interchangeable.

The core features of life are conserved. A working mechanism may be selectively adapted but is seldom overhauled.

That is not to say that the basic wheels of life from the earliest forms have not gained new hubcaps from time to time. New biological traits, expressed from novel genes and proteins, have repeatedly later evolved independently in distinct species (convergent evolution).

Evolution is in many ways a conservative process. ~ English anthropologists Roger Lewin & Robert Foley

The basic biochemistry that first evolved for genetics and cellular organization have changed by tweak at most. The fundamentals are conserved. This clearly indicates an intelligent design force behind Nature.

Old forms may take new functioning, or old functions new form, but all-in-all adaptation is incremental. Major morphology changes can transpire via modest genic alteration: the mechanism is often selective genetic expression.

Having spent untold effort making maps, geneticists were chagrined to learn that mapping genes was just like learning the alphabet. Biological development and adaptation are intricate processes physically displayed in DNA and their expression, but genetics does not explain motive forces or mechanics.

Genetics is not the language of evolution. The complexes surrounding DNA are only physical evidence: artifacts, not agency. As an ongoing process the architect of evolution is the natural force of a localized coherence which is entangled with a universal field.

Weak Linkage

There is a weak regulatory linkage between genetic code and its expressive effect. A minor edit – either in DNA or epigenetically – can vector a distinctive development. While the core genetic foundation is maintained, an adaptive tweak can produce a profound effect.

Bacteria rapidly adapt their enzymes for available food supply. French molecular biologist Jacques Monod offered a culture of E. coli bacteria a choice of sugars: glucose and lactose. The culture grew for a while on glucose, paused, then started in on the lactose. From repeated exposures, Monod found that enzyme adaptation was not simply a matter of activation, but synthesis of a new working enzyme. Weak linkage allowed quick adaptation.

Monad discovered that living cells selectively control their protein production via a feedback cycle. Most biological processes regulate by feedback, either to accelerate and inhibit. The immune system is exemplary. Relatively simple physiological feedback circuits afford rapid adaptation by gene expression while conserving the core code.

Bacteria and archaea are under frequent attack from foreign genetic elements. These prokaryotes evolved immune responses early on based upon memory.

When encountered, foreign DNA fragments are tucked away for later reference. That way, using specialized proteins, a microbe can recognize something similar by pattern matching previously saved DNA with the new encounter. To thwart foreign gene expression, defense is activated via an RNA interference-like technique.

The prokaryotic immune store-and-compare pattern-matching technique became the primary mechanism for vertebrate adaptive immune systems billions of years later, albeit using cell surface protein patterns rather than genetic fragments. In whatever form, such signature recognition is the only feasible solution.

Nerve cells date back to Ediacaran jellyfish. Nerve cells are all a combination of chemical conveyance at interfaces and electrical conduction within. Neurons are an exquisite example of weak linkage, by being a poised binary communication conduit: on or off, but with wide-ranging room for variation.

There is no physical connection between neurons. No tight fit is required. As the output is basically binary – signal or not – how that signal is obtained or tempered, and how conveyed at the interface, as well as how connections are laid out, allows distinct nerve cells types, with different receptors, different neurotransmitters, and near-infinite variety in connective matrices; a conserved core with an ideal architecture for adaptability in intercellular communication.

The genome of multicellular life is itself structured to facilitate the evolution of new genes as creative expressions. The possibilities are practically infinite, as the sum-total of life’s diversity throughout this planet’s history testifies. This owes to the weak linkage among the protein-encoding domains in the genome. New genes are created by fusing various pieces of other genes, with unlimited possibilities.

Folding as a functional attribute of proteins adds another realm of adaptive flexibility. Moreover, the regulation of gene expression is a related, but altogether separate, aspect of the genomic dynamic: conserving the core mechanics while creating an additional layer of evolutionary elasticity.

The weak linkages found in genes, proteins, and neurons are exemplary of a basic biotic paradigm. Weak linkage is itself a conserved core feature of biology, underlying many organic processes.


Humans have about the same number of genes as mice (21,000) and share 97.5% of the same working DNA. The difference between the human and chimpanzee/bonobo genome is scant indeed: most edits are epigenetic. The most significant disparity from other primates affects early brain development.

Most DNA in humans comprises backup copies of pre-vious evolutionary advances. They appear to present day judgmental geneticists as “junk”: nonfunctional vestige and redundancy. Instead, this is genetic conservation at work.

Researchers are only now beginning to appreciate the treasure in the apparent genic trash pile. An axiom of evolution is conservative bio-layering: novelty while retaining weak linkage interdependence with biological legacy. Bio-layering is the mechanism behind reversion evolution.

 The Easy Route

Some traits are easy to evolve – formed by many different combinations of mutations. Others are hard to evolve – made from an unlikely genetic recipe. Evolution gives us the easy ones, even when they are not the best. ~ American molecular biologist Matthew Cowperthwaite et al

Via computer modeling and statistical inference, Cowperthwaite and his colleagues concluded that evolution may be short-sighted, yielding some good in the short run, but painting evolution into a corner in the long run.

In the long run we are all dead. ~ English economist John Maynard Keynes

That evolution consistently delivers life is well beyond probabilistic. Considering the intricacy and myriad dynamics involved, life itself is astonishing. That biological systems inherently possess robust conservation coupled with unimaginable flexibility, and have done so since life emerged, is nothing short of miraculous.

Statistical models are well-known for bell-curve bias: taking the average bulk as the message in toto and ignoring the tail (the statistically improbable). Taking a narrow view, Cowperthwaite and company overlook the statistical odds that life could have even formed and ignore weak linkage.

Innumerable impressive real-world adaptive speciations splay such statistical musings as spurious. Any value judgment as to which mutations may be “best” is at best a parlor game for silly evolutionary biologists and makes no sensible impression toward understanding the real world.

The point of this story is that Nature cannot accurately be atomistically characterized, as empirical scientists are wont to do. The Matryoshka nature of Nature belies an overarching design. Trade-offs do occur, but adjudging optimality necessarily involves a skewed perspective. If there is one descriptor that best fits biological evolution, it is “adaptive.”

A New Trait

The parallel genetic changes underlying similar phenotypes in independently evolved lineages provide empirical evidence of adaptive diversification as a predictable evolutionary process. ~ American evolutionary biologist Matthew Herron & Canadian evolutionary biologist Michael Doebeli

A trait is an organic expression. The routes to realizing a new trait are multifarious. One path begins with genetic copies (alleles) being made that have the genesis of the emergent trait. The ancestor of these alleles has the rudimentary potential for the new trait which is, at best, undeveloped.

Amplification of alleles proceeds with different variants emerging. Through progressive selection, alleles with trait improvement continue to evolve and are further amplified, while less functional copies become inactive or even eliminated. The process continues until there remains the conserved ancestral gene with the parent activity and an allele that encodes the new trait in functional form. The divergence between the gene that scripted the old trait and the allele for the new trait signifies evolution.

This process is necessarily adaptive in aiming at a needed functionality. Otherwise there would be no criterion upon which progressive selection could proceed.

Researchers experimentally observed such evolution in Salmonella bacteria. Surgically deprived of its primary means for producing the amino acid tryptophan, the bacteria re-evolved the needed capability within 3,000 generations through the described process.

There is more to inheritance than genes. ~ English evolutionary biologist Kevin Laland et al

The material mechanics of evolution happen at the molecular level. Mutations of genes are the coarsest means, and by far the least common way that organisms evolve.

Tweaking the genomic database through epigenetic changes which regulate gene expression occurs throughout life. It is basis for development in many complex organisms.

Epigenetic alterations are inheritable. While prolific manipulators of their genomes, plants often carry their legacy epigenetically.

Changing alleles may seem more profound, but its import is the same as altering DNA sequences. Selection of epigenetic alleles underlie many complex traits in eukaryotes.

In bursts of creative problem-solving, new alleles are often created which are not immediately used. Instead, the reserved variations provide a ready database of possibilities if adaptive need arises.

Evolution retains many mysteries at the empirical level. Animal population sex ratios is exemplary.

 Sex Ratios

At the moment of conception, the sex ratio in humans is 1 to 1. Yet more boys than girls are born: ~105 males for every 100 females.

Girls develop more quickly in the womb but are also more likely to die there, at least in the first few months. Out of the womb, boys are more prone to death throughout life, tending the ratio to return to 1 to 1.

Boys face a triple whammy. They are more likely to be born preterm, and if they are, they have a greater risk of death, disability or blindness. And even when they are full term, they have a higher risk of birth complications. ~ English physician Joy Law

While sex ratio skewed toward males is common in several animal species besides humans, researchers cannot account for this balancing, as no feedback cycle is apparent.