Hydrogen is a complicated thing. Despite it’s apparent simplicity this most humble element, a single electron orbiting a single nuclear proton, is still beyond our complete understanding. Modern science has made great headway in studying of the atom in the last century, from the early Bohr’s model of electrons orbiting around a nucleus, to the probabilistic atomic orbital fields espoused by de Broglie and Schrödinger, through to modern quantum mechanical and string theories being probed at CERN’s Large Hadron Collider, and yet it’s only recently with advances in quantum computing that we’ve been able to accurately model even such apparently “simple” systems as Hydrogen or Helium, and complicated molecules remain beyond our reach (1). Humanity is just beginning to model and probe the nature of matter and the sub-atomic world. It is reasonable to suspect more surprises are on the way.
Nonetheless, we accept that the everyday world around us is made of these unseen atomic units interacting with one another, producing not only the planet we live on, but the highly complicated, well-arranged, self replicating molecules of life. Moreover, if we go one step further down the rabbit-hole to subatomic level, all the different chemical elements are composed of but three particles; protons and neutrons in the nucleus, and a probabilistic field of electrons rippling/buzzing around at some 2200 kilometers per second (2). These three particles make up not only Hydrogen, but the Carbon, Nitrogen, Oxygen and every other element in our bodies, in trees and rocks, cars and satellites, and every single atom throughout the entire Universe. How do we get such complexity and structure from such simple units?
In science and philosophy, this is a phenomenon known as emergence, the interactions of smaller, simpler entities following local rules thereby producing larger entities with unique properties not found in the smaller units individually. That is, new properties ’emerging’ from the interaction of simpler units without those properties. To paraphrase Aristotle, the whole is greater, and different, than the sum of it’s parts. Consider flocking behaviour in birds (3), or schooling in shoals of baitfish, as they move seemingly in unison to avoid a predatory swoop from a falcon, or perhaps for the baitfish, the hungry torpedo attacks of sleek, powerful tuna. The entire flock/school expands as one and a hole appears in the middle, avoiding the danger then closing to form a tight, secure ball once more.
How do those individual prey animals on the opposite outer edge of the predator, blinded from the incoming attack by their compatriots, know to make space for the incoming threat? How do those facing the threat tell the rest of the school/flock to make way for gnashing teeth or claws? Luckily, they have no need to. Individually, each animal need only maintain a certain distance, speed, and orientation from their nearest neighbour for this kind of schooling behaviour to occur (3). As those closest to the threat move to avoid being captured, their neighbours will move in response to them, and so on through the entire group. There is no pre-organised group strategy, just birds or fishes following their own simple behaviours at a local scale. Bunching, splitting, avoidance, opening/closing the flock, these typical characteristics of a flock of birds are emergent properties of groups of animals with each individual following local behavioural rules.
It should come as no surprise that biology is full of emergent phenomena (4; 5). After all, living organisms are intricately complicated and structured matter made of anywhere from one to billions upon billions upon billions of cells, all working towards the survival and reproductive success of the organism and the copying of it’s DNA. Within us large, multicellular life forms, we can address life’s complexity at many scales. Starting from atoms we get the macromolecules of life, namely DNA, RNA, and proteins, as well as a variety of other structural and functional elements such as sugars, carbohydrates, and too many more to name here in full. These are all used to build cells with a massive variety of different sizes, surfaces, shapes, and of course, functions.
By varying and grouping cell types we come to, mainly, four different tissues; muscle, epithelial (skin/outer membranes), connective, and nerve tissues. These tissues form the organs of our bodies, for example the heart is muscular with connective fibres and membranes controlling the blood flow in the atria and ventricles, controlled by motor-neurons and monitored closely by sensory neurons. Organ systems are the product of multiple organs, such as the cardiovascular system, comprising the heart, lungs, blood vessels, and kidneys, not to mention the controlling neurology from the associated central nervous system. Through emergence, 100 billion neurons in the human brain give rise to not only various behaviour patterns but at least in theory, contentious though it may be, to the phenomenon of human consciousness (6). Take together these phenomena form organisms like ourselves, but the hierarchy of life can be extended even further to populations, followed by multiple interacting populations forming meta-populations and community structures, and finally, whole ecosystems featuring abiotic (non-living) and biotic (living organisms) elements.
At each level, though somewhat arbitrary and constructed by our human understanding, it is interesting to imagine how these new, unique properties emerge whether at the cellular level or that of flocks/populations. Various fields are dedicated to studying life at these different scales, such as microbiology/cellular biology focusing on the very small while ecology focuses on ecosystems as a whole, though there is of course significant crossover, as in the field of molecular ecology. This crossover is of course natural, as phenomena at higher levels emerge from interactions at lower ones, and thus the lower level interactions can be instructive to biologists.
While we can always look at lower levels, all the way down the subatomic, or even perhaps to vibrational strings from which these properties arise (see 7 for an extended review), the organisation of life emerges at the level of macromolecules, the nucleic acids DNA and RNA. Let’s have a brief refresher on the machinery of life; segments of sequences of massive DNA polymers form genes which are transcribed to a messenger RNA (mRNA) intermediary. This is transported out of the cell nucleus, the central information storage organelle, to the construction machines called ribosomes and there translated to a sequence of amino acids, creating what we call proteins. From the interactions of these proteins we get the structures of our cells and tissues, as well as enzymes, the catalytic promoters of specific biochemical reactions in the body. These complex interactions create a plethora of emergent phenomena (8; 9; 10), often variable and unpredictable, but produced by local interactions of proteins under direction from genes.
Consider the amino acid Cysteine, one of 20 amino acids naturally occurring in the genetic code. Amino acids are coded for by triplets of nucleotides, the four rungs of the DNA ladder which we denote as A,T,G,C. If an mRNA Polymerase molecule, itself an enzyme and the end-product of DNA, is directed towards a certain gene by various promoters upstream of the sequence it will start reading the code as it moves along the DNA strand until it encounters a three-nucleotide sequence, which we call a codon, in this case ATG. At this point it will start assembling a complimentary mRNA molecule until it reaches one of three STOP codons (e.g. TAG).
Once completed and transported to the cell’s endoplasmic reticulum, the ribosome will recognise the first translated start codon (nucleic ATG transcribed as AUG in mRNA form, where Thymine is replaced by Uracil) and begin creating a sequence of amino acids corresponding to the sequence of mRNA codons. Any codons of UGU or UGC tell the ribosome, “Hey buddy, add a Cysteine!” and so on, creating a cacophony of instructions at an immense scale; in the common household bacteria E. coli some 10-100,000 ribosomes can encode around 20 amino acids per second, while in the nucleus 1,000-10,000 RNA Polymerase molecules transcribe 40-80 nucleotides per second (11). This constant stream of information in and out is required not only to control homeostasis and replication of the cell but a massive slew of other tasks depending on in it’s type and environment.
Why are we so interested in what emerges from the simple interactions of Cysteines? Bear with me, for this humble amino acid can do some amazing things. Not only does it have enzymatic properties, acting as a “nucleophile” in reactions (donating an electron pair to an “electrophile” in reactions), but it can also oxidise to form a disulfide bond with another Cysteine residue. This handy feature means a chain of amino acids with two Cysteines within a certain distance of one another will form a loop as the two residues bond, and more than one loop is possible (9; 10). In fact, through folding or even cross-linking separate amino acid sequences at their free Cysteine residues, these disulfide bonds and looped amino acids are employed in many proteins for structural roles, generally secretory proteins which act outside the cell due to the reductive environment inside the cell which interferes with oxidation.
It is also possible to have many Cysteine loops as well as free, non-bound, enzymatic Cysteine residues, as is the case for the Cysteine Rich Secretory Proteins. These so-called CRISPs (not to be confused with the current DNA editing sensation CRISPR/Cas-9, see 12) are essential for a wide variety of functions, such as mammalian reproduction and fertilization, or alternatively as venom components of a broad range of snake species (10). Snake venoms are an extracellular secretory protein. Venom glands contain tissues made of secretory cells which produce a cocktail of toxic protein products transported outside the cell. This gland is compressed by the snake’s musculature, forcing these proteins along the venom ducts, past accessory glands and through the hollow fangs into, ideally for the snake, an edible prey item. Cysteines are important for not only the structure of many venom proteins but their enzymatic properties as well. The venom protein ophanin from Ophiophagus hannah, the King Cobra, contains 8 disulfide bonds in addition to 16 conserved Cysteine residues, and inhibits voltage-gated calcium channels to interfere with smooth muscle contraction (10; 13). CRISPs in this venom cocktail can have a variety of toxic impacts on their targets, blocking calcium channels such as those on nerve membranes, inhibiting induced smooth-muscle contraction, blocking cyclic nucleotide-gated ion channels, all interfering with the nervous system.
All these actions of CRISPs in venom, not to mention other biological roles, are heavily dependent on and arise from the local acting properties of amino acids such as Cysteine (9). The property or “phenotype” of toxicity to a prey item’s nervous system, stopping electrical signals to, for example, the diaphragm controlling the lungs, is a product of these local actions. And here, we finally approach the crux of the matter. Emergence is important to understanding phenotypes, the variable characteristics produced by genetic variation in organisms, and how far they may extend beyond their local environments. Cysteine is, after all, just an amino acid acting locally, often with other amino acids, yet the product is a venom which can kill and subdue another organism. Through emergence, the presence/absence of such an amino acid pair has a greater consequence than simple folding or unfolding of the protein.
This phenotypic ripple effect continues throughout the population of snakes, and into other organisms, such as in the immune system genes in prey items, or in potential snake predators such as hawks which might receive defensive bites while hunting. The way organisms behave is a huge factor in their survival and reproduction, and behaviours are the emergent properties of a massive network of individual neurons (and certain accessories such as Glial cells), themselves the product of genes and proteins. Behaviours then are the extension of neuronal phenotypes directing the body how to respond to incoming stimuli. This becomes even more interesting when the stimuli are produced by another organism i.e. are produced by other genes. For example, signaling behaviours such as seasonal colouration or song-patterns in male birds trigger neuronal changes in female birds, effectively manipulating their neurology to become reproductively receptive, releasing a cascade of hormones in the female’s brain (14). Here the male’s song phenotype, specifically tuned by natural selection to release gonadotrophins and other hormones in brains of con-specific females, is an emergent property extending beyond the male’s own form. Female reproductive receptiveness is an extended phenotype of male genetic variation.
This idea of the Extended Phenotype (EP), first proposed and popularised by Richard Dawkins in 1982 (14), is central to modern evolutionary biology. Put simply, the genes of an organism have phenotypic effects which extend further than the organisms physical boundary, that is, further than it’s own body. In fact, it is somewhat arbitrary to treat phenotypes as acting within an organism only, since organisms are but one level of the emergent phenomena resulting from gene replication. Genes, through the behaviour of organisms, extend their phenotype into the environment to produce spider webs, beaver dams, termite mounds, and more (14, 15). All are the emergent properties of genetic sequences improving their own inclusive fitness, the ability to successfully pass on it’s genes to the next generation, whether in it’s own body or that of close relatives which share the same genes. Which genes are “successful” is chosen by proxy, by the ability of the emergent phenomena they produce to aid in replicating themselves through reproduction, however far from the source their phenotype may extend.
If mate-calling songs (and other behavioural manipulation), termite mounds, beaver dams and so on are EPs, what about more complicated structures such as houses, skyscrapers, and cities? How far do phenotypes extend into the environment? Here we reach a point of some contention among the neo-Darwinian crowd. Let us follow convention and place EPs into three categories; constructed EPs such as dams or nests, host-parasite interactions, and genetic “action-at-a-distance” involving behavioural manipulation from afar. While the latter two categories explain some complex phenomena (14; 16), they involve organisms manipulating other organisms and are generally more straightforward. The first category, involving abiotic constructions, causes some extra difficulties.
What constructions can be considered an EP? Here, we come to the somewhat controversial Niche Construction theory (NC), which tries to consider the effect of many organisms altering their environment and, therefore, the selective environment in which they live (17). This in turn influences which genes pass to the next generation, and which genes alter the environment, a feedback between environments modifying organisms and organisms modifying environments. In NC theory we not only inherit genetic variation but also our adaptive environment from our ancestors, as well as heritable epigenetic mechanisms. Accordingly, one might consider cities, buildings, houses and so on, to be part of our inherited adaptive environment, and part of our extended phenotype.
There are some difficulties with the NC theory. Dawkins and the EP proponents state that there must be genetic variation associated with the phenotype for selection to act upon it (16; 17). While epigenetic changes can be heritable, they can only moderate the expression of what alleles are present in the underlying DNA sequences. Such epigenetic changes can also be reversible in one generation. Nonetheless, team EP agree that organisms can and do modify their own adaptive landscapes and are certainly subject to selective feedback, however for selection to act there must be some variation in the EP associated with it’s genes, whether in the sequence itself or the epigenetic control of its expression.
When it comes to structures such as cities, they may modify our selective environment, but there is unlikely to be much genetic variation associated with town planning and architectural design. These are learned behaviours, conscious and collaborative design efforts, less under genetic control of an individual than emerging from cooperative and educational environment. Moreover, good city design by an individual is as likely to improve the success of many others in the population as it is the genes of the designer or its direct relatives. Putting aside any shared Jungian archetypes in our species’ collective unconscious, even if there were specific “genes for town planning” the personal fitness benefit is effectively shared among those who use the town.
If such town planning skills are the product of intelligence with a heritable basis, this intellectual capacity is not restricted to city design, although this may undervalue the impact of some yet undetermined heritable variation on our design ability and it’s direct relationship to individual fitness. Such theories of course work on averages and leave room for the possibility of social merit and architecture/town planning groupies who arguably improve the reproductive prospects of successful designers, though I imagine the rarity of such events leaves little for natural selection to act upon (see HIMYM for extended details/rebuttals). It is interesting that while Extended Phenotypes are themselves emergent phenomena, at a certain distance emergence might usurp the power of extension. At some level of increasing hierarchy, the complexity of life means the emergent phenomena they produce will not be directly related to the reproductive success of specific genotypes. Emergence, not limited by having to score reproductive/inclusive fitness points, extends further than phenotypes can. Thus satellites, space stations, and cities are certainly emergent phenomena, but too far extended to be referred to as Extended Phenotypes (17).
For many, the idea of emergence can be uncomfortable, and rightly so. New properties simply ‘arising’ seems like too much of a good thing, a free lunch which surely violates some physical law or rule of causality. Are not these emergent phenomena reducible to some kind of units or rules which let us understand them? This is often the case, and the idea of emergence doesn’t necessarily rule this out (18). In what is termed “weak emergence”, at any level of organisation in complex hierarchical systems there will be emergent states based on the intricate, unexpected, but potentially comprehensible (perhaps by massively complicated computer modeling) interaction of “microstates” at a lower level of the hierarchy. While this rests on our understanding of the interaction of these microstates, the point remains; one might deduce the constituent microstates, units, and physical laws which produce this novel emergent property. The reverse, predicting an emergent property based on lower level interactions, is much more difficult though still within the realm of possibility.
I should mention that “strong emergence”, where new properties are entirely unpredictable in any way, not even in principle by some high powered computer, might also occur (18). While some insist such “strong” emergent phenomena are in fact impossible as all things have underlying causes, others have suggested many such systems exist in nature. One example is water. In spite of the painstaking efforts made by scientists to understand the elements Oxygen and Hydrogen, simply bind one of the former with two of the latter, repeat, stir, and the properties which emerge continue to defy our understanding. Or perhaps despite our efforts we’re being subjective and are simply incapable of comprehending such an interaction of simple atoms on mass, requiring greater minds (with greater computers) to achieve such understanding. Perhaps we are restricted to referring to “emergence” by our non-understanding of these highly complex systems, at least with our current neurology, a somewhat humbling thought. Hydrogen is, after all, a rather complicated thing.
References
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Snakes On The Brain 