“Complexity and the Individual” [1]
“In considering the study of physical phenomena, not merely in its bearings on the material wants of life, but in its general influence on the intellectual advancement of mankind, we find its noblest and most important result to be a knowledge of the chain of connection, by which all natural forces are linked together, and made mutually dependent upon each other; and it is the perception of these relations that exalts our views and ennobles our enjoyments.”
Alexander von Humboldt [2]
There is a problem with our concept of the individual. As humans, we live inside our little heads and we have this illusion that we are separate from the world and our bodies, the so-called mind-body problem. This mental separation means we need a “Theory of Mind,” a realization that there are other minds out there and a great deal of our conscious effort is in trying to figure out what these other minds are thinking. I have argued before [3] that the human concept of individuality is only a recent concept and individuality is now the current dominant cultural consensus for much of the world. Arguably there is a great deal of good in this. There are however conceptual limits that can hold one back. Nowhere is this seen more than in the biological sciences. Biology has always been a descriptive science and it is only in the last 50 years that mathematics has made inroads into the biological sciences. Because biology is so complex the mathematical descriptions start simplistic and biological simplicity doesn’t have the force of say, the basic relationships of physical laws. Biology has very few general principles and those that exist always have special cases. Complexity theory is an attempt to understand complex processes, including those of biology. Complexity theory is not really yet a theory but a set of ideas for building models, simple ways to test basic relationships. Talking about models rather than laws is a better way to understand biological processes. Models can be useful until they are not, then they get replaced by hopefully better models. Darwinian evolution is a model that has become so useful that it has become a framework from which other models are built. In evolutionary theory there are now several models:
the Price equation, [4]
The Price equation was first derived in 1972 by George R. Price as a theoretical response to William Hamilton’s kin theory. [5] The equation is a general, formal definition of selection. It is not a predictive equation. It has been used to show that both kin selection and group selection are equivalent and used as a basic model for the evolution of cooperation. As a general definition, it has also been used to model evolutionary scenarios in such things as human culture or technology. Since selection is modeled as a statistical relationship between a unit of selection and the fitness of a character under selection it has been accused of being a strictly linear relationship, something which defenders challenge. [6]
the replicator equation [7]
The frequency of type i increases when the fitness of i is greater than the average fitness of the population. [8] In 2002, Karen Page and Martin Nowak showed that the Price Equation and the replicator-mutator equation, a generalization of the replicator equation, were functionally equivalent. In addition, this paper showed that this equation provided a general framework for the mathematics of evolutionary theory. [9] This has not been without controversy, especially Nowak’s application of this framework to biological problems. More on this later.
There is also a computational method using a language called "Avida", [10] [11] that allows researchers to program different evolutionary scenarios and then let them loose and see what happens.
In biology, what an individual is and what “individual” means is another murky term like “gene”, “fitness”, or “species.” Or what is “life?” Last summer I took a course on “The Emergence of Life” from the Santa Fe Institute’s Complexity Explorer. [12] One can define what life does but it gets harder to describe what life is. Life came from somewhere, it arose out of abiotic (non-life) processes over 4 billion years ago. Unfortunately, living things have pretty much consumed whatever bridging processes there were between life and non-life. Or we haven’t as yet found them. This divide between living and non-living has led some to give life a special property, a magic spark, called vitalism. The mathematician and physicist Roger Penrose sees this spark as a quantum property and a form of universal consciousness and the self-assembly processes in a cell as proof of this. [13] Others have argued that we don’t have the physics presently to understand this transition. They, like Penrose, have been accused of vitalism. Biological models start with the idea of an individual or a population of individuals and how these individuals or populations change over time. But what exactly is an individual? Richard Dawkins has coined the term, “selfish gene.” [14] This sees genes as the individuals in biological reproduction, individuals whose only task is to make copies of themselves, hence selfish. Furthermore, they are replicators, the only entities important in Darwinian evolution. The phenotype, the organism, and the objects the organism produces to modify its environment (Dawkins calls this the “extended phenotype”) are all products of genes as replicators. Dawkins was a big promoter of etiology, the study of cause and effect. Genes cause biological diversity by being selfish. There are even genes that are pure parasites, inserting copies of themselves randomly in the genome. But what are genes? Genes are collections of strands of DNA, copied and edited and used to make proteins. Genes are not really physical entities but a physical structure, a space of sequences, embedded in a physical thing (DNA) which allows for the construction of specific proteins. Genes cannot exist outside the biochemical machinery and like viruses, cannot be considered alive. Dawkins is trying to abstract Darwinian evolution, to reduce it to the transfer of an informational object. This is one of many necessary steps to understanding the origin of life. He also coined another word, “meme,” and applied it to cultural evolution, Darwinian evolution abstracted and applied to human culture. My main problem with Dawkins is that he wrote a popular book using a provocative, anthropological, and frankly political term, “selfish.” This has confused the public and deflected central questions: Is this a useful model for evolutionary theory? Is this a useful model for generalizing Darwinian evolution? Developmental biology is the study of how biological entities grow and change, and their life history. Development was basically ignored by the synthesis of Darwinian evolution and genetics in the 30s. One reason was that developmental biology was at that time dominated by German scientists, some of which had become Nazis. Another was that there was still much magical thinking swirling around the field. A third is a general difficulty in understanding biological development. It has been only recently that the technology exists to resolve some of the issues raised by developmental biologists. [15] There has been a continuing critique of issues with the synthesis. One of the main issues is perspective, holism (gestalt) vs reductionism. I don’t like binary concepts because it is so easy to put dual labels on them like “good or bad” or“right or wrong.” Mention holism to most biologists and you will get a very unpleasant response. Reductionism has been a very successful perspective for doing biology. But it does have limits that can’t be reduced away. Mathematical advances have changed all that. Nonlinearity, cybernetics, dynamical systems, systems thinking, and model building, are all concepts that fall under the general domain of complexity theory. Complex systems can be reduced to some extent and they can be probed for general concepts. But there is so much more. In 1996 Robert Lewontin formulated a relationship between a replicating individual (or population) and its environment. Put in modern form by the biologist and philosopher of science, Peter Godfried-Smith it reads:
[16] [17]
O is the organism and E is the environment. The next replication of the organism is a function of both the parent organism(s) and the past environment. The next iteration of the environment is also a function of both the parent organism(s) and the past environment.
In this, life doesn’t react passively to a hostile environment but actively changes it. The replicator and the environment are coupled, they can’t be uncoupled. It used to be that the evolution of life was thought to be like a ladder of increasing complexity leading to the ultimate, humans. This doesn’t work anymore, life has always been complex. What life has done is expand its domain to modify and encompass the planet. Perhaps humans are a solution to expand life’s domain outside the planet. Perhaps we will fail and another solution will arise and succeed. Perhaps if we succeed we will encounter very different solutions. We humans have more bacterial cells in our bodies than we have human cells. We live in a world created and modified by bacteria, we are surrounded by bacteria. Bacteria arose as the first life forms, and we have been around as a mere blip. So the difference is in time, young and old, not a ladder or a tree but a web of relationships in time and space.
Location of Pando Tree at Fish Lake, Utah [18]
In the mountains of central Utah is an ancient natural lake formed in a crack between parallel faults, a geological formation called a graben. This lake, unimaginatively named “Fish Lake,” has its own subspecies of land-locked salmon. Near the southwestern shore is a stand of Aspen forest that has been named “Pando.” [19] Pando spans 106 acres which seems large but is dwarfed by larger stands further up the mountains. This forest has been bisected by a highway and on one end the state of Utah has built a campground. Pando was discovered in 1977 and in 2008 it was verified that the stand is a single clone that is perhaps 800,000 to a million years old. [20] Aspen is a mainly clonal species and every single tree is connected to all the others by a root system. Unlike other clonal trees like oak, aspen root systems don’t separate into individual trees. The individual stems can only live for about 120 years due to all the other species that inhabit and feed off of it. But the clone lives on. Aspen can also reproduce sexually and several miles north on the lake I discovered for the first time aspen flowers. So what is the individual, Pando the clone, or the separate trees? Or is the ecological niche around Big Lake the individual? Or part of the Ponderosa pine forest that covers most of western North America? Forests and other ecological entities like chaparral, deserts, or grasslands are linked underground and on the surface by bacterial filaments. Some think that these create a chemical form of communication network throughout a forest. [21] Everything is embedded in a web of life, an environment both locally and globally created by life.
An aphid giving birth to live young. Her granddaughter is already growing inside.[22]
Aphids have a complex life history. Female aphids are hatched from an egg in the spring. They are born with all their ovaries fertilized and a wingless female clone immediately begins to develop inside. Inside the female clone is another female clone beginning to develop. By the time of live birth, the newborn is almost ready to give birth herself. Each female gives birth to their clonal daughters and granddaughters at the same time. In the fall, given some environmental signal, winged females called sexuparae are born and these fly off to congregate with other unrelated sexuparae (2 – 6) to start bearing sexually active males and females who have no mouth parts. These mate, the females lay eggs, and both die. The eggs overwinter then the whole thing starts over again. So what is the individual? The original female? The replicating final forms? The egg? Males can mate up to 14 times but females reject mates after two matings. Each mated female lays only one egg. Aphids in this study are unusual in that they actively mate with clone siblings. The paper I am referring to was written in 1992 [23] and they didn’t follow the newly hatched eggs over the winter. This is a part of a long controversy as to whether aphids can recognize kin and about the incest taboo, often linked to female choice. There have been situations like this in other species where sibling sperm is somehow actively rejected. Also, among some 4000 species of aphids, only a few can be studied in the laboratory, and laboratory conditions are not real-life conditions. In the 1990s aphids were thought to not recognize kin. Now they are. Same with sibling eggs that don't hatch. A loss of fitness has been found. Perhaps by predation. Mixing bad eggs with good a predator eating a bad egg actually helps fitness. Aphids are symbiotic with the bacteria Buchnera aphidicola. They have inside them a sack of cells called bacteriocytes which house the bacteria. Without these symbiotes, the aphids won’t survive and the relationship is some 400 million years old. The bacteria is passed directly from mother to daughter, so-called vertical transmission. Aphids have one or more additional symbiotic bacteria that are transmitted by infection or horizontal transmission. [24] These are not necessary but enhance survival and different species of aphids have different sets of these bacteria. Looking at aphids and their corresponding Buchnera genomes, it is clear, except for a few noticeable jumps, that the two evolved together. [25] Every eukaryote has at least two genomes and the aphid has three unique ones and perhaps many others. Genomes seem to like to hang together, within the cell, between cells, and between organisms. Maybe one should talk about the cooperating genome as opposed to the selfish gene. Or maybe these binary choices are getting in our way.
But what of bacteria? These are, for the most part, free-living (planktonic) single-cell and single-genome organisms. Right? Turns out this is not the case.
Staphylococcus aureus biofilm on an indwelling catheter [26]
Planktonic is just one phase of a bacteria’s often complicated lifestyle. What we know about bacteria is from the limited number of species we can grow in a lab under ideal conditions. Bacteria don’t grow the same way under normal conditions. They form communal clusters encased in a gel matrix called a biofilm. It is believed that all land-based bacteria and 70% of sea-based bacteria form biofilms. [27] Little is currently known about most sea-based bacteria so this number could be low. One common ocean genus that is considered free swimming, Pelagibacter, has a streamlined genome, suggesting a loss of genes perhaps used for biofilm formation. [28]
Mature Biofilm Structure [29]
Biofilms consist of a form of matter called a gel. Gels have both liquid and solid properties and a structure consisting of some type of polymer molecule. All cells are also gels and the internal structure is made up of polymer tubes called tubulin. Cells within the biogel develop different states or specialties. Specialties include resistance to certain diseases or chemicals or a specialized metabolic function. These cells can come from one species of bacteria or several different species of different genera or even from one or more eukaryotes.
5 Stages of Biofilm Development [30]
initial attachment
irreversible attachment
maturation I
maturation II
dispersion.
The cells attach, form clumps, and the clumps gather together to form the biogel. All the outside structure comes from compounds secreted by the cells themselves. The structure of the biogel creates a membrane and a tough, resistant cover. Biogels are hard to kill. Also, spontaneous channels can form within the structure to facilitate the flow of materials. Among the compounds secreted into the biogel are strands of DNA. This extracellular DNA (eDNA) often will migrate into another cell and combine with its genome, a form of horizontal transfer. In Gammaproteobacterium, eDNA can form the polymer structure. This bacteria could be quite ancient since its genome is deep branching and it has very few relatives. [31] The cells communicate through a method of communication called quorum sensing. This is a form of chemical communication that allows the cells to come together and create the biofilm. So what is the individual? Each individual bacteria/eukaryote or the biofilm? In a way, this is the start of a multi-celled organism.
Colony of thermophilic bacteria at Mickey Hot Springs, Oregon. [32]
Notice the fibrous outer skin consistent with a dried hydrogel.
Cells and biological individuals need a certain degree of autonomy, and this implies competition. So there is a paradox here, which came first, the individual or the quorum? Most biological models have cooperation evolving out of individuals, but the question could just as easily be turned around. Maybe we are asking the wrong question. Cooperation can’t exist without computationally autonomous agents and computationally autonomous agents can’t exist without cooperation.
Prairie Voles: rare mammals that practice social monogamy [33]
Nowhere is the problem of the individual more acute than in the study of biological behavior. Behavior is what an individual does, how it modifies and reacts to its environment, and how it associates with other individuals: for reproductive sex, with members of the same species, and with other species. Association can run a spectrum from a bird landing for a time in a tree, a bacterium living in nodules in a root, insects living in a gall, disease, to something eating some or all of the tree. Usually, there are several interlocking spectrums of association involving hundreds of different species. But if one reads the behavioral literature it is all about binary choices and one on one associations. Starting in the 1960s, a group of British and American mathematicians and biologists, John Maynard Smith, George Price, William Hamilton, and Richard Dawkins set the groundwork for new theoretical models of behavior and the genetic roots of behavior. This period saw the start of evolutionary game theory and evolutionary dynamics. Game theory is the modeling of the interaction between two or more agents given payoffs based on at least two playing strategies. In evolutionary game theory, the payoffs relate to fitness. Behavior is the association between two or more biological individuals. There are two major questions about behavior: [34]
How does it evolve?
How is it maintained?
One behavior is altruism or cooperation. Why would an individual reduce their fitness for the sake of others? One of the simplest and most famous games is Prisoner’s Dilemma. Two people are charged with a crime. Since the prosecutor does not have enough to convict, they are each offered a deal. If one confesses and the other doesn’t the rat will go free while the other will receive a maximum of 10 years. If neither confesses they will go both get 1 year. If both confess they will both get 7 years. The cooperative goal is to not confess but the rational goal, the one with the best potential payoff, is to rat on the other. For this and other games, cooperation always loses out.
The general mathematical setup for a two-person two-strategy game with relationships between the payoffs for the Prisoner's Dilemma. C means cooperate, the prisoner refuses to confess, D is the default, and the prisoner rats out the other.
This was the situation in 1964 when both kin selection and selfish genes were proposed. Kin selection basically says that altruism evolves when then a population of associates is related. This is Hamilton’s Rule: [35]
where r is relatedness, B is the fitness benefits of relatedness, and C is the cost of altruism. Hamilton’s Rule has dominated behavioral biology to this day.
In 1978 the sociologist, Robert Axelrod proposed a tournament. Playing the Prisoner’s Dilemma over and over, can one strategy lead to cooperation? It turns out there was a winner. The strategy is called Tit-for-Tat. Do what your opponent does last. Axelrod published a paper with William Hamilton in 1981 [36] and wrote a popular book in 1983. [37] There is a second possible way for cooperation to evolve, called reciprocity. Later, it was found that the Tit-for-Tat strategy had flaws, and mistakes could defeat it. In the 1990s Robert Nowak and Karl Sigmund did a systematic computer simulation of the iterated Prisoner’s Dilemma. [38] They found a set of linked iterative strategies and a (semi) stable one. The following is a drawing of an image in Nowak’s book: [39]
Oscillations of cooperation and defection
TFT is Tit-For-Tat, GTFT is Generous Tit-For-Tat, ALLD is All Defect, ALLC is all cooperating, and WSLS is Win Shift Lose Shift. WSLS occasionally will collapse to ALLD under unknown conditions.
This result shows both how cooperation evolves and how it is maintained. Nowak has looked at evolutionary game theory from the standpoint of the number of single-turn strategies being larger than two, games on graphs, finite populations, and spatial games. All of these show the complex dynamics of strange attractors, chaos, and the onset of cooperation. People have taken the results of the Prisoner’s Dilemma to mean that cooperation is both difficult to create and fragile to maintain. To me, the results show that even in the most dismal bleak, and simple scenario, cooperation can exist. Evolution is dynamic and variation must be maintained so a rich ever-changing mixture of cooperators and defectors is optimal.
E. O. Wilson, the great ant biologist, among other things, coined the name “Sociobiology” and wrote a famous book on the subject in 1975. [40] The idea that humans, as animals, had behaviors linked to their biology, struck many as a return to social Darwinism and racist ideology in the sciences. It caused a major rift at Harvard that culminated in Wilson having a jar of ice water dumped over his head during a talk in 1978. [41] What Wilson was defending was the right to study behavior as a biological problem. Fortunately dangerous ideas like a ‘gay gene’ have been thoroughly debunked and the biology of behavior is firmly in place as a real science. Wilson accepted and promoted inclusive fitness (kin selection) and Hamilton’s Rule, but he never gave up the idea of group selection, a hierarchy of selection by populations of groups over individuals. The inclusive fitness people have always argued that kin selection and group selection are equivalent but over the years Wilson became more and more dissatisfied. In 2010 a paper was published: The Evolution of Eusociality [42] by Martin Nowak, Corina Tarnita, one of Nowak’s post-docs, and Wilson. In it, the authors argue that there is more than one path from altruism to cooperation, five I believe. The response was an explosion of controversy. Nowak was accused of trying to put religion back into science, [43] mainly because he has taken money from the Templeton Foundation. In 2017, Wilson, Nowak, and others published The general form of Hamilton’s rule makes no predictions and cannot be tested empirically. They make several points, but the final paragraph is worth repeating. I took out all the reference marks for clarity:
“Indeed, we should not expect that interplay of population structure and social behavior can be reduced to a simple rule with three parameters. Social interactions, which are typically multilateral and nonlinear, cannot be expressed by a single benefit and cost. Complex population structures cannot be captured by a single relatedness quantity. Assortment among relatives often has a positive effect on cooperation, but in other cases it has a negative effect or no effect at all. A good understanding of these questions, like all great problems in science, will require careful empirical observation in concert with meaningful mathematics.” [44]
E. O. Wilson died in December of last year and problems with him, behavioral biology and race are still cropping up. [45] Nowak’s career took a serious dive not because of science and religion but because of his relationship with one Jeffery Epstein, something I documented in a footnote here. He seems to have recovered and is publishing again. Tarnita left mathematics for biology. Whatever happens with Hamilton’s Rule and group selection, it will be she and other researchers that will make the difference. In southeast Arizona is the small community of Portal, at the base of the Chiricahua Mountains. It is a major birding and naturalist area and further up the mountain is the Southwest Research Station of the American Museum of Natural History where many biologists do their summer field research. There is a small gift shop and they always have books from local authors and from visiting scientists. It was here that I picked up Deborah M. Gordon’s Ant Encounters. i There are currently about 11,000 known species of ants plus another estimated 10,000 that haven’t been described. Only 50 species have been thoroughly studied and only a few can be studied in a lab. Ants are incredibly diverse, in size, colony size, and behavior. Because just a few species were studied at first, many of the current ideas about how ants act are not correct. For one thing, the idea of caste seems incorrect, even in species that have different sizes, a situation far from universal, in most species except for the queen, most ants are the same size. Ants don’t have a set task their whole lives. An ant’s task is determined by the rate of contact with other ants. A high enough rate of contact with other ants doing a certain task will switch an ant over to doing that task. Ants are covered with a greasy coating of a mixture of different hydrocarbons that are spread over the ant's body by grooming. This mixture tags the ant as being both a member of the colony and have a specific task. The memory of each contact lasts about 10 seconds. The is also some evidence that ants have some long-term memory but it is unclear how this is maintained. An individual ant can live for about a year but a colony can live much longer, the harvester ants that Gordon studies have a colony lifespan of between 20 to 25 years. The network of interactions between the ants in a colony forms a collective memory that allows the colony to respond to changes in its environment. Evidence of this is that mature colonies are more stable to environmental perturbations than less mature colonies. The colony matures even though the individual ants come and go. Interactions of semi-autonomous individuals naturally lead to cooperation and a complex structure that exists in space and time. This structure can also be modeled as an individual, Gordon considers the colony as the reproductive individual, not the queen herself. So evolution acts on populations of colonies, something that is just beginning to be studied. Hamilton’s rule has been useful but no longer sufficient for the complexities involved. It seems that a new queen has to mate with at least two males to successfully start a new colony. Also, what is relatedness when some species steal the broods of others to use as slave workers?
Birds have complex mating and brood-rearing systems. Often this can include generations that stay in the nest and help raise new generations, thus suppressing their own reproduction. This is termed cooperative breeding and how this evolved and is being maintained is another study of cooperation. In 2016, a compilation of studies in cooperative breeding was published. Cooperative Breeding in Vertebrates, [47] edited by Walter D. Koenig and Janis L. Dickenson includes 15 bird studies, one fish, and 3 mammal studies. Koenig’s introduction specifically targets Nowak and Wilson’s critique:
“Explicit tests of Hamilton’s rule (Chapters 2 and 3) provide evidence that further documents the value of kin selection and inclusive fitness thinking. This large body of evidence supporting the importance of kin selection in helping stands in direct opposition to challenges based on modeling efforts and spotty interpretation of empirical evidence (Nowak et al, 2010).”
I intend to say more about this in future blog posts and the whole book could use a critical summation but here is what I’ve noticed so far:
Mating strategies are very heterogeneous and fluid yet all seem to have some sort of monogamy, mostly social, as the default. Social monogamy means that a mating pair might mate for life yet a certain percentage of the chicks born do not belong to the father. In some this is about 10% or less, in others, it can be as high as 44%. Thus, many chicks are not related to the father.
How kinship is recognized and remembered is still a mystery.
Environmental effects are real and diverse, they can change the sex ratio and also the extent of cooperative breeding.
It is unclear what constitutes hierarchy. Is it the nest? Sometimes nests are distributed, like in Mexican Blue Jays. [48] The larger group can be kin-based or not. The replicating individual can be thought of as the nest(s) or the larger flock.
Fitness is hard to quantify.
The series of books Masks of God, [49] by Joseph Campbell is based on the premise that the modern concept of the individual evolved from mythological roots. To him, the individual didn’t exist in the past. To some, the Western concept of self-started with the German Romantics at the end of the 18th century and centered around the university town of Jena in what is now Germany. [50] I’ve always been sympathetic to this idea. Lately, I’ve come to realize that it is a bit more complicated. In biology, boundary and what is enclosed within this boundary as an autonomous agent of computation and replication is central. Also central is the embedding of these agents in hierarchies of boundaries and thus hierarchies of computation and replication. Human individuals always existed, so maybe it is consciousness, the discovery that we are individuals, that is evolving.
To summarize:
Evolution works on populations of individuals.
The definition of an individual is arbitrary. An individual can be defined along any hierarchy of replication.
Evolutionary dynamics are non-linear and complex.
Cooperation can arise from any and all different game theoretic dynamics.
In these dynamics, mixed populations of cooperators and non-cooperators are the norm.
In the biome, the concept of individual and group is only useful as a model, there is no way to actually separate the two, except as a way to probe the system.
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