Chapter 3: The Evolution of Intelligence on Earth
In Chapter 3, we’re going to briefly turn away from the concepts of neurodiversity and evolutionary medicine so that we can dive into the story of evolution. It’s a meaningful narrative that helps set the context for issues we are going to discuss in upcoming chapters. When you think of disorders, such as schizophrenia, I don’t want you to think of them in the context of movies, television shows, and popular books and articles. I want you to think about them in terms of the epic of evolutionary history. In this epic, the characters are self-replicating molecules.
Self Replicators
It is easy to see that all living organisms on our planet today are replicators. Each plant,
animal, fungus, protist and bacterium is here now because its ancestors were able to
escape death, and successfully pass their genetic material on to their offspring. Since
the beginning of life on earth every member of each of the five kingdoms has been fine
tuned to accomplish one ultimate objective, replication.
Chemically, the genetic material used by all organisms on the earth is so uncannily
similar that most scientists believe that we all came from a single ancestor. Even organisms as dissimilar as humans and bacteria share the same chemical systems for
replication, in fact we even share many of the same genes. The very first replicators on our planet were most likely microscopic, organic molecules. These were strands of chemicals that attained the ability to copy themselves sequence by sequence. Most experts assume that the first chemicals to achieve this ability were strands of ribonucleic acids or RNA.
The basic constituents of RNA, and DNA for that matter, are four different nucleotide
molecules. A, C, T, and G. The compounds that these nucleotides form have chemical affinities for one another, and they tend to group together creating long strands. The RNA world hypothesis, a well-accepted theory for the origins of Earth’s first denizens, suggests that these chemicals existed in miniscule amounts near the bottom of the ocean and that, over time, the long sequences of nucleotides developed a way to make identical duplicates of themselves. Because the earth is such a dangerous place for large organic chemicals, any RNA strand that could not duplicate itself would eventually be worn down or destroyed. In a volatile physical world, rapid replication would have been the only path that allowed these RNA strands to perpetuate themselves.
The way in which these first strands of nucleotides replicated was probably very similar
to the way that our DNA replicates itself within our own bodies. Replication is
achieved using chemical catalysts called enzymes which travel down the
length of the DNA or RNA strand and duplicate it nucleotide for nucleotide. The enzyme
that our bodies employ to complete this task is called DNA polymerase. It is not clear
what enzyme was used by our oldest ancestors, but it was surely similar to DNA
polymerase in structure and function. Luckily for us, the mistakes inherent in
replication, also known as mutations, allowed these early replicators to be adaptively modified from their original forms and to respond to the rigors of their environment.
The errors made during replication are committed by DNA polymerase, and often these mistakes are not caught by the figurative spell checker, DNA repair enzyme. Usually these accidents are either neutral, debilitating, or fatal. However, sometimes they can be beneficial. When these mistakes prove useful, they can create genetic variability in a gene pool and thus allow organismal populations to change with time. Theorists believe that natural selection began to act on these RNA strands on the bottom of the ocean, weeding out the poor or slow replicators and allowing the robust ones to proliferate. After some time, competition for resources must have caused these original replicators to develop new survival strategies.
It is thought that the environment drove these RNA strands to compete with one another. For instance, a scarcity of resources may have caused these replicators to use
chemicals to destroy one another. If they were in fact successful at destroying other RNA strands, then they not only kept other strands from taking scarce resources, but they also had immediate access to a nucleotide corpse they could use to create a replicate of themselves. It is thought that this “chemical warfare” caused them to develop protein enclosures to protect themselves from other strands and from the harsh environment. Today, we know these protein enclosures as cells, the smallest units of life. Simple cells changed, evolving to perform complex functions, all of which came about to ensure and increase replication.
Cells began to be grouped together in giant communities or that today are recognized as multicellular organisms. Multicellularity evolved and evolution began to experiment with body plans. The replicators that survived were those that built the most fit body for themselves to inhabit. Every multicellular animal is a plodding, subservient robot doing the bidding of its genes in service of replication. Put simply, our bodies are vectors for replication. But it is important to point out that neither genetic nor behavioral complexity is not necessary for successful replication. Bacteria are the least intelligent forms of life, but the most prevalent. Not only are there far more individual bacteria on the earth than there are individual humans, but bacteria also make up a larger proportion of the earth’s biomass than all members of the human species combined. The evolutionary success of humans and bacteria shows that nature can allow many different reproductive strategies.
As reproductive strategies go, there seem to be two very successful kinds. One, used
by bacteria, is reliant on the transference of genes alone. The other, employed by
humans, is reliant on the transference of genes as well as the transference of memes.
Memes are units of cultural or social information, and they are passed or taught from
parent to child. Humans are reliant on memes. Without language, knowledge,
and skills humans cannot survive on their own in a natural environment. Bacteria, plants and many other organisms, however, have no use for memes. All the behavior that they need to reproduce is already contained in their genes and in their bodies at birth.
It is interesting to note that memes can be thought of as another form of replicator. Just
like genes they are passed from parent to child and usually only the ones that increase
survival and reproductive success can persist. It turns out that there are two
antagonistic strategies used by organisms to perpetuate themselves, one is the r
strategy and it is reliant on genetic transference alone and the other is the K strategy
which is reliant on both genetic and memetic transference.
| Millions of Years Ago | Eon | Era | Period | Notable Events |
| 4600 | Hadean | Precambrian | Earth forms | |
| 4000 | Archean | Life begins as bacteria | ||
| 2500 | Proterozoic | Multicellular life develops | ||
| 542 | Phanerozoic | Paleozoic | Cambrian | Early animals evolve |
| 488 | Ordovician | Plants & animals move to land | ||
| 423 | Silurian | Jawed fish appear | ||
| 416 | Devonian | First amphibians | ||
| 359 | Mississippian | Trilobites decline | ||
| 318 | Pennsylvanian | First reptiles | ||
| 299 | Permian | First mammal-like reptiles | ||
| 251 | Mesozoic | Triassic | First dinosaurs and true mammals | |
| 200 | Jurassic | Giant dinosaurs dominate | ||
| 145 | Cretaceous | First primates appear | ||
| 65.5 | Cenozoic | Paleocene | Dinosaurs go extinct | |
| 55.8 | Eocene | Early modern mammals | ||
| 34.0 | Oligocene | Grasslands and herds develop | ||
| 23.0 | Miocene | Apes appear | ||
| 5.30 | Pliocene | Human-like primates evolve | ||
| 2.40 | Pleistocene | Humans develop |
Table 3.1 Geological time scale showing the major periods in earth’s history and some of the notable events this book will refer to.
Our subspecies redundantly emphasizes our sapience: homo sapiens sapiens.
| Taxonomic Classification for Human Beings (Homo sapiens sapiens) | ||
| Kingdom: | Animalia | A living organism that is multicellular, has muscles and a nervous system |
| Phylum: | Chordata | Has a spine (or simpler notochord), a spinal cord (or nerve cord) down its back, pharyngeal slits, and a post-anal tail |
| Class: | Mammalia | Uses mammary glands to provide milk for young, has fur, a neocortex, and three middle ear bones |
| Order: | Primates | Has large brain, visual acuity, color vision, mobile shoulder joints, and dextrous hands |
| Suborder: | Haplorhini | Dry nosed primates (contrasted with strepsirrhini or wet nosed primates) |
| Infraorder: | Simiiformes | Group of higher primates containing monkeys and apes |
| Family: | Hominidae (hominids) | Great apes |
| Subfamily: | Homininae | African apes (humans, chimpanzees, bonobos, gorillas, and related extinct apes, excludes orangutans) |
| Tribe: | Hominini (hominins) | Humans, chimpanzees and bonobos (excludes gorillas) |
| Genus: | Homo | Humans along with extinct archaic humans species |
| Species: | Homo sapiens | Includes multiple extinct human subspecies |
| Subspecies: | Homo sapiens sapiens | All surviving humans |
Table 3.2 Taxonomic classification for human beings
Life Arose from Matter
As a brief recounting of our history shows, our bodies exist to ensure that our genes perpetuate. Modern measurements place the beginning of our universe at 13.8 billion years ago. Fourteen billion years ago, there was no space, time, matter, or energy. A disturbance in this nothingness created space and time and produced massive amounts of energy. Cosmologists use the term “the Big Bang” to describe the event, a tremendous explosion of energy from a single point. Much of the energy released from this explosion was in the form of highly energetic photons of light. These high-energy photons condensed into atomic matter, mostly hydrogen. Unlike light, matter has gravity and these atoms pulled themselves into large balls of gas that grew dense and hot enough to ignite. As these stars burned, they converted hydrogen and helium into all the heavier elements of the periodic table creating the material for planets, asteroids, comets, and life.
The atoms in our bodies are derived from three or four generations of stars that burned out long ago. Our sun and its planets accreted from a giant nebulous ball of material, remnants of an earlier star that exploded in a supernova. Our Earth formed about 4.5 billion years ago, and life is thought to have begun around 3.4 billion years ago. How did it begin? Life emerged spontaneously from interactions between molecules on the prebiotic Earth in a process commonly referred to as abiogenesis.
Abiogenesis: Life from Matter
All living organisms are composed of atoms that themselves are not alive. It is the fantastically complex structural composition of cells that organizes inert atoms into incomprehensibly intricate, miniature factories. How did this fantastic chemical complexity come about? It was crafted slowly and incrementally by the hand of natural selection. But what was the starting point? All scientific evidence suggests that we descend from simple molecules that accidentally developed the capacity to self-replicate.
In order to persist through billions of years something must either be incredibly structurally stable or it must be able to duplicate itself. Tiny replicating molecules in the earth’s primordial seas were not stable, they could be broken apart easily, but their capacity to make nearly exact copies of themselves allowed their form, if not their original embodiment, to endure through the eons. These “entities” were much like today’s viruses. How did these complex molecules arise de novo from the primordial soup? Heat in the oceans give the atoms in water kinetic energy, which creates opportunities for molecules to collide, and in so doing, form and break molecular bonds. Constant molecular tinkering taking place in hundreds of millions of square kilometers of water must have chanced upon the right combination. The first replicator was assembled accidentally.
A number of laboratory experiments have demonstrated that simple inorganic elements, under the right conditions, can combine to form complex organic molecules. Some of the most important molecular building blocks of life have been shown to assemble spontaneously: 1) amino acids (the building blocks of proteins), 2) purines and pyramidines (the A, T, G and C building blocks of DNA and RNA), and 3) spherical cell-like membranes (micelles). Scientific experimentation has shown that the basic organic components of life can form randomly from simple chemicals with no human intervention. It has not been shown, however, that these can assemble into self-replicating polymers. Until this changes we take this on faith.
Most of life’s important molecules are linear macromolecules called polymers. Polymers are made of subunits that attach like beads on a string. The way in which these first macromolecules replicated was probably very similar to the way that our DNA replicates itself within our own bodies. The molecule acts as a template attracting its molecular subunits (floating freely in the ocean around it) to create a matching polymer that corresponds precisely with its own molecular sequence effectively creating a duplicate of itself. This would actually be a relatively passive process, the replicator could not reach out and grab these molecules. The molecular building blocks would mostly float into the position where they could be captured to form the needed bonds. The matching and pairing would continue until the replicator had been completely duplicated, but it would then be bonded to its duplicate. It was necessary to have a way to force these two chains to split resulting in two equivalent replicators, each of which can go on to create more.
Organic chemists believe that the first replicators were ribonucleic acids (RNAs) because RNA has all of these necessary properties. RNA has the capacity to perform the chemical manipulations necessary to duplicate itself (autocatalyze its own synthesis) and then split or divide in two (perform self-cleavage). Because the new RNA strand is now itself a template, such systems can exhibit exponential growth over time.
The “RNA world hypothesis,” a generally accepted theory of the origins of earth’s first replicators, suggests that life on Earth descends from an RNA world. Because the earth is such a dangerous place for large organic chemicals, any RNA strand that could not duplicate itself would eventually be worn down or destroyed. In a volatile physical world, rapid replication would have been the only path that allowed these RNA strands to perpetuate themselves. These molecules were never meant to last forever, they were selected to last long enough to make a few copies of themselves, and thus eventual death was built into this system from the beginning.
Evidence indicates that these replicating molecules have persisted in a relatively conserved form since the Archean eon over 3.5 billion years ago (shortly after the Hadean eon in which the earth was essentially molten). At this time, the moon was much closer to the earth, and it loomed large in the sky. The sun was not as bright, the days and nights were much shorter, the seas were green rather than blue, and the sky was orange.
The mistakes inherent in replication, also known as mutations created variations for natural selection to act upon. This allowed these early replicators to be modified from their original forms and to become more complex in response to the rigors of their environment. Copies were selected for longevity, fecundity and accuracy of replication. Competition for resources must have caused these original replicators to develop new survival strategies. They began building a cell membrane around themselves to serve as a shelter and a vehicle to further their continued existence. They went from floating about naked in the seas, to being ensconced in protective sheathes. Today, we know these enclosures as cells, the smallest units of life. These simple cells changed and evolved to perform complex and meaningful functions, all of which came about to protect the RNA (and later DNA) and to increase the productivity of replication.
Once earth’s early replicators began to be able to gather energy, they could complexify and do work. The espousal of an energy gathering system allowed them to overcome the second law of thermodynamics (entropy) and maintain structure and order over time, developing a metabolism, homeostasis, and life in general. The first live, energetic organisms derived their energy from chemicals (chemoautotrophic). Some later evolved to derive energy from the sun like plants (photoautotrophic), and others, like us, derived their energy from the consumption of other organisms (heterotrophic). Living organisms developed the capacity to budget energy, save it during times of rest, and expend it during times of need. Most of the disorder that we discuss in this book stem from tradeoffs in energy expenditure.
These survival machines developed an ability to reflect upon their universe, themselves and their place in the universe.
Figure X.X:
Charles Darwin predicted that the abiotic production of simple organic molecules must have been the initial step in the creation of life. He believed that a “warm little pond” on the early earth may have allowed the right conditions to produce the precursors of life that would undergo complex changes to become the life we know today. Since, scientists have found that many of the complex molecular building blocks of life have a tendency to “accidentally” assemble under the right conditions. By passively mixing together chemicals thought to have existed in earth’s early oceans scientists have observed the formation of: 1) amino acids (the building blocks of proteins), 2) purines and pyramidines (the A, T, G and C building blocks of DNA and RNA), and 3) spherical, layered, cell-like membranes (micelles). Science has shown that the basic organic components of cells can form from simple chemicals with no human intervention.
In 1953, Stanley L. Miller and Harold C. Urey, performed a now classic experiment demonstrating how inorganic elements, under the right conditions, could combine to form some of the precursors of organic chemicals. This experiment began the study of how biological life could arise from abiotic matter through natural processes (abiogenesis). Miller sent electric discharges through a flask containing some of the gasses that would have been abundant three to four billion years ago. These included methane, ammonia, hydrogen, and water. The experimenters repeatedly condensed and vaporized the mixture for a full week and found that at the end of seven days about 15% of the carbon had formed organic compounds. Upon further examination they found that about 2% of the carbon in the experiment had formed the fundamental building blocks of all proteins and thus of all cellular life… amino acids.
The complex components of genes can form spontaneously. It has not been shown, however, that these can assemble into self-replicating polymers. Evolutionists are forced to take this on faith. But how did this polymer, this rudimentary first gene, evolve into us? It actually changed and mutated a little during each replication due to copying mistakes. Certain mistakes were made in the copying process and the mistakes that created more efficient variants of the replicator became more numerous. Theorists believe that copy mistakes that helped the replicators copy faster, with fewer errors were the ones that proliferated. Within a short period these primeval forms of life could develop vast diversity of form and function. But like a virus, the first replicators were not alive. Cellular biologists don’t count anything as living unless they constitute or are constituted by cells.True animacy (the subjective impression that a being is alive) developed in single cells. True agency (the subjective impression of a willfulness and goal direction) developed in animals with brains.
After these molecules espoused cellularity their very structure took on a different function. They still acted as templates for their own replication, but they began to hold genetic information. At some point before they evolved into bacteria, they came to hold instructions for how to perform cell division, act as a blueprint for building and maintaining organisms, and also contain the information necessary to make the various proteins necessary for the organism’s survival. The DNA in our cells today performs these exact same functions.
We are not only related to every other animal on the earth, but every form of life on the earth. In order to not be related to another form of life it would have had to start off as a replicator, from chemicals, on its own. It is possible that another life form copied our way of making genes and proteins exactly but is astronomically improbable.
Radioactive dating places the age of the earth at 4.47 billion years. The first microbes seem to have appeared 3.7 billion years ago. Dinosaurs ruled for 135 million years before they were wiped out by a ten-mile-wide asteroid that fell into the Gulf of Mexico 65 million years ago at the end of the Cretaceous period. Primates were just differentiating themselves at this point, but mammals had been around for a long time. Mammals are thought to have diverged from reptiles 300 million years ago. The oldest stem primate fossils found date back to just before the extinction of the dinosaurs and were similar in size and shape to modern squirrels (which were themselves less distinct rodents at the time).
Self-replicating nucleic acids are a form of propagating information. They are propagating in the sense that they are moving through space and time. In this way, genes represent data that is conserved and maintained intact on the surface of the planet. In a way this genetic information is equivalent to memory – it holds instructions for how to duplicate themselves, and since they espoused cellularity they hold instructions, memories, for how to make the proteins that are necessary for their survival. And like memories they change and have new components added. Evolution by natural selection changes genes slowly in a way that is very much like learning. Genes are molded to better fit their environment as memories are molded to ensure that an animals behavior fits with their environment.
The Selfish Gene
Albert Einstein described the propagation of light from light’s point of view. Richard Dawkins described the propagation of genes from a gene’s eye view. Dawkins said that all organisms are “survival machines,” devices intended to endure the environment and perpetuate the cold, greedy, psychopathic molecules known to us as genes. This echoes Samuel Butler’s aphorism that “a hen is only an egg’s way of making another egg.” Dawkins argues that DNA is fundamentally selfish because it created us, and all life on earth, to serve their purposes. Dawkins showed that this analogy, although only one way of looking at life, is valid at many levels of biological examination. Unlike most organisms, humans have the capacity to create their own agendas, but in the grand scheme of things these are subordinate to our primary objective, which is to survive and reproduce. Today most adults can appreciate that their innate urges toward sex, eating, self-preservation, and the attainment of resources have a commanding and pervasive effect on our behavior.
In his book “The Selfish Gene,” Dawkins clearly illustrates how the DNA is not only the fundamental unit of heredity but also the fundamental unit on which natural selection acts. Thus, genes are not just the blueprint for our bodies, they are the programmers, the navigators, and the original captains before the invention of the ship. Any full account of the meaning of life must at least mention this as a caveat. Genes can be thought of as units that outlive many individual survival machines. Their legacy structures our biology and gives us perspective from which to interpret our innate behavior. These molecular replicators evolved to the point where they employed animals and even us as their ephemeral encolosures, given one chance to do their bidding. In this way, competition between self-replicating molecules is responsible for creating our civilization, our intellectual heritage, and everything man-made we see around us.
In the late 1800s, evolutionist August Weismann pointed out that, in multicellular organisms, inheritance only takes place by means of the germ cells (gametes such as the egg cells and sperm cells). Other cells of the body – somatic cells – do not function as agents of heredity. This paints a picture where our bodies are mortal baton carriers and the germ cells are the baton in a relay race that stretches back billions of years. Our ovaries and testicles contain remnants of an immortal line of unbroken continuity stretching back 3.5 billion years. They were passed down to us by our parents and we pass them down to our children. Many biologists see our eggs and sperm as the seeds, and the rest of our bodies as a “disposable husk.”
The condiiton that damns us is that we came from selfish replicators. That is the true original sin that dooms us to some degree to inevitable selfishness.
Dawkins takes the selfish gene concept further, to its logical conclusion, that genes compete with each other to remain in the genepool, and that genes not individuals are the units of selection. In doing so he disabuses biologists of the idea that natural selection acts to promote the species, or the group. Since, most evolutionary biologists formulate their adaptationist hypotheses in terms of individual selection.
Replication is life’s imperative. Natural selection acts as a wheel or rudder that steers changes in a species over time, but it is not the driving force of biology. Replication is. In fact, biology and even psychology can be seen as just elaborate extensions of replicative chemistry. Every organism’s original purpose in life is to pass on their DNA in as effective a manner as possible to the next generation. To this end, all organisms have adopted various methods, called life history strategies, which enable them to fulfill this purpose efficiently given their body type and ecological niche.
The Tree of Life
- RNA and DNA; B. RNA synthesis and replication; C. Earth’s early oceans
The Great Tree of Life
For centuries it has been hoped that scientists could precisely determine dates for the branching points in the evolutionary tree of life. This dating has now been accomplished. In just the last few decades, scientists have finally assigned time periods to our line of descent from, not only other animals, but from plants, fungi, and bacteria. To determine relatedness, geneticists measure the number of molecular differences in the DNA between species. When a geneticist tells us that we are more than 98 percent chimpanzee that means that if we lined a matching strand of our DNA right up next to theirs, less than 2% of the sequence of molecules would be non-identical, and the rest would match our sequence exactly. Comparisons can be made with all animals, and all forms of life for that matter, to determine relatedness and time since divergence.
Table 3.1 below lists estimated dates for our divergence from other living groups of animals (Dawkins, 2004). It is easy to misinterpret such a list so allow me to give you some caveats. The last entry on the list indicates that we shared a common ancestor with chimpanzees, our closest living relative, only 6 million years ago. This does not mean that we were chimpanzees at that time, just that the common ancestors of humans and chimpanzees were members of the same breeding group of individuals and had not yet split apart and evolved into distinct species. The same goes for our relationship with each of the other modern groups listed. If the illustrations accompanying this list contained images depicting the actual forms that our lineage took during its history, it would look considerably different. However, in many cases the sketches provide a rough approximation for how our ancestors would have appeared all those years ago. As you look over the entries, you will see that our lineage went from single-celled organisms to plant-like animals, to worm-like animals, to fish, to amphibians, to reptiles, to mammals.
Dogs are not ancestral to cats or vice versa. Similarly, rats are not ancestral to humans. Each represents a different evolutionary lineage. Aside from differences in body plans and appearances, animals are built from highly conserved elements at the cellular and molecular level of analysis.
The fact that this list details the interrelationships between us and all living organisms on Earth makes it profoundly thought provoking for me. What type of information would have been more interesting to ancient thinkers, or to renaissance scholars? Even just 40 years ago humanity didn’t have anything like this. To me it is a kind of Holy Grail. We have it now, you are holding it in your hand. Please continue to refer to this table as we discuss similarities we share with other species.
Table 2.1 Time Since Divergence with Other Presently Living Organisms
3.? bya Molecular Replicators
2.? bya Eubacteria
2 bya Archaebacteria
1.25 bya Plants
1.2 bya Amoebozoans
1.1 bya Fungi
1 bya Drips
900 mya Choanoflagellates
800 mya Sponges
750 mya Placozoans
700 mya Ctenophores
650 mya Cnidarians
630 mya Acoelomorph Flatworms
590 mya Protostomes
570 mya Ambulacrarians
580 mya Sea Squirts and Salps
575 mya Lancelets
550 mya Lampreys and Hagfish
460 mya Sharks, Rays, and Skates
440 mya Ray-finned Fish
425 mya Coelacanths
417 mya Lungfish
340 mya Amphibians
310 mya Sauropsids
180 mya Monotremes
140 mya Marsupials
105 mya Afrotheres
95 mya Xenarthrans
85 mya Laurasiatheres
75 mya Rodents, Rabbits, and Hares
70 Tree Shrews and Colugos
63 mya Prosimians
58 mya Tarsiers
40 mya New World Monkeys
25 mya Old World Monkeys
18 mya Gibbons
14 mya Orangutans
7 mya Gorillas
6 mya Chimpanzees
The table below organizes this information slightly differently and offers examples of animals that belong to the larger taxonomic groups specified.
| Millions of Years Since Humans Shared a Common Ancestor | |||
| Years | Animal Group | Examples | Acquired Features |
| 0 | Humans | All contemporary races of human | Loss of fur |
| 6 | Chimpanzee | Chimps & Bonobos | |
| 7 | Gorillas | Mountain gorilla, Lowland gorilla | |
| 14 | Orangutans | Bornean orangutan, Sumatran orangutan | Flexible wrists and arms |
| 18 | Gibbons | Siamang, Silvery gibbon, black crested gibbon | Loss of tail |
| 25 | Old World Monkeys | Colobus, langur, proboscis, guenon, macaque, baboon | |
| 40 | New World Monkeys | Spider, howler, woolly, capuchin, squirrel, night, owl monkey | Menstrual cycle, diurnal, nails, single pair of mammaries |
| 58 | Tarsiers | Dian’s tarsier, pygmy tarsier, spectral tarsier | |
| 63 | Lemurs | Loris, bushbaby, potto, aye-aye | Forward facing eyes, grasping digits |
| 70 | Tree Shrews & Colugos | Tupaia, common tree shrew, pen-tailed shrew | |
| 75 | Rodentia & Lagomorpha | Pikas, rabbits, hares, rats, mice, gerbils, squirrels, porcupines | |
| 85 | Laurasiatheres | Shrews, hedgehogs, moles, bats, hippos, whales, camels, pigs, deer, sheep, cats, dogs, seals | |
| 95 | Xenarthrans | Sloths, anteaters, armadillos, aardvarks | |
| 105 | Afrotheres | Elephants, manatees, moles, shrews, aardvarks, dugongs | Full placenta |
| 140 | Marsupials | Opossums, wombats, kangaroo, koala | Live birth, nipples |
| 180 | Monotremes | Echidnas & platypus | Milk, sweat, fur, nocturnal |
| 310 | Sauropsids | All reptiles and birds | Diaphragm, keratin, no gills, shelled eggs, adrenal glands |
| 340 | Amphibians | Frogs, toads, salamanders, caecilians | Tongue, saliva, bladder, glottis, loss of fins, eyelids, tears |
| 417 | Lungfish | Marbled lungfish, gilled lungfish, West African | Walking, protolimbs |
| 425 | Coelacanths | Sulawesi coelacanth & African coelacanth | Lungs, preliminary ribs |
| 440 | Ray-finned Fish | Tuna, catfish, clownfish, eel, seahorse, goldfish | |
| 460 | Sharks, Rays & Skates | Great white, hammerhead, manta ray, sting ray | Jaw, scales, teeth, stomach, spleen |
| 530 | Lampreys & Hagfish | Sea lamprey, northern lamprey, Pacific hagfish | Ears, camera eyes, taste, pineal gland, skin layers, blood |
| 560 | Lancelets | Amphioxus, Branchiostoma floridae | Brain, smell, gills |
| 580 | Sea Squirts & Salps | Sea vase, sea pineapple, Didemnum vexillum | |
| 570 | Ambulacrarians | Sea urchins, starfish, sand dollars, acorn worms | |
| 590 | Protostomes | Insects, crustaceans, nematodes, mollusks, annelid worms… | |
| 630 | Acoelomorph Flatworms | Sterreria rubra, Nemertinoides elongatus | Heart, anus, bilateral symmetry |
| Cnidarians | Jellyfish, corals, anemones | ||
| 800 | Ctenophores | Comb jellies, venus girdle, lampocteis | Organs, nerves, muscles, skin, mouth |
| Placazoans | Trichoplax adhaerens & treptoplax reptans | ||
| Sponges | Demosponge, Giant barrel sponge, sycon | ||
| 900 | Choanoflagellates | Monosiga brevicollis, salpingoeca rosetta | |
| Drips | |||
| Fungi | Mushrooms, molds, yeasts, rusts, & mildews | ||
| Amoebozoans | Amoeba, entamoeba, mycetozoa | ||
| 1250 | Plants | Green plants, red algae | |
| Remaining Eukaryotes | Brown algae, protists, and protozoans | Organelles (nuclei, mitochondria, etc.) | |
| 2000 | Archaea | Halophiles, methanogens, thermophiles | Cell membrane, DNA, RNA, ribosomes |
| Eubacteria | E. coli, cyanobacteria, salmonella, bacillus | ||
This list of our relatives by evolutionary distance creates the false impression that the evolution of life has been one of progress and increasing intelligence. Some people see this and assume that this is proof that evolution leads to complexification. However, keep in mind that this is merely the list for humans. Every species has a similar list of divergences arranged in a different order. It is also important to point out that scientists fine tune and update the data that this list is built from, so it is not completely set in stone.
The next section will prove to you that evolution actually “prefers” to tend toward simplification.
Spiegleman’s Monster
When replicating molecules compete for the building blocks from which they are constructed, the fastest out-replicate the slower ones so that the slower replicators disappear over time. Self-replicators are naturally selected to become as short as possible because shorter molecules replicate faster. But, since the beginning of life, organismal DNA has tended to grow longer. This is because replicators can be selected to become longer if it increases their likelihood of survival. This allowed more sophisticated structure and behavior.
A molecular biologist by the name of Sol Spiegelman performed a fascinating experiment that helped elucidate what the prime directive of a replicator is. He took a simple virus out of its environment, placed it in a test tube, and allowed it to replicate. Because it was taken out of the wild, and given ample resources, it didn’t need its complex shape to survive. Most of its genes became superfluous. The length of its RNA shrunk dramatically. Seventy-four generations of replication reduced the original strand from 4,500 nucleotides to only 218. Follow-up studies have shown that in a specialized laboratory environment with no need for complexity, viruses can decrease in length to merely 54 nucleotides (the minimum required for the binding of the replication enzyme).
These dwarf viruses do their jobs much more efficiently than we do. They can self-replicate in a tiny fraction of a second, whereas humans generally take over a decade. They have a few dozen nucleotides, whereas the human genome is around 3 billion nucleotides long. It was natural selection that built our genome up, just like it was natural selection that pared Spiegelman ‘s viral genome down.
Sol’s virus is so astonishing and bizarre that it has since been called “Spiegelman’s monster.” It has shown us that replicators are “driven” to find the most efficient way to reproduce, given their surroundings. They can embrace complexity when environmental demands are complex. But when demands disappear, natural selection cuts the frills and maximizes simplicity.
The Simplified Slime Animals
The same natural process whittled an ocean dwelling animal down to its nuts and bolts. Myxozoa is a group (subphylum) of aquatic animals. The name means “slime animal.” It contains the smallest animals ever known to have lived. Many have no mouth, gut, or nervous system. There are more than 2000 species of them. One myxozoan species is a contender for the smallest animal genome ever. They are now so simple that they exist as a single cell for much of their life cycle. For comparison, following fertilization, human exist as a single-celled zygote for around one day. At one point in time, they were much larger and more complex, appearing like modern jellyfish. However, they were maximized for simplicity after they became parasites.
Molecular clock studies show that myxozoans share a common ancestor with their closest living relatives, medusazoans (jellyfish with medusa-like stinging tentacles), over 650 million years ago. They even have the perfunctory jellyfish stinging structure called a nematocyst. However, they don’t use it to sting. They use it to attach to the host they parasitize. It’s one of the few physical features it retained as it regressed. It is common for parasitic animals to lose many of the features of an autonomous animal. Because they are piggybacking off someone else, they can afford to drop features that their hosts can supply them with. These animals even shed their entire nervous system. They lost so much complexity that they barely count as animals anymore.
The trend toward simplicity seen in Spiegelman’s monster and the myxozoans is sometimes known as regressive evolution. It happens when animals seem to regress to a more primitive form. In Chapter 2, we saw this with the cavefish blinded by natural selection. As we continue, we will see more examples of regressive evolution.
A Quick Crash Course in Genetics
Cells are essentially protein robots. Proteins are dead structures that make life possible. There are 21 amino acids that form the alphabet of proteins. In this analogy, you can think of each amino acid as a different letter. A few dozen amino acids strung together to create a long linear molecule forms a protein. You can think of a protein as a word composed of amino acid letters. Proteins interact and perform work often in sequences or cycles, called cellular pathways. In our analogy a cellular pathway is equivalent to a sentence. It’s necessary to know about 8000 words in a human language to speak it well. In the human protein language, there are around 20,000 words. In English the average word has five letters, whereas proteins average around 375 amino acids. The protein for insulin contains only 40 amino acids whereas the longest protein in humans Titin I has over 28,000. One percent of your DNA is made up of genes. Each gene is a blueprint for how to sequence amino acids to create a specific protein. Your functional genes are the dictionary for your body. And the rest of your DNA is not useless, but contains information about which proteins need to be built, when, how many and how they interact, this is like a book of grammar. The cell speaks the language. The 21 different amino acids each have different electromagnetic charges. When the amino acids are chained together, these charges cause them to fold in on them selves. This changes them from a one-dimensional string, two or three dimensional structure. Their specific shape determines their function. Because it determines how they interlock with an interact with other proteins and cellular constituents. They can snap together, change, each other’s charge and properties, dismantle each other, convey information, and form complex micro machines. Cellular pathways are cascades of interactions between proteins that can have dozens to hundreds of steps. Your cells are bags of proteins and the grammar that determines how they interact is chemistry. Cells are mindless automatons, but working together have emergent properties and they form organs which form the organism. The cells or speakers speak to each other and create bio molecular conversations.
DNA is a chain of nucleotides bases. The nucleotides are A, C, G, and T (adenine, cytosine, guanine, and thymine). They are chained together to create a long, linear molecule (a polymer). There are 23 individual chromosomes, each with a different set of genes. You inherit two copies of each chromosome, one from each parent. Thus, DNA is partitioned into 46 chromosomes consisting of 23 pairs. Both copies of the 53rd gene on your 7th chromosomes, for example, code for the same protein, but it is likely that you inherited a slightly different copy from each parent. So, because you have two pairs of each chromosome, you have two copies for the blueprint of every protein. Sometimes they represent different strategies. They can even contradict each other. Some are dominant, some are recessive, but they usually blend together and play nicely.
British ethologist Pat Bateson used the analogy of cooking. He said that the raw ingredients and their measurement are equivalent to genetics and that the preparation and cooking represents the biological, environmental, social, and psychological influences during development.
Your entire DNA genome is replicated each time a cell divides. The DNA is “transcribed” into a new copy which is placed inside the new cell. This happens when you need to grow a new cell such as when you develop a fresh layer of skin cells, intestinal cells, or new brain cells. This type of cell division, known as mitosis, copies all 46 chromosomes. However, when our bodies create sperm and eggs that type of cell division, known as meiosis, only 23.
The DNA is used by the cell to build the proteins it needs. Generally, each gene corresponds to a single protein, each with a different function. When a specific protein is needed the cell transcribes the gene for that protein from DNA to RNA. From there the RNA travels outside the cell nucleus and is “translated” into protein by cellular machines called ribosomes. The ribosome travels along the RNA sequence and uses it as a recipe for building the protein corresponding to that gene. This recipe calls for a series of amino acids to be strung together into a protein which is another long, linear molecule (polymer). The ribosome grabs free-floating amino acids from all around it. These amino acids are available there because you ate them earlier in the form of protein. Your digestive tract broke down those proteins into their constituent amino acids, and now a cell is putting them back together in a different order to create a new protein. The central dogma of molecular biology states that information flows from DNA to RNA to protein.
So, when someone brags about having “good genes” they are really bragging about the shape of their proteins. The protein’s shape determines its behavior inside (and outside) the cell. A mutation in a gene will produce a differently shaped protein that will interact with the cellular environment a bit differently and of course this can be advantageous or detrimental. Evolution has been making miniscule modifications to the shape of our proteins for over three billion years. Even slight deviations in the shape of a protein can cause large changes in function.
Because genes are retrieved and translated into protein when they are needed, they are the means by which creatures can be flexible. Genes are actively responding to the environment every moment of our lives. They do direct the general construction of the body in the womb. But even in utero, they are constantly dismantling what they have built and rebuilding upon it. Genes preprogram our bodies, but even after we stop growing, they are still active. Environmental cues are constantly commanding the expression of genes that otherwise would remain silent (or silencing genes that would otherwise continue to be expressed).
The DNA in just one of your cells is composed of 3.2 billion base pairs. This means that writing down their full sequence would fill 800 copies of the Bible. Remember when I said it was a long molecule? The DNA in just one cell would stretch to about 6 feet long. The DNA from all 37 trillion cells in your body would stretch across the solar system and back again.
The human genome was first mapped around the year 2000. It was sequenced and cataloged nucleotide for nucleotide. It is not exactly clear how many genes humans have but it seems to be around 20,000 protein coding genes.
This process of exchanging bits of chromosome is known as crossing over. Point mutation a small singular error. Inversion, a whole sequence is inverted or misplaced.
“Predator-induced phenotypic plasticity describes the ability of prey to respond to an increased predation risk by developing adaptive phenotypes. Upon the perception of chemical predator cues, the freshwater crustacean Daphnia longicephala develops defensive crests against its predator Notonecta spec. (Heteroptera). Chemical predator perception initiates a cascade of biological reactions that leads to the development of these morphological features. Neuronal signaling is a central component in this series, however how the nervous system perceives and integrates environmental signals is not well understood. As neuronal activity is often accompanied by functional and structural plasticity of the nervous system, we hypothesized that predator perception is associated with structural and functional changes of nervous tissues. We observe structural plasticity as a volume increase of the central brain, which is independent of the total number of brain cells. In addition, we find functional plasticity in form of an increased number of inhibitory post-synaptic sites during the initial stage of defense development. Our results indicate a structural rewiring of nerve-cell connections upon predator perception and provide important insights into how the nervous system of prey species interprets predator cues and develops cost-benefit optimized defenses.” Graeve A, Ioannidou I, Reinhard J, Görl DM, Faissner A, Weiss LC. Brain volume increase and neuronal plasticity underly predator-induced morphological defense expression in Daphnia longicephala. Sci Rep. 2021 Jun 15;11(1):12612.
Introns are spliced out between transcription and translation so that only the exons, the working parts of the gene are used for protein synthesis. But exons can be spliced out too leading to different variants on the gene product. In fact, many genes have shown that they can be spliced many different ways, leading to more genes than we were led to believe we had from the DNA sequencing method.
The virus that causes AIDS is a retrovirus. Retroviruses find a way into your cells and incorporate their own DNA into your DNA within the chromosomes within the nucleus of some of your cells. They do this so that human cellular machinery will take over and replicate them and they can be safe and stay dormant for a while. With AIDS this happens in blood cells but not in sperm or egg cells, so the viral genes cannot be passed to offspring. Retroviruses have incorporated their DNA into ours in the past though. This is known because the human genome contains many different copies of complete retroviral genomes, recipes for making more viruses. These are called HERVs (human endogenous retroviruses), and they sit among our own genes as parasitic intruders. Every time one of our cells divide, we replicate their junk DNA. Happily, their DNA has been shut down by a process called methylation. Our DNA is a graveyard for ancient, inactivated retroviruses.
Some of the most intriguing discoveries are probably still ahead, but many of those age-old questions that were begging us to answer them have partial answers now. We are moving out of the age of discovery and into the age of technological mastery.
Since some parts of DNA mutate at a relatively regular pace, they act like a “molecular clock.”
There are thousands of genes (single nucleotide polymorphisms that make a contribution to determining intelligence. Recent studies have shown that they are over 1000 SNPs associated with high intelligence. This was discovered by genome wide association study (GWAS) that performed a statistical analysis of 1.1 million genomes. The statistical findings have been used to create polygenic scores that allow IQ to be predicted from DNA, even before birth.
Transcription factors are proteins, coded for by genes, that attach themselves to regions of DNA called promotors. Promotors can be either upstream or downstream of the gene itself and many genes have a few different promoters each of which has an affinity for a different transcription factor. Once the transcription factor binds to the promoter it will influence the expression of the gene, either increasing or decreasing its expression. Transcription factors do this by either promoting or blocking the recruitment of RNA polymerase (the enzyme that performs the transcription of DNA to RNA, the first step in building a protein). They work additively and many genes will not be affected until several of their promoters have received transcription factors. Thus, many genes work to turn other genes on and off. DNA promoters work in the fourth dimension, through time. Allowing more dynamics to genetics. Most differences between closely related species come from the duration and timing of protein expression, not all from the physical differences between the proteins as might be expected. Much of the difference between the chimp and human brains is thought to stem from extended expression of nerve cell growth factors. Our neurons look like their neurons, it is the number and extent of growth that is different.
Darwin’s Legacy
The intellectual heritage passed down to us from Charles Darwin, although static in its foundations, continues to be a dynamic force for academic and scientific exploration. Darwin (1809-1882) was a Victorian gentleman educated as a minister who famously pursued an occupation as a self-educated naturalist. His theories have been elaborated on generously and have yet to be modified significantly, even though it has been nearly 150 years since his first book, On the Origin of Species, was published. This book and subsequent works by Darwin have provided the platform for several new fields of biological science.
Like any theorist in the sciences, Darwin was forced to make dozens of explicit and implicit suppositions while writing. Time has revealed that most of the assumptions that his theories relied on were valid. Conclusions that he reached, primarily through thought-experiment and inductive logic, have caused revolutions in scientific and philosophical thought, permitted humanity to find its place in nature, and both shaken and shaped our deepest religious and philosophical convictions. Although Darwin achieved success in his lifetime, there were still some questions he could never answer and some findings he could never explain. The continued research of scientists, paired with advancements in technology, has brought much of what Darwin saw as the “unexplained” to light.
Darwin was one of the first educated natural historians to see the world with his own eyes. His trip around the Earth on the H.M.S. Beagle was truly formative for him and gave him a cosmopolitan perspective on biology that few scientists of his time had. A close friend and mentor advised that he spend his idle time during the voyage reading and recommended two books. Darwin read them on the boat and later spoke about their influence on him.
The first book was Charles Lyell’s “Principles of Geology.” This opus suggested that the Earth is slowly but constantly changing and that the geological changes proceeded no faster or slower in the past than they do in modern times. This idea that geological changes happen too slowly to appreciate in a year or even a lifetime resonated with Darwin. Second, Thomas Malthus’ “Essay on the Principles of Population” and its arguments related to population surpluses, limited resources, and the competition to survive similarly affected Darwin. Malthus’ essay was primarily concerned with economics. There wasn’t a sentence about biology, but Darwin derived his first postulate of natural selection from its wisdom. This underscores the importance of interdisciplinary thought in his work, and not surprisingly, the interdisciplinary approach continues to be taken by present-day evolutionary biologists.
Several theorists proposed evolutionary theories before Darwin did. Individuals like Georges-Louis Buffon, Jean Baptiste Lamarck, and Charles’ grandfather, Erasmus Darwin, wrote about the interrelatedness of all living organisms. This work set precedence for the Darwinian revolution. The capacity for evolutionary change in animal populations is a concept that can be traced all the way back to Greek philosophy. However, we credit Darwin because he logically delineated how this change occurs in the natural world, a concept that proved elusive for all who came before him.
In the 19th Century, it was largely thought that “acquired” traits, characteristics brought about through use or disuse, could be heritable. Jean Baptiste Lamarck based his theory of evolution, which preceded Darwin’s, on this faulty premise. Although Darwin thought traits could be acquired, he didn’t see acquired traits as the source of variation that natural selection acted on. He felt it acted on variation in inheritance. He could not say where this variation stemmed from, however. Interestingly, Lamarckism was refuted and ridiculed in the 20th Century, but it has been, more or less, exhumed in the last few decades. Recent studies have proven that genetic traits can be acquired and passed on to offspring. This fascinating, new branch off of genetics is now called “phenotypic plasticity” and will be discussed much more in coming chapters.
Darwin understood that lowly organisms continue to persist because “natural selection, or the survival of the fittest, does not necessarily include progressive development; it only takes advantage of such variations that arise and are beneficial to each creature under its complex relations to life.” Here, he addressed what has become one of the most misunderstood facets of evolution. Many people learning about evolution tacitly assume that it is a “progressive” process. He foresaw this mistake and was very careful to address it.
Many scientists embraced Darwinism early on. However, it evoked strong protests from both scientific and ecclesiastical circles. For instance, Louis Agassiz, who enthusiastically countered Darwin, declared that individual animals fall into discrete groups without intermediary forms and that each group was unique since it was created by God independently. He based much of his argument on the idea that birds were an example of this fact, that many groups have clearly defined boundaries. Such boundaries separate them from other groups regarding skeletal structure, behavior, appearance, and position in the fossil record. Amazingly, just a few years later, in 1868, the fossil, Archaeopteryx, a perfect example of an intermediate between birds and reptiles, rendered Agassiz’s point moot.
Since its publication, hundreds of seemingly rational objections to Darwin’s Origins have been overturned by new fossil findings, genetic discoveries, and biology experiments supporting nearly everything Darwin had to say about natural history. Today his theory of natural selection, or as he called it early on, the “transmutation of species,” has been reconciled with many other fields of biology, including anthropology, cellular biology, ecology, genetics, microbiology, paleontology, and dozens of others. Darwinian evolution has spawned many subdisciplines that could have hardly existed without it: Darwinian medicine, evolutionary psychology, exobiology, molecular taxonomy, phylogeny, sociobiology, and systematics, just to name a few.
Darwinian evolution hasn’t always enjoyed such influence and success. It took a backseat to genetics in the early 20th Century. This was partly because so many advances were being made in genetics, as Gregor Mendel’s “laws of inheritance” were being rediscovered, and partly because Darwin could not join his ideas with what was then known about heritability. He couldn’t even explain where these variations in traits were coming from. Darwin and others of his time assumed that “particles of inheritance” were passed through sperm and eggs. However, it took the first half of the 1900s for scientists to understand evolution in the language and phenomena of genetics and vice versa. This detailed reconciliation between the two disciplines, which happened decades after Darwin’s death, came to be known as Neo-Darwinism.
Darwin correctly assumed that “particles of inheritance” could determine how an organism will develop, but he had no idea how they might accomplish this. Today we know that these particles that Darwin theorized about are contained in all cells and are passed from cell to cell every time a cellular division occurs. We now know the particles as D.N.A., Genes are recipes for proteins and are “used by the cell as a template to mass produce proteins which perform chemical functions, and guide development.” D.N.A. comprises small molecular subunits called nucleotides, made of a few dozen atoms. As of 2000, we know there are around 3 billion nucleotides and nearly 30,000 genes in the human genome.
At the time, DNA had not been discovered, and Darwin had no authority to turn to for an explanation of biological inheritance.
The confusion stemmed from the difference between discrete traits and continuous traits. Some heritable traits can be controlled by a single gene (a discrete trait), and others are controlled by the interaction of multiple genes (a continuous trait). Natural selection generally acts on continuous traits, yet Mendel’s laws had not been extended to explain such traits. These “polygenic” traits were much more complicated, and so Darwin was not truly vindicated until the 1920s when mathematicians R.A. Fisher, J.B.S. Haldane, and Sewall Wright were able to show that continuous traits, the kind that selection acts on, are truly heritable. Their success led to a modern synthesis that combined Mendel’s laws of inheritance along with Darwin’s natural selection and is now referred to as Neo-Darwinism.
Since the 1920s, the fundamental tenets of Neo-Darwinism have remained intact, but much has been contributed. Some of the most notable contributions came from Ernst Mayr, who helped explain how different groups of animals, all molded by natural selection, came to become separate species. He suggested that a subpopulation of animals could be separated genetically from an ancestral species by geographical isolation. Mayr reasoned that if a subpopulation was kept from interbreeding with the species that it came from, whether by a mountain range or a river or great distance, then over time that subpopulation would change in physical appearance and genetic makeup. When different populations of the same species are separated for an extended time, they can become reproductively incompatible. It is generally thought that both natural selection and speciation are responsible for the great diversity of life we see on our planet.
We have come a long way in describing the molecular basis of life, and we have even uncovered the evasive source of variation that Darwin’s theories once precariously stood upon. Before a cell can divide, it must copy its entire nucleotide sequence so that both “daughter” cells can carry the entire complement. During this copying process, mistakes are sometimes made, and these errors are the source of gene pool variation that Darwin must have spent many hours contemplating. About “1 mistake is made for every 10,000 nucleotides copied,” and this equates to (excluding the many mistakes which will be repaired) about 100 mutations per generation. These mutations create the variability in character that natural selection picks and chooses from to guide each species on different trajectories. Darwin reasoned that new types of heritable particles must somehow find their way into the gene pool. However, because the technology of his time was far less advanced than ours today, he could never have known that this was accomplished through mutations.
Examining Darwin’s writings, considering the answers he didn’t live to hear, and analyzing the discoveries in evolutionary science is a fascinating area for many historians and scientists today. Even now, evolution is a cause of discomfort and contention, mainly in the U.S. However, it is widely accepted by educated people worldwide and has helped us make sense of what we are, where we came from, and how we are interrelated with other animals.
Adaptive Neurodiveristy 