Level 8: Life — \(\text{M}\) years
Cells
Size: \(\text{pm}\)
Initial state: Proto-prokaryot cells
Production process: abiogenesis, evolution
Meta-stable equilibrium: Prokaryots, protists, fungi, plants, animals
Stable future: Animals (ctenophora, sea sponge, brachiopod, velvet worm, nautilus, jellyfish, horseshoe crab, coelacanths, elephant shark...), plants (gingko tree, horsetail plant...), plus many others.
Biosphere
Size: \(\text{MPc}\)
Initial state: habitable natural environment
Production process: population by life / biodiversity
Meta-stable equilibrium: dynamic ecosystems (forming a biosphere)
Stable future: dead or artificialized ecosystem (otherwise there’s always disturbance, random genetic mutation at the very least).
The principal concept of this new Era in our progression, and in particular of this stage, is Life. We have evoked biomolecules already, assembling into larger and larger biopolymers, and we know that they are on the verge of forming something else, something more: a qualitative leap over a cliff towards a new world.
Unfortunately, that cliff is also very hard to define. The problem was vexing already when we knew precious little about the life sciences; we have now accumulatd a staggering amount of biological knowledge but are no less stumped/
Of course, we can always use the serviceable folk definition which, in the vein of "you know it when you see it", simply states that a thing is alive if and only if it is a living cell or made of such cells. But that does not help us to navigate edge cases, like possible extra-terrestrial life, yet unknown past lifeforms or even our own creations.
More rigorous textbook definitions normally take a functional approach, citing capacities shared by living organisms: homeostasis, organisation, metabolism, adaptation, reactivity, growth & reproduction. That is better, but still lacking in conceptual elegance. It is unclear how this motley crew came to be associated in all organisms, and which one(s) may be a ground for the others. Most attempts at a better characterization fall in one of two categories: autopoietic and evolutionary definitions. They reflect the two main aspects of biological phenomenology - metabolism and evolution.
The picture of life based on metabolism, or more precisely autopoiesis (self-maintenance and reproduction), is borne from systems theory and more generally from physicists’ views on the topic (notably, Schrödinger’s), putting a spotlight on the thermodynamics of living beings. They are seen as far-from-equilibrium islands that use energy to locally reduce entropy, which implies a physical boundary, and, in Valera’s word, continuously regenerate and realize the network that produces them. This class of definitions can easily account for individual cellular and supra-cellular life-forms in the here and now, but they cast a wide net, and could struggle to exclude many candidates that don’t fit the "folk picture" (for instance, planet Earth).
The picture of life based on evolution, to the contrary, is historical and collective at its core. It espouses a geneticist’s bias that metabolism and autopoiesis are necessary by-products of selective dynamics applied to a family of replicating molecules: Darwinian evolution. A living system is thus one that can replicate with heritable variation, and be subject to natural selection.
Abiogenesis and the origin of cellular life
Both pictures of life are ultimately entangled, each one seeing itself as the causal ground for the other. Starting with the latest common ancestor of current life forms, the two viewpoints are pertinent and complementary. But before that fabled being, a self-sustaining, evolving system, must have arisen, somehow, from a primordial soup of biopolymers. For that abiogenesis the syncretic approach hits its limits.
Before we consider the difference in approaches, let’s mention the common starting point. Any protocell body is first and foremost characterized as a closed volume. That is actually a "cheap" feature from a chemical and complexity perspective. We have seen how lipid vesicles can spontaneously form thanks to the amphiphilic nature of fatty acid. Not only can lipids create closed spheres reminescent of cells, they can undergo division under gentle mechanical stress (like a wave), and also absorb specific molecules, depending on the chemical nature and geometry of the boundary, while rejecting others. Even before genetics or biochemistry come into play, we then have at least a close volume that concentrate biomolecules within its boundary, and spontaneously divides after reaching a certain size.
The next step brings us back to our dichotomy.
In the metabolism/autopoiesis picture, biochemistry comes first: we need enough biomolecules in a proto-cells to kickstart self-sustaining chemical cycles. Of course, all such reactions are endothermic; to actually "live" long enough, a proto-cell would have to find enough molecules to "feed" and extract the required energy in the same way organisms do, or benefit from specific environments, for instance natural proton gradients (acidic vs neutral discrepancy between the inside and exterior of the proto-cell) that provide it.
The replication apparatus would then have appeared over time, possibly using PNA (peptide-nucleic acid) as a rough, but robust, information carrier, before stumbling onto RNA.In the evolutionary picture, genetics come first, at least a simplified version of it in the form of an RNA world. RNA (ribonucleid acid) is relatively fragile, but incredibly versatile molecule. In living systems as we know them, DNA carries information, encodes a copy of it into RNA, which is then decoded by ribosomes to produce proteins. But RNA is able to play all roles: it can be a primary information carrier, albeit an imperfect one; like proteins it can also act as a catalyst for may biochemical reactions including crucially, the copying of other RNA strands.
Since ribosomes are built on an RNA core, and ATP, the universal energy currency, is an RNA derivative, it is quite a seductive idea to imagine an RNA-only world progressively evolving into the machinery we now know. The instability of RNA molecules is a concern, since it makes them more sensitive to parasitic sequences out-competing useful ones. In principle, this could be alleviated by the membrane’s border post role, making the proto-cell a petri dish of quickly evolving "healthy" RNA.
Prokaryotic cells
The earliest unambiguous fossils of cellular life are around 3.5 billion years old (about \(1\) billion years into the Solar Era). Proto-cells left no trace and those fossils already resemble modern cells, more precisely prokaryotes.
That term means "before the nucleus", and it describes the simpler of the two current cellular architectures:
A membrane that separates the interior from the outside world and controls the traffic.
The cytoplasm, a gel-like aqueous medium filling the cell.
The nucleoid, a region (not bounded by a membrane) where the cell’s information, carried by DNA, resides.
Ribosomes, the molecular machines that synthesize proteins by reading RNA code.
Various external appendages: flagella for motility, pili for attachment and exchange of genetic material...
Prokaryotes today still represent more than 90% of individual cells on earth, although they only make up less than 20% of the biomass due to their smaller size. Two of life’s three taxonomical domains contain only prokaryotes: archea and bacteria.
Metabolism
Every cell, prokaryotic or not, must accomplish two things to sustain itself:
Obtain energy to power its activities: that is a job for catabolism, which breaks down complex molecules into simpler ones
Process matter to build its structures: that is anabolism, the use of energy to synthetize complex molecules from precursors.
Together, the whole set of chemical reactions and cycles is called metabolism. Metabolism requires three inputs:
an energy source to power the process (remember that by building organic materials, the cell is decreasing entropy, which cannot happen in a vacuum). That energy source can be solar: cells who can harness light in this way are called phototrophs. Or it can be chemical (chemotrophs).
electron donors from reductants: compounds that can be easily oxidized (building organic materials is a fundamentally reductive process). Those can come from organic sources like glucose (organotrophs) or inorganic ones like ammonia (lithotrophs).
carbon sources: all life forms on earth are primarily made of water, but their dry weight is generally about half carbon. Most organic materials that need to be built under the metabolic process are largely carbon, which is then the most sought-after element by cells. Some can fixate it from atmospheric (autotrophs), others get it from organic sources (heterotrophs).
Prokaryotes cover all possible combinations in this taxonomy, but it’s not the case for pluricellular organisms, as we’ll see. Plants are almost all photolithoautotrophs: they get energy from light, carbon from and get reductants from minerals in the soil. Animals and fungi are all chemoorganoheterotrophs: they get their energy, their reductants and their carbon from food.
Let’s go more precisely over what is happening:
the energy source triggers the oxidation of the electron donors.
electrons are passed on to electron carriers.
this process catalyzes the phosphorylation of ADP (adenosine diphosphate) into ATP (adenosine triphosphate), life’s energy currency.
the catabolic part of the process is over when the electron carrier can be "re-generated", that is, pass on its electrons. How that is done depends on the catabolic model:
in aerobic respiration, the electron acceptor is , the oxygen molecule. It takes on extra electrons and makes up two molecules of water by interacting with the free protons that always existing in a water solution.
in anaerobic respiration, the electron acceptor is some other inorganic molecule.
in the absence of any electron acceptor, fermentation can pass on the electrons to an organic molecule from the cell.
not all electron carriers give up their electrons at the end of the catabolism stage. Some continue on. The transition between catabolism and anabolims is characterized by the transfer of both metabolic currencies: energy (via ATP) and reducing power (via electron carriers).
in the anabolic phase, ATP gets hydrolized back into ADP, freeing enough energy to enable the reduction of biomolecules and their assemblage into new, more complex structures.
It is important to note that every pathway in this process is catalyzed by enzymes, specialized proteins play no small role since they can accelerate reactions by factors of millions to billions.
The central dogma: information, replication, and division
The twin pillar of metabolism in cellular like is information. Every cell carries a set of instructions, its genome, encoded in the sequence of bases along its DNA, which specifies the complete repertoire of proteins that the cell can make, and therefore determines its structure and capacities.
The flow of genetic information is the same in all known cells and has been called the central dogma of genomics.
\[\text{DNA} \xrightarrow{\text{transcription}} \text{RNA} \xrightarrow{\text{translation}} \text{Protein}\]
A segment of DNA called gene is copied into a complementary strand of messenger RNA (mRNA) by the enzyme RNA polymerase.
The mRNA travels to the ribosome, where translation occurs: its sequence is read three bases at a time (each triplet is a codon), and for each codon, a specific transfer RNA (tRNA) delivers the corresponding amino acid.
The amino acids are joined one by one into a polypeptide chain, which then folds into a functional protein.
This code is universal across all life. The same 64 codons specify the same 20 amino acids (plus start and stop signals) in bacteria, archaea, protists, fungi, plants, and animals.
Now, we had mentioned before that the RNA world hypothesis pictured protocells where RNA would the information carrier. Should that be true, the process whereby DNA supplanted it is still unknown, but it is clear that DNA, with its characteristic double helix structure is much more robust.
Carrying information is not enough, it allso needs to be replicated. DNA replication starts with the double helix being unwound, and each strand serving as a template for the synthesis of a new complementary strand by the enzyme DNA polymerase. The immediate result is two identical copies of the original DNA molecule.
Or, should we say, "likely identical"... Mutations do occur: DNA polymerase makes about one error per billion base pairs copied, and additional mutations arise from UV radiation, reactive oxygen species, etc. Most mutations are neutral, some are harmful, and occasionally one confers a benefit. That is the raw material of evolution.
DNA replication enables the process of cell division in prokaryotes. The cell replicates its (usually single) DNA strand, the two copies migrate to opposite ends of the cell, and the cell pinches in two, producing two genetically identical daughter cells...
Viruses and prions
Before moving on from the earliest cellular life in our chronology, we must address bio-agents. By most definitions they are not alive, but play an important role in the story nevertheless.
A virus, in its simplest form, is a piece of DNA or RNA, wrapped in a protein coat called a capsid, and sometimes further enclosed in a lipid membrane; that is all. Outside a host cell, it is an inert chemical compound, no more alive than a grain of salt. But once it encounters a compatible cell, a virus can hijack its entire machinery to replicate itself thousands, even millions of times, often destroying the host in the process.
The origin of viruses is deeply uncertain. Although the virus-first scenario is part of the many (unprovable) hypotheses, it seems improbable that viruses could exist before cells since they don’t have any independent replication apparatus.
Whatever their origin, viruses have become a formidable evolutionary force. Although they are not alive, they are unescapable in the history of cellular life:
viruses can accidentally pick up genes from a host when replicating themselves, or conversely integrate some of theirs in the host’s genome, thus contributing to horizontal gene transfers between cell lineages (an estimated 8% of human genome is of viral origin).
their noxiousness makes them automatically an evolutionary force since organisms need to evolve to strengthen their immune systems.
the impact of viruses on bacterial life in particular is so significant that it can affect the earth on a geochemical level.
A step further still from life are prions. Not a cell, not a virus, not even a strand of nucleic acid, a prion is simply a misfolded protein. Its aberrant shape triggers a chain reaction whereby it converts neighbouring proteins into copies of itself. This RNA-free replication has disastrous consequence for the host.
Evolution
The emergence of cells is also immediately the beginning of biological evolution.
We have seen that any form of life features:
a store of information, coded in DNA — that is the genotype.
observable physcial features and behaviours, called the phenotype.
a way to reproduce that always involves the genotype’s replication.
The elements of phenotype that are directly grounded in genotype are called inheritable traits. Biological evolution simply designates the variation in inheritable traits between generations.
In the case of prokaryotes, there are three main processes at play:
Mutation are permanent alterations of a cell’s genotype. They happen spontaneously during DNA replication, which is a near-perfect, but not perfect, process. They can also be triggered by mutagens in the natural environment. Only some mutations affect inheritable traits.
Gene flow is mostly a feature of prokaryotes. Unlike later organisms, they have a much greater ability to accept external DNA, which can be acquired (1) directly from the environment (freestanding DNA, for instance from a dead cell), (2) through direct cell-to-cell exchanges, or (3) from a virus.
Natural selection is not a physical or chemical process, but rather a logical consequence of these facts:
Mutations and gene flows ensure there will be great variations between individual genotypes, and thus phenotypes, within a population.
Prokaryotes’ high reproduction frequency ( 1 division per hour on average) ensures there will always be more individuals produced than can be sustained by the environment.
Distinct phenotypes have different survival expectations.
Therefore, we can expect certain inheritable traits to be selected by the evolutionary pressure, and passed on to the next generations.
Evolution quickly led to an extremely diverse range of prokaryote species.
Photosynthesis
The most momentous event known to us from the billion years of prokaryotic evolution follows the appearance of oxygenic photosynthesis. A new group of prokaryotes appeared, cyanobacteria, that could harness light energy absorbed by chlorophyll to produce glucose from \(\text{CO}_2\) and water, with oxygen (\(\text{O}_2\)) as a byproduct. For the first time, a metabolic process was releasing free oxygen into the environment, rather than using it.
Initially, this oxygen was absorbed in the oceans and by reduced minerals on land. But eventually, these sinks were saturated, and it began to accumulate in the atmosphere. This Great Oxidation Event around 2.4 billion years ago (2 billion years SE).
Not only were the consequences star for the still enormous population of anaerobic organisms, for whom oxygen is a poison: natural selection quickly made their numbers dwindle. The composition of the atmosphere gradually changed, influencing the earth’s climate and, crucially, creating an ozone (\(\text{O}_3\)) layer. Ozone absorbs UV radiation, shielding our planet’s landmass, which ultimately made land-based life possible
Eukaryotic cells
Around 2 billion years ago (about 2.5 billion years SE), a new type of cell appeared and with it a third domain of life (besides the prokaryotic bacteria and archea): the eukaryote. The name means "true nucleus", which is indeed its defining feature: a membrane-bound nucleus housing the cell’s DNA. But the differences with prokaryotes go far beyond that.
Eukaryotic cells are 10 to 100 times larger in linear dimensions, and they are packed with organelles: specialized, membrane-bound compartments that perform specific functions. The major organelles include:
The nucleus, as mentioned, which contains the chromosomes (linear DNA molecules, wrapped around histone proteins), separated from the cytoplasm by a double membrane.
The endoplasmic reticulum (ER), an extensive network of membrane-enclosed channels and sacs. The rough ER is studded with ribosomes and is the site of protein synthesis. The smooth ER synthesizes lipids and is involved in detoxification.
The Golgi apparatus, a stack of flattened membrane sacs that receives proteins from the ER, modifies them, and dispatches them to their respective destinations.
Lysosomes, vesicles filled with digestive enzymes that break down macromolecules.
Mitochondria, the cell’s metabolic centre, which carry out respiration or fermentation. They have their own small, circular DNA and their own ribosomes, and can replicate within the cell.
In photosynthetic cells, mitochondria have a counterpart in chloroplasts, which carry out photosynthesis, and also have their own genes and replication apparatus.
The cytoskeleton, a dynamic network of protein filaments that gives the cell its shape and enables movement.
Vacuoles, large sacs used for storage and waste disposal.
The origin of the eukaryotic cell is still a puzzle, but the prevailing theory, endosymbiosis, proposes that key eukaryotic organelles originated as independent prokaryotic cells that were engulfed by a host, and entered into a permanent symbiotic relationship.
Eukaryotes still represent a minority of living individuals today. Their numbers are roughly \(10^{28}\) on earth, vs an estimated \(10^{30}\) prokaryotes. Of course each eukaryote is on average around a thousand time heavier, so those cells dominate in terms of biomass (\(77\text{Gt C}\) in prokaryotes vs \(480\text{Gt C}\) in eukaryotes).
Eukaryotic reproduction: mitosis and meiosis
Eukaryotes’ DNA is organized differently from brethren’s, as we have alluded to. Prokaryotic DNA is a single circular strand, which we could see as a single chromosome. Eukaryotes’ nuclei typically have multiple chromosomes, sometimes hundreds, and their DNA strands are wrapped around a specific shape.
For that reason and others linked to their internal structure, eurkaryotes have developed their specific process of division, mitosis.
Mitosis is preceded by the DNA replication and several checks and controls, before unfolding in six phases:
Prophase: Chromosomes condense and become visible; the mitotic spindle forms.
Prometaphase: The nuclear membrane breaks down, and microtubules attach to chromosomes.
Metaphase: Chromosomes align at the cell’s center.
Anaphase: Sister chromatids (replicas) are separated and pulled to opposite poles.
Telophase: New nuclear envelopes form around the two sets of chromosomes.
Cytokinesis: The cytoplasm divides, creating two distinct daughter cells.
Despite its more complex structure and its organelles, a eukaryote can then achieve through mitosis the same goal as a prokaryote: to create a perfect (in principle) genetic replica of itself.
However, 1.5 billion years ago, eukaryotes would also develop a second form of cell division, opening the way for sexual reproduction. The eukaryotes’ nucleus is indeed a blessing and curse. It is a much better cocoon to preserve the genotype’s integrity, and mitosis ensures better replication quality. However what is positive in the short term turns negative over evolutionary timeframes. Because eukaryotic genes mutate less and gene flow is reduced to a bare minimum, individual variation rates are much lower, slowing down biological evolution and making eukaryotes a "sitting duck" for rival bacteria and archea in a changing environment.
Sexual reproduction makes up for these flaws, and then some. The key fact is that almost all sexual organisms are diploids, meaning that their chromosomes come in pairs. The few that are not diploids in the first place can become it before the reproduction process starts.
Here are the key steps for a diploid cell with \(n\) chromosome pairs:
Like in mitosis, the whole DNA is fully replicated. We still have \(n\) pairs of chromosomes, but each is made of two sister chromatids.
The chromosomes from each pair undergo genetic recombination, shuffling their genes in chromosomal crossovers. This happens between non-sister chromatids, so that each of the \(4\) chromatids from each chromosome pair ends up being unique
During meiosis I, chromosome pairs are separated and pulled to opposite poles of the cell before a division occurs. This results in two haploid cells (with no chromosome pairing, but still two sister chromatids per chromosome).
During meiosis II, each of these haploid cells undergoes another division, mechanically similar to mitosis, where the sister chromatids are separated. This results in a total of \(4\) haploid cells with no sister chromatids and \(n\) regular chromosomes each, called gametes. Each gamete is genetically distinct and carry a unique combination of the parent’s genotype.
Gametes alone are an evolutionary dead-end. Nothing follows without the last step: fertilization — the fusion of two gametes from different individuals to produce a diploid offspring.
Sex comes with obvious drawbacks: systematically diluting the genome prevents selected phenotypes to "stick" to the same extent. It also requires to find mates (some organisms can reproduce with themselves (self-fertilization) as a strategy, but not a durable one since it ony leads to poor genetic variation). The quest for compatible mates can be a costly and limiting endeavour in many environments.
But the benefits from genetic recombination in selecting fit individuals and eliminating harmful mutations still largely outweigh these issues. That is clearly evidenced by a census of the current biosphere: 99.9% of eukaryotes today reproduce sexually.
Genes, chromosomes, and heredity
It is worth revisiting the basic concepts of genetics and heredity after the emergence of sexual reproduction. A sexual organisms carries two copies of each chromosome, one from each parental gamete. The two copies are not identical —they carry the same genes in the same order, but may carry different alleles (versions) of those genes. An organism is homozygous at a given gene if both alleles are the same, and heterozygous if they differ.
The relationship between alleles and observable traits is the domain of genetics, a field that began long before the molecular nature of genes was understood: what was called genes is now identified with a specific area from the genome. The key discovery of early genetics is that one version of the same allele may be dominant (it is expressed in the phenotype even if only one copy is present) while another may be recessive (its effect is masked unless present in both chromosomes).
Reality, of course, is more complicated than this simplified picture:
Most traits are influenced by many genes simultaneously (polygenic inheritance).
Many genes influence more than one trait (pleiotropy).
Alleles can show incomplete dominance (the heterozygote is intermediate).
Alleles can show codominance (both are expressed simultaneously).
Gene expression is modulated by the environment.
There are interactions between genes (epistasis).
Acquired epigenetic modifications can influence gene expression without altering DNA.
Nonetheless, traditional genetics in which genes are discrete units, transmitted according to probabilistic rules, remains the main bridge between molecular biology and evolutionary theory.
The leap to multicellularity
Especially after sexual reproduction took over, the eukaryotic world, though still single-celled, became a staggeringly varied grab-bag of very diverse organisms, which today we call protists. Marine phytoplanktons, grazer zooplanktons, amoebae, flagellates, parasites, and the likes have deeply influenced their ecosystems and made their mark on the biosphere.
Although to this day, most eukaryotes on earth are still single-celled organisms in their own rights (around 75% of them), they have been remarkable in their capacity to assemble and form multi-cellular organisms. At least, it seems important to the multi-cellular organism who is writing these lines...
It is a fine line to define true multicellularity, that is at the hear of defining organisms. There is evidence of cell colonies, or of 8- or 16-cells algae going back billions of years, perhaps even before eukaryotes appeared. Individual cells can evolve to emit and detect signals from their brethren, deduce the cell density in certain areas, and coalesce in groups. But the key missing development in those structures is cell differentiation. Cells from a colony are still functionally identical to each other, and fully able to survive on their own, if they need to revert to single-cell status.
True multicellular bodies develop specialized cells that can only thrive in the organism that engendered them. How can that come about, if genotype is the making of phenotype? The answer lies in differential gene expression. All cells in a multicellular organism carry the same genome, but can activate different subsets of genes, producing different proteins and therefore adopting different structures and functions. This is controlled by a complex interplay of transcription factors, signaling molecules and epigenetic modifications.
Yet, all multicellular organisms still develop from a single cell a fertilized egg, in the case of sexually reproducing species, or a spore, or a cell from the parent body. Development proceeds through repeated rounds of cell division (mitosis), accompanied by progressive specialization.
The oldest, unambiguous multicellular fossils (not cell colonies nor undifferentiated algae) appear around 1 billion years ago.
The sex binary
Note that I have talked of sexual reproduction, but have not used the words male or female. Of course, similar singled-celled organisms produce gametes with the same characteristics. This is also true of all the early multicellular organisms which we call isogamic, a minority today.
Indeed, a significant example of cellular differentiation has been that of gametes. The quasi-universal distinction is a binary between smaller, bare-bones, mobile and abundant male gametes, and heavier, nutrient-rich, static and rare female gametes. The mechanism that led to this binary is not fully clear — it appears that isogamy may be an unstable equilibrium under evolutionary pressure and that any discrepancy may converge to the current system.
This differentiation at the level of gametes does not imply sex-driven differences between organisms. Most multicellular beings today are hermaphrodites (for instance, most plants): they can produces both types of gametes. Of course, many variants can exist in more complex beings: the male and female organs can be in close proximity (in the same flower, for plants), or in different parts of the organism; there can be varying degrees of self-fertilization depending on various factors, etc.
The most familiar situation to us human beings, that is the wont of most animal species, is that individual organisms can only produce one type of gamete. Sexual reproduction then always requires mating between two individuals, another form of pressure with a long evolutionary tail, which ultimately lead to sex differences in the phenotype (ranging from mild to extreme depending on the species).
It is important to note that the a sex binary in individual organisms is a priori an extreme drawback: only the female half of a population can produce children. With a compounding effect over generations, it seems that isogamic or hermaphrodite species would be at an immense evolutionary advantage. And yet, species like ours, if not prevalent in the biosphere, have grown to dominate the animal world, so the benefits from this specialization must be material.
The three kingdoms of multicellular life
With the exception of a few protist lineages (some algae, slime molds), all complex multicellular organisms on earth belong to one of three great kingdoms: Fungi, Animalia, and Plantae:
Fungi are heterotrophs that feed by absorption: they secrete digestive enzymes into their surroundings and absorb the resulting small molecules, acting as decomposers.
Animals (metazoa) are heterotrophs that feed by ingestion: they take in food and digest it internally. Their cells lack walls, giving them flexibility of shape and the capacity for movement.
Plants are autotrophs that feed by photosynthesis. Their cells have rigid walls made of cellulose and contain chloroplasts.
The three Kingdoms represent three different strategies to navigate the problem of obtaining energy and carbon, which has shaped these organisms’ anatomy and ecology.
Development: from single cell to organism
Regardless of kingdom, every organism begins life as a single cell. In sexually reproducing species (the vast majority), the cell that is the result of fertilizing gametes is a zygote. In asexual ones, it may be a spore, a bud, or a fragment of the parent body.
The subsequent development into a fully-formed organisms varies a lot of course, but still proceeds through several universal stages.
The first is cleavage: rapid rounds of cell division (mitosis) that partition the zygote into many smaller cells without overall growth.
The cells then begin to rearrange and specialize, in a phase named morphogenesis. Cells move, fold, and sort themselves into layers and structures.
As development proceeds, cells become undergo determination, then full differentiation, when they adopt their final structure and function.
Fungi and plants follow the same development logic. Their cells are locked in place by their rigid walls, so they cannot migrate. Morphogenesis relies entirely on the direction and rate of cell division and on differential cell expansion. Another key points is that the growth process is never meant to stop. Plants, for instance, always maintains regions of permanently undifferentiated cells called meristems, located at the tips of roots and shoots, and growth continue from there following the same pattern. In practice, growth of course stops due to death or unfavorable environmental factors, but it is not genetically programmed to.
In animals, the key phase is gastrulation, the single-layered blastula (a ball of undifferentiated cells) sees cells starting to migrate and differentiate.
In the simplest animals, sponges (porifera) cell roles stay highly plastic and no clear layers emerge. For more complex animals, the blastula folds inward to produce germ layers.
Some animals, like cnidarians (jellyfish, anemones, coral...) follow a radial body plan and have two germ layers: the ectoderm (outer) and the endoderm (inner).
Other animals follow a bilateral body plan and have a third layer, the mesoderm (middle); the bilateral symmetry means that they have a front and back, dorsal and ventral sides, which are preludes to cephalization (the concentration of sensory organs to the front) and motility.
Germ layers constitute the starting material from which all tissues and organs later develop. Lastly, in contrast with plants and fungi, animals reach a genetically and nutritionally determined adult size and cease to grow.
Tissues
As cells differentiate, a new layer of organization emerges: tissues, groups of similar, neighbouring cells that work together to perform a specific function.
Fungal tissues
Fungal cells assemble into tubular shapes named hypae, then develop regions with different density, shapes and functions (like the characteristic stern, gills or cap of mushrooms). These structures could be considered as distinct tissues but in any case, are not nearly as differentiated as tissues observed in the other kingdoms.
Plant tissues
In plants, the main tissue systems are:
Dermal tissue that covers the plant’s outer surface (its "skin"), ranging from a thin epidermis for young shoots to a thick periderm for older, wooden plants.
Vascular tissue provides long-distance transport of water, nutrients, minerals...
Ground tissue fills the space between dermal and vascular tissues and performs a number of functions, including photosynthesis, starch storing or repairs.
Animal tissues
We have seen before that sponges did not develop germ layers — as a result they do not have proper tissues.
Other animal groups have distinct tissues. In advanced animals, they are incredibly diverse, but can still be classified in four types:
Epithelial tissue covers body surfaces and lines internal cavities. It forms barriers (skin, gut lining, blood vessel walls), controls what passes across those barriers, and secretes substances (mucus, hormones, enzymes). Its cells are tightly packed, with minimal extracellular material.
Muscle tissue is specialized for contraction.
Nervous tissue is specialized for the transmission of electrical signals. It consists of neurons and supporting glial cells.
Connective tissue supports, connects, and separates other tissues. It is characterized by abundant extracellular matrix. In advanced animals it forms a diverse bunch: subcutaneous and adipose tissue, tendons, ligaments, cartilage, bone, blood... Its not present in animals with a radial body type like jellyfish, but exists in most bilaterians.
Organs
Tissues then combine into organs: structures composed of multiple tissue types that work together and perform a specific function.
Fungi do not have organs in the conventional sense. As we’ve seen, there are distinct structures at the organism’s levels but tissues are hardly differentiated and there is no clear delineation that could be said to define organs.
Plants generally, however, have organs, which are all composed of the three tissue types. Vegetative organs include the root (anchoring and absorption), the stem (support and transport), and the leaf (photosynthesis and gas exchange). Reproductive organs include flowers (pollination and fertilization), fruits (maturation and dispersal), and seeds (embryo protection and nourishment).
Organs are much more diverse in animals, and more easily listed in the context of organ systems.
Organ systems
In complex organisms, organs get more specialized and can work in concert with each other to fulfil a broad physiological function, in which case they belong to a same organ system. Fungi and plans do not really fit that bill, but animals do.
The principal organ systems (whose presence or absence vary according to species, of course) are:
The digestive system (mouth, esophagus, stomach, intestines, liver, pancreas): ingestion, breakdown and absorption of food.
The circulatory system (heart, blood vessels, blood): transport of gases, nutrients, wastes, and hormones.
The respiratory system (lungs or gills, airways): gas exchange with the environment.
The nervous system (brain, spinal cord, peripheral nerves, sensory organs): rapid signaling, sensory processing, coordination.
The endocrine system (pituitary, thyroid, adrenals, gonads, pancreatic islets): hormonal regulation.
The musculoskeletal system (bones or cartilage, skeletal muscles, tendons, ligaments): support and movement.
The immune system (thymus, spleen, lymph nodes, white blood cells): defense against pathogens.
The excretory system (kidneys, bladder, ureters, urethra): waste removal and homeostasis.
The reproductive system (gonads, uterus, etc.): production of gametes and, in many species, gestation of offspring.
The integumentary system (skin, hair, feathers, scales, glands): protection, thermoregulation, sensation.
Nervous systems
At this stage, we shall turn to the most consequential innovation in the history of animal development: the emergence of nervous systems, and with them, the capacity for behavior, perception, learning, and the emergence of mind.
We have seen that the simplest animals belonged to the loose, composite groups we call sponges. They do not have a nervous system of any kind. Sponges are mostly passive, but they still share with other animals the capacity to move — they can contract their pores in response to physical stimulation, or to expel debris. However, these responses are mediated by individual cells acting semi-independently, communicating through chemical signals that diffuse sluggishly from cell to cell. An individual sponge can then react to the world, like inanimate objects, cells and many plants do. However it cannot sense the world, perceive it or learn anything from these interactions.
We have seen before that animals other than sponges were roughly divided according to their body plans: radial for the cnidarians, bilateral for the bilaterians. The first neurons appeared in their common ancestors, 600 to 700 million years ago. Neurons are specialized cells geared for the rapid transmission of electrical signals. To achieve that, their defining features are:
an excitable membrane, with the ability to generate a short-lived, propagating, electrical potential.
synapses: specialized junctions at which the resulting electrical signal can be converted to a chemical one, in the form of biomolecules called neurotransmitters, or conversely, where neurotransmitters from other neurons can be detected, and their energy harnessed to build an electrical potential.
An individual neuron is then a node in an electrochemical relay. The obvious benefit is the speed of transmission, which is incomparably faster than with pure chemical signaling.
The cnidarians’ nerve net
In cnidarians jellyfish, sea anemones, corals.. neurons are arranged in a diffuse nerve net: a mesh of interconnected neurons that spreads throughout the body, with no central processing point. This allows simple coordinated behavior, like a jellyfish can contract its bell rhythmically to swim. Signals spread outward from the point of stimulation in all directions; the response varies based on in signal intensity, but is essentially the same regardless of the precise nature of the stimulus: contract, retract, withdraw.
Worms and the birth of centralization
The transition to bilateral body plans brought a fundamental reorganization of the nervous system. An animal that moves in a consistent direction, that has a front and a back, benefits from concentrating its sensory apparatus at the front end, the part that encounters new environments first. This is called cephalization, and is accompanied by centralization: the gathering of neurons into dense clusters and longitudinal cables, rather than a diffuse net.
The simplest bilaterians, flatworms, display the simplest outline of that strategy. A pair of neuron clusters at its head end, the cerebral ganglia function as a primitive brain. Close by, they can receive signals from the worm’s proto-sensory apparatus (simplistic light and chemical detection). Further down the body, two nerve cords can distribute signals through the body: as they progress longitudinally from the head to the tail end, they can also propagate transversally through nervous commissures (think of the rungs of a ladder).
A bit higher on the complexity scale, we find annelid worms, segmented bodies like earthworms or leeches. They reproduce the same nervous organization as their flat brethren, but in a modular, decentralized fashion. Each body segment has its own segmental ganglion and ladder-like structure, while the head end still has cerebral ganglia acting as master coordinators. That structure — central command with semi-autonomous local units — proved incredibly scalable and is the basis of all that followed.
The behavioral impact of centralized or modular nervous systems is immediately visible when one compares worms to jellyfish or anemones. Worms can learn how to navigate a maze and "remember" a favorable path. Some, who retreat and shrink when detecting a shadow, can habituate and stop responding if the shadow is shown repeated ly without consequences. Although simplistic ones, these are forms of learning that indicates clear behavioral patterns,
Arthropods: the rise of specialized senses
The next group we shall examine is the one that may have witness the original emergence of the brain: the arthropods.
The arthropods are by far the most successful and ubiquitous living beings in our biosphere by any measure. They include insects (the dominant group), arachnids (spiders), myriapods (centipedes and milipedes) and crustaceans (crabs, lobsters, shrimps, prawns...). Their body plan differs markedly from worms’, with its rigid exoskeleton and jointed appendages, as does their nervous system.
Arthropods’ ganglia have fused and specialized over time. Head-end pairs of ganglias have merged into a single, complex brain. Ganglias in key areas of the bodies have also fused, for example in the thoracic area, where they have specialized control centers for the legs and wings.
Combined with their sensory apparatus, featuring compound eyes and a diverse set of receptors, the arthropods’ comparatively tiny brains support a level of behavioral complexity that has seemed startingly advanced to humans who have studied they ways:
The waggle dance allows honeybees to inform nestmates of the distance and direction of a food source.
Jumping spiders stalk their prey with detour strategies that require mental model of the target’s path and of the surroundings.
Paper wasps can learn and recognize the individual faces of their nestmates.
Cephalopods: a parallel experiment in intelligence
Arthropods do not represent a uniquepeak of cognitive complexity in invertebrate animals. Another group has developed even more impressive abilities: the cephalopods (octopuses, squid, cuttlefish...), part of phylum Mollusca. And yet, the two groups have been treading entirely different evolutionary paths: their common ancestor is an early flatworm. That fact’s significance cannot be overstated: we may not know of any extraterrestrial life yet, but we have proof that the biological basis for complex cognition has evolved more than once, suggesting it can be a common byproduct of the right evolutionary pressures rather than a one-time fluke.
Cephalopods can routinely have several hundred million neurons, more than any other inverterbrate individual, and than most vertebrate. They do have central brains, like arthropods, but two-thirds of their neurons are distributed through the arms, each of which contains a semi-autonomous ganglionic network, enabling complex movements (reaching, grasping, exploring) independently from the central brain. An octopus can almost be said to have nine brains.
The implications in terms of behavior are remarkable. Cephalopods learn rapidly: they can solve mazes, use simple tools (coconut shells as shelters), and distinguish between individual handlers (treating a gentle feeder and a rough one differently). They are capable of observational learning: an untrained octopus that watches a trained one perform a task can subsequently perform it without trial-and-error. Their mastery of visual communication, by altering the color or texture of their own skin, is also put to good use for camouflage, deceiving or courting.
Chordates and the vertebrate body plan
Chordata is the last major animal phylum to be evoked here, and the one this author, as well as, presumably, any reader, belong to.
Chordates are defined by four features:
a notochord (flexible rod providing axial support)
a dorsal hollow nerve cord (spinal cord and brain)
pharyngeal slits (openings in the throat region, later gills, ears or pharynx)
a tail.
The original chordates and their least-changed descendants are humble, soft, sea creatures. We would not be talking of chordates though, if it was not for the evolution of the subphylum Vertebrata.
Vertebrates developed a special notochord called the vertebral column: a segmented series of bones or cartilage surrounding and protecting the spinal cord. This structural innovation enabled a dramatic increase in body size, activity level, and ecological reach. The most notable vertebrate classes, in order of evolutionary appearance, are:
Agnatha (jawless fish): lampreys and hagfish.
Chondrichthyes (cartilaginous fish): sharks, rays, skates...
Osteichthyes (bony fish): the vast majority of fish species.
Amphibia: frogs, salamanders, caecilians, destined to be the first terrestrial vertebrates.
Reptilia: turtles, lizards, snakes, crocodilians.
Aves: birds (descended from theropod dinosaurs).
Mammalia: mammals.
We will now briefly present the main features of vertebrates’ anatomy and physiology.
Skeleton and musculature
The vertebrate endoskeleton, internal, made of bone or cartilage, contrasts with the arthropod exoskeleton. An endoskeleton does not need to be shed, grows with the animal, can support much greater masses, and provides internal attachment points for muscles. Vertebrate muscles, arranged in antagonistic pairs around a jointed skeleton, allow a range and precision of movement unmatched among animals of comparable size. The skull, a unique feature of vertebrates and a few other craniates, protects the brain.
Circulatory and respiratory systems
Vertebrates have a closed circulatory system: blood is confined within vessels (arteries, veins, capillaries) and pumped by a muscular heart. This is more efficient than open ones (in invertebrates, the blood bathes the organs directly in an open cavity), particularly for large, active bodies that demand rapid and targeted delivery of oxygen and nutrients.
The respiratory system evolved in tandem. Fish extract dissolved oxygen from water using gills: thin filaments through which blood and water flow in opposite directions. The transition to land required a different solution: lungs, internal sacs where air and blood are brought into close proximity across a moist membrane.
Thermoregulation
Most animals are ectotherms: their body temperature fluctuates with the environment. Within the vertebrate groups, endothermy arose: the capacity to maintain a stable, elevated temperature through metabolic heat. The cost is enormous (endotherms must eat roughly ten times more than an equivalently-sized ectotherm), but endothermy is transformative: muscles contract faster and more reliably at elevated temperatures, enzymatic reactions proceed at a more predictable rate, and the animal can remain active at night, during winter, in cold water, when ectotherms tend to be sluggish or immobile. Endothermy is supported by body insulation (feathers, fur or fat) and physiological feedback loops (sweating, shivering, panting,...).
The digestive and excretory systems
The vertebrate digestive system is a far cry from the simple gastric cavity of many a predecessor. It is a long tube in which food is processed in stages by specialized organs. The mouth initiates mechanical breakdown and, in mammals, chemical digestion with salivary enzymes. The stomach provides an acidic environment that denatures proteins and activates proteases. The small intestine is the primary site of chemical digestion and nutrient absorption, its inner surface vastly expanded by brush-like projections. The large intestine reabsorbs water and electrolytes and harbors dense communities of symbiotic bacteria that ferment fibers, and synthesize vitamins. The liver processes absorbed nutrients, detoxifies harmful substances, and produces; the pancreas supplies digestive enzymes and regulates blood sugar through insulin and glucagon . This assembly line allows vertebrates to extract maximum energy and and matter from an extraordinary diversity of diets.
The excretory system handles the metabolic waste thus generated. The kidney filters the blood, recovering useful molecules and water while excreting nitrogen-containing wastes (urea or uric acid) and excess salts. They also play a central role in homeostasis: regulating blood pressure, acidity, and the concentration of electrolytes. That is one of the vertebrates’ major ability: to create a controlled internal milieu in which the exquisitely sensitive biochemistry of neural and muscular activity can proceed reliably.
The immune system
Every single one of an organism’s cells is a potential meal for parasites, bacteria, fungi, and viruses.
Vertebrates have evolved a two-layer immune system. The innate immune system provides immediate, nonspecific defense: physical barriers (skin, mucous membranes), antimicrobial proteins, and phagocytic cells that engulf and destroy invaders. The adaptive immune system adds specificity and memory. It relies on lymphocytes: B cells, which produce antibodies (proteins that bind specifically to the molecular features of a particular pathogen), and T cells, which either kill infected host cells or coordinate the broader immune response. The adaptive immune system can generate antibodies against virtually any molecular structure, including ones it has never encountered, through a remarkable process of random gene rearrangement and clonal selection. Crucially, it also remembers past infections: upon re-encountering a pathogen, the response is faster and stronger, a feature called immunological memory.
The endocrine system
Alongside the nervous system, vertebrates possess a second body-wide coordination protocol: the endocrine system, which communicates via chemical messengers called hormones. Where the nervous system operates in milliseconds and targets specific cells, the endocrine system operates over minutes to months and affects broad populations of cells throughout the body. The two systems are deeply intertwined: the hypothalamus, a brain structure, controls the pituitary gland, the "master gland" of the endocrine system, which in turn regulates the thyroid (metabolism), the adrenals (stress response, salt balance), the gonads (reproduction), and growth processes.
The interplay between hormones and neural circuits means that an animal’s behavior is shaped not only by its immediate sensory input and past learning, but by its internal physiological state: hunger, fatigue, arousal, reproductive readiness, stress. This is a major mechanism through which evolution tunes behavior to circumstance.
The vertebrate brain
The primary coordination system in vertebrates remain their nervous system, the most complex in the animal kingdom. The architecture can be outlined as follows:
The central nervous system (CNS) includes
the brain
the spinal cord: carries sensory information up to the brain and motor commands down to the muscles, and also mediates rapid reflexes independently of the brain.
The peripheral nervous system (PNS): connects the CNS to the rest of the body.
Somatic division: voluntary movements (skeletal muscles).
Autonomic division: involuntary functions.
Sympathetic branch: mobilizes the body for action.
Parasympathetic branch: promotes "rest and digest" functions.
The interplay between the sympathetic and parasympathetic branches maintains the body in a state of dynamic equilibrium, constantly adjusting physiological parameters in response to the demands of the moment.
As to the brain, it develops from three embryonic swellings:
The hindbrain (rhombencephalon),which gives rise to the medulla oblongata (controlling vital functions: heartbeat, breathing, blood pressure) and the cerebellum (coordinating movement, balance, and motor learning).
The midbrain (mesencephalon), originally a center for processing visual and auditory information, which in mammals has become a relay station between the hindbrain and forebrain.
The forebrain (prosencephalon), which gives rise to the thalamus (a central relay station, routing sensory information to the appropriate cortical areas), the hypothalamus (controlling the endocrine system), and the cerebrum, whose outer layer, the cerebral cortex, is the seat of higher cognitive functions in mammals.
This three-part architecture is conserved across all vertebrates, but the relative sizes and elaboration of its components vary enormously and tell a story of progressive expansion, particularly of the forebrain. In mammals, the cerebral cortex has ballooned to dominate the brain as a whole.
Senses and perception
A nervous system’s primary input is the information received from sensory organs, whose receptor cells can transduce external stimuli of various types into electrical signals. Let’s go through the major modalities by which these stimuli manifest.
All sensory perception begins with transduction: the conversion of a physical or chemical stimulus into an electrical signal that the nervous system can process. Different receptor cells are specialized for different modalities. The major sensory modalities are summarized below.
Mechanoreception
Sensitivity to mechanical stimuli is the most universal sense. Even single cells respond to those and can be deemed to have some primitive sense. In vertebrates, mechanoreception has diversified into several sub-modalities:
Touch, with various specialized cells within the skin, best able to detect different levels of pressure or force.
The lateral line system in fish and other aquatic beings detects water currents and vibrations.
Balance: the sense of equilibrium and orientation, mediated within the inner ear.
Hearing: the detection of airborne sound waves. The range of detectable frequencies varies enormously, from elephants, who communicate with infrasounds, to bats and dolphins who use ultrasound for echolocation.
Photoreception
Sensitivity to light is also ancient, starting with simple eyespots in flatworm, detecting direction and intensity with little nuance. Later, arthropods had developed extremely sophisticated compound eyes.
The vertebrate eye, is camera-like, with its adjustable lens, variable aperture (the iris), and a retina densely packed with photoreceptors (rods for dim-light vision, cones for color and fine detail). Color vision depends on having multiple types of cone cells, each sensitive to a different wavelength — most mammals have dichromatic vision (two cone types), but primates’ eyes are trichromatic, and many birds or reptiles are tetrachromatic.
Chemoreception
Sensitivity to chemical signals encompasses both olfaction (smell, detecting airborne or waterborne molecules) and gustation (taste, typically requiring direct contact). The olfactory system can be extremely sensitive: a male moth can detect a single molecule of a female’s sex pheromone from miles away; dogs can distinguish individual humans by scent, etc.
Other sensory modalities
Electroreception: the detection of weak electrical fields.
Magnetoreception: the detection of the earth’s magnetic field, used for long-distance navigation.
Nociception: the detection of tissue damage, which underlies the sensation of pain.
Proprioception: the sense of one’s own position and movement.
Thermoception: sensitivity to temperature.