The Universe

This chapter of the Atheist Bible describes the current scientific view of the Universe, including the Big Bang, the genesis of life, and the evolution of humans. The chapter consists of the following sections:

The Universe: Describes the Universe and the Earth.
Life: Explains the genesis of life.
Evolution: Explains how organisms evolve.
Humans: Traces the evolution of humans.
Complexity: Explains the nature of complex systems.
Questions: Treats common objections to this view of the Universe.
References

This chapter is also available as an audio-book, read by an Artificial Intelligence

The Universe

The Earth

To tie our exploration of the Universe back to our theory of truth from the previous chapter, we start with rather basic notions: We call “the Earth” the planet on which humans reside (i.e., on which we perceive ourselves). Already in the 4th century BCE, Greek philosopher Aristotle postulated that the Earth takes the form of a huge ball2. Around 250 BCE, his compatriot Eratosthenes even measured the circumference of the Earth2. Today, modern science can deliver evidence in the sense of this book for the hypothesis that the Earth is round:

The Earth appears as a disc on photographs taken from space regardless of the vantage point. Anything that appears as a disc from all vantage points is a spherical ball. Also, the shadow of the Earth on the Moon during a lunar eclipse is always a circle.
It is possible to circumnavigate the world, i.e., you can travel around the world and return to where you started, even when you travel straight ahead — no matter in which direction and at which point you start. If one always arrives at the same point after traveling the same distance in the same direction, the surface is spherical.

The spherical Earth can then explain the following facts:

The Sun and the stars are lower in the sky as you travel towards the poles. For example, when traveling northward, stars such as Canopus, visible in Egypt, appear lower, and finally disappear from the sky.
You can see the sunset twice if you first see it on the ground, and then travel up very fast (for example, by an elevator at the Burj Khalifa building in Dubai3).
Two airplanes that start in a 90° angle from any point on Earth will meet again at a 90° angle. Two streets that start in parallel in the same direction will eventually meet.

The Church says that the Earth is flat, but I know that it is round — for I have seen the shadow of the Earth on the Moon and I have more faith in the shadow than in the Church.
Ferdinand Magellan, ascribed

The Sun

Mars traces a loop in the sky© Tunç Tezel, with permission

We observe that there are other things in space than just Earth — for example the Sun and the planets. People first believed that the Sun and the planets revolved around the Earth. This theory, however, predicted certain things that did not coincide with perceptions. For example, planets change their position relative to the other planets. They seem to slow down, reverse their direction, and then accelerate again in the original direction. Despite attempts to account for this retrograde motion by positing deferents and epicycles, precise observations of planetary motion contradicted the geocentric theory. This was one of the reasons why astronomers of the 16th and 17th centuries began to doubt that the Sun and the planets revolved around the Earth .

The Earth (blue) overtakes Mars (red) while both turn clockwise. In this process, Mars seems first left, then right, then left again, and then right.

Today, we know that the Earth revolves around the Sun. How do we know this? Mainly because we can see how the Earth moves around the Sun, much like we can see that a train moves by looking out of the window. In this analogy, “looking out of the window” means observing the stars around us. If we look at the stars each night for a year, we see that they move exactly as trees and houses move when we look out of the train window. Stars that are farther away move less than stars that are closer (a phenomenon known as parallax)4. The fact that the Earth moves around the Sun can then explain the movements of the planets: Both the Earth and the other planets revolve around the Sun. When the Earth overtakes a planet on an outer orbit, that other planet appears to make a backward-forward movement (see illustration). The revolving Earth also explains solar eclipses, lunar eclipses, and the shape of the Moon at different times of the month. Once every 175 years, the four outermost planets (Jupiter, Saturn, Uranus, and Neptune) are aligned — a fact that allowed the Voyager 2 space probe to visit all four planets in the 1980s5.

Elizabeth Anscombe: I can understand why people thought that the Sun revolves around the Earth.
Ludwig Wittgenstein: Why?
Elizabeth Anscombe: Well, it looks that way.
Ludwig Wittgenstein: How would it look if the Earth revolved around the Sun?

The Universe

There are other stars and planets in the Universe. Some of these objects emit or reflect light that we can see. We can even estimate their distance to Earth, as follows: We measure the angle at which the star is visible in December. Then we measure the angle again in June. Since the Earth has traveled around the Sun in these 6 months, the angles are slightly different. From these two angles and the distance of the Earth to the Sun, we can compute the distance of the star. This technique works for stars that are relatively “close”.6

For stars farther away, we can proceed as follows: Astronomers are able to spread out the white light of stars into its constituent “rainbow” of colors. This is called the stellar spectrum. Using the stars within the 300 light year range, astronomers have shown that stars with similar spectra have similar intensity of brightness and are at a similar distance from Earth. This allows scientists to predict the distance of stars beyond the 300 light year range based on the spectra. The spectrum of the star is photographed and compared with the spectra of nearby stars whose distance is known. Measuring the apparent brightness (the farther it is, the less bright it will seem), the astronomer can then determine the distance of the star. This method can be used for stars up to tens of thousands of light years away from the Earth.4 Nowadays, we can also measure the distance of the stars by launching satellites. Gaia, a European space observatory, was able to build a precise three-dimensional map of our galaxy in the 2020s7.

These techniques have led to the following conclusions: The Earth orbits the Sun in an elliptical curve at a distance of 150 million kilometers. The light of the Sun needs roughly 8 minutes to reach us. The farthest comets orbiting the Sun are 50,000 to 100,000 times farther from the Sun than Earth, making up what is known as the Oort cloud8 9. The Sun’s field of gravity then gives way to that of surrounding stars around an estimated 1.6 light years from the Sun. This area is our Solar System.10

The Solar System is just one of many such systems. Each system revolves around one or more stars. A galaxy is a collection of such star systems. Our galaxy, the Milky Way, spans a gigantic distance of 100,000 light years11. This means that even if we could travel at the speed of light, we would need a third of the time that humans have existed on the planet Earth to cross it. The Milky Way is estimated to have between 200 and 400 billion stars12, so there are more than 25 stars for every person on Earth.

The Milky Way is located in the so-called Local Group, which spans some 2 million light years13. This group lives in the Virgo cluster, which spans 5 million light years14. The part of the Universe that we can observe is made up of many such superclusters. It is around 100 billion light years across15. This means that if a star at the fringes of the observable universe dies, it would take 50 billion years to see that the light had ceased. As a result, the Universe that we see is the Universe that existed billions of years ago. According to current scientific opinion, we cannot know how the Universe is now, because no signal can travel faster than light.

The Earth is at the center of the observable universe because what we can observe is 50 billion light years around us in all directions. This does not mean that the Earth would be at the center of the entire Universe. We do not know how big the Universe is beyond what we can observe.

So far it is athwart the blue
to where that star appears,
that for its light to reach our view,
it took a thousand years.
It may have languished long ago,
then perished in the skies,
and yet, we still perceive its glow
right there before our eyes.
The image of the star survived,
to rise each night anew.
We could not see it while it thrived.
Now that it’s gone, we do.
Mihai Eminescu in “La Steaua”, translated by Corneliu M. Popescu and Fabian M. Suchanek

The Big Bang

We all have experienced the Doppler Effect (named after Austrian physicist Christian Andreas Doppler): When a fire engine passes, the pitch of the siren is higher when as the vehicle approaches, and lower when it has passed. This is because sound is a wave. When a sound-emitting body moves towards us, the waves arrive in a compressed form, which makes them sound higher. When the body moves away from us, the waves are dilated and the sound appears lower.

The same observation can be made for light. Light can be understood as waves. When these waves are dilated, they do not turn “low-pitch” (as sound waves), but they turn slightly more towards the red end of the spectrum (a phenomenon known as red shift). Since light travels extremely fast, these effects are visible only when the light-emitting body moves away from us at an extremely high speed. We know roughly what the color of the stars should be, because this color depends on the nuclear reactions in them and on their size and luminosity. Now here is the surprise: All distant stars are slightly more red than they should be. This means that they are all moving away from Earth at the speed of hundreds of billions of kilometers per hour. This holds no matter where we look in the Universe.16

Does this mean that we are the center of the Universe? Not necessarily. When you draw dots on a balloon and you inflate it, all points will move away from each other, and yet no dot is in the center any more than the others. What it does mean is that the Universe is continuously expanding at incredible speeds. Ever since American astronomer Edwin Powell Hubble and his colleagues made this observation, the hypothesis of the expanding Universe has been confirmed by a large number of other observations, including cosmic background radiation and predictions from Albert Einstein’s relativity theory.

Now if the Universe is expanding, this means that if we go back in time, the Universe was smaller. If we go back really far, then the Universe was most likely a single ball of extremely dense matter. This ball then exploded to give rise to the expanding universe — an event called the Big Bang. Based on how fast the stars are moving away from us, that Big Bang must have been roughly 14 billion years ago17. Even though the Universe is 14 billion years old, the observable universe is larger than 14 billion light years. This is because space itself has expanded in these 14 billion years.

Scientists have investigated the conditions of matter at the time after the Big Bang, and today, we can even replicate the conditions near the beginning of the expansion of the Universe in large particle accelerators.

Space is big. Really big. You just won’t believe how mindbogglingly big it is. I mean, you may think it’s a long way down the road to the chemist’s, but that’s just peanuts to space.
Douglas Adams in A Hitchhiker’s Guide to the Galaxy

Before the Big Bang

We have seen that the Universe most likely started by a sort of big bang. A natural question of course is “What was before the Big Bang?” Unfortunately, we do not have an answer to this question. Several theories have been proposed, including an oscillating universe or parallel universes. Time could even have stalled, so that there would be no beginning at all.

A gradual halt of time is not completely illogical. To see this, consider again Albert Einstein’s relativity theory. Technically speaking, this theory is a set of rules, and these rules predict that time runs slower in a field of large gravity. For example, time runs slower at the center of Earth than in the sky. Absurd as this theory may sound, it has always made true predictions: GPS satellites offer proof that time runs indeed slightly slower closer to the Earth than far away from it18. Now if the single dot of mass really existed at the beginning of the Big Bang, its mass must have been extremely large. This could entail that, as we move closer in time to the beginning, time runs slower and slower from our perspective19 — so that we never actually arrive at any beginning at all. The chase for the start of the Universe would then resemble a mathematical function that converges to a value but never reaches it — or to a donkey that chases a carrot on a stick. As British cosmologist Stephen Hawking put it: “Time was always reaching closer to nothing but didn’t become nothing.”20

Still, this leaves open the question of why the Big Bang happened. The problem with science is that it can propose only theories that produce verifiable predictions. As long as no such theory has been found, science keeps searching. Until then, the answer to the question of why the Big Bang happened remains unknown.

Science starts being most interesting where it ends, actually.
Justus von Liebig

The birth of the Sun and the Earth

The current scientific consensus is that the Big Bang produced a large amount of hydrogen and helium. These were pulled together by gravity, and gave rise to the first stars. Heat and pressure within stars caused smaller atoms to smash together and merge into new, larger atoms21. After several generations of stars, this material formed interstellar dust and gas called the solar nebula. Gravity, inertia, and centrifugal forces formed the center of the nebula into a rotating cloud. Gravity pulled the cloud together to form a ball, giving birth to the Sun22. The resulting compression heated the center, and this caused the start of nuclear fusion. Fusion occurs when protons of hydrogen atoms violently collide in the Sun’s core and fuse to create a helium atom, releasing a large amount of energy in the form of heat23. The Sun fuses 620 million tons of hydrogen each second.24 25

How the early Earth might have lookedCC0 NASA

The rest of the nebula was still rotating around the Sun, and as was the case with the Sun, gravity pulled together parts of the cloud and clumped them together to form planets (a process called accretion). This process formed the Earth and the other planets. Much like for the Sun, the accretion heated up the center of the planets. However, the Earth attracted much less debris, was smaller, and hence nuclear fusion did not start in its core. Over time the outer layer cooled down and formed a crust.26

At the time of the formation of the Earth, volcanism was rampant, and heat and materials from the inside of the Earth were spit out to the surface. These included water vapor. As the planet cooled, this vapor turned into water and oceans started forming27. The crust of the Earth consisted of tectonic plates, and these moved around, floating on the liquid layers below. The plates moved several times before forming the continents that we know today — and they are still moving.28

The discovery that we are just one particular species on one particular planet in one particular galaxy in our universe is making me much more humble than any burning bush ever could.
Christopher Hitchens, rephrased

The age of the Earth

The Methuselah Tree in California, the oldest living tree, is 4800 years old.CC-BY-SA Chao Yen, cropped

Naturally, the Earth has to be younger than the Universe, i.e., younger than 14 billion years. Based on biblical sources, people have estimated the age of Earth to be around 6000 years old. Biblical sources also tell us that the stars were created after the Earth (on the fourth day of creation[Bible: Genesis 1:14-1:19]).

Now here is the rub: Given that some of the stars are billions of light years away, and that we can see them, they must be billions of years old. Hence, they cannot have been created after an Earth that is 6000 years old. Therefore Biblical claims about the age of the Earth relative to the age of the stars must be false.

Ancient trees tell us a lot about the age of the Earth. A tree adds one ring to its trunk every year. If we count the rings in a tree cross section, we can know when the tree was born. Some trees are thousands of years old. For example, we have found a Bristlecone Pine aged over 4800 years (pictured)29. But the rings also tell us more: In a year with good climate conditions, rings are thicker than in years with bad climate conditions. Thus, the thickness of rings gives us a pattern. Trees in the same geographic region experience the same climate conditions. Thus, all trees in the region exhibit the same pattern of ring thickness.

Now let’s say we find a tree that died this year and that is 4000 years old. In its first 100 years, it exhibits a particular pattern of ring thickness. Let’s assume that we find another tree that died long ago, and that exhibits the very same pattern of ring thickness. However, this pattern now appears on the outer rings, closer to the death of the tree. Then we assume that the death of this tree coincides with the first 100 years of the first tree. Thus, we can calculate backwards when the second tree was born. In this fashion scientists have found trees that were born over 13,000 years ago. Thus, the Earth must have existed at least 13,000 years ago.30 31 A similar method can be used for layers of rock28.

Scientists have also developed more sophisticated methods of dating objects. The most common is radiometric dating: Some types of atoms are unstable and will spontaneously decay into other kinds of atoms. While the moment of decay of each individual atom is completely random, in a large sample the rate of decay has been shown to be constant. The rate of decay of the radioactive atoms is specific to that particular element. This decay is normally given in terms of half-life, which is the time it takes for half the original amount of atoms (the “parent” atom) to decay to another type of atom (the “daughter” atom). The decay rate of the various particles had been determined experimentally. Thus by comparing the relative amount of parent and daughter atoms in a rock sample, a geologist can determine the age of that particular sample.

There are many naturally occurring radioactive elements with known half-lives on Earth. For example, potassium-40 decays to argon-40 with a half-life of 1.26 billion years. Argon is a gas that does not ordinarily combine with other elements, and so when a mineral forms it will be initially argon-free. If the mineral is then found to contain locked-in argon, it must have come from radioactive decay. The ratio of argon to potassium can then be used to estimate the age of the mineral28 . By using these radioactive “clocks”, the oldest rock yet found on Earth (from northeastern Canada) is dated at 4.3 billion years old. Analysis of these along with other geologic and astronomical evidence led scientists to conclude that the Earth was formed about 4.5 billion years ago32. Thus, the scientific estimate of the age of the Earth is larger than the one given by the Bible by a factor of roughly a million.33

What was God doing before he created the world?
Was he just hanging around?
Anonymous

Life

One of the characteristics that distinguishes our planet from the others we know is that there is life. Different from inanimate entities, living beings can grow, reproduce, exchange substances with the environment, and transmit genetic information to their descendants. This applies to both complex life forms (such as birds or humans) and simpler ones (such as bacteria, archaea, or fungi).

According to the current scientific consensus, life started fairly early (a few hundred million years) after the formation of Earth, but evolved relatively slowly. Some of the earliest evidence for life are stromatolites — structures created by photosynthetic bacteria called cyanobacteria. The oldest stromatolites were found in Western Australia, and are 3.5 billion years old34, indicating that life on Earth is at least that old.

We will now trace the genesis of life step by step.

Chemical reactions

All matter is made of atoms. Atoms can attach to one another, and the resulting structure is called a molecule. For example, two hydrogen atoms (abbreviated by “H”) can bind together to form a molecule of two hydrogen atoms. We denote this process by

H H → H — H

The left-hand side of this equation says that we have two separate hydrogen atoms. The right-hand side says that we still have two hydrogen atoms, but that these plugged together to form a molecule. This molecule is called dihydrogen, and is abbreviated “H₂”.

Such molecules can again link together to form larger molecules. They can also split up into atoms, or transform into other molecules. For example, water is formed when one oxygen-pair combines with two hydrogen pairs into two water molecules, as shown in the figure.35

Such a chemical reaction may require heat or energy in order to proceed. In the example of water, the process requires energy to split the oxygen pairs and the hydrogen pairs. However, a chemical reaction may also emit energy. Reactions usually also require the presence of other molecules (so-called catalysts) to proceed.

In the terms of this book, a chemical reaction is a theory that says that if certain chemical substances are brought together, and if energy and/or catalysts are present as required, then a new chemical substance will form. Such theories are often testable, i.e., they can be reproduced in the laboratory. They have also been validated extensively, because chemical reactions happen in real life around us all the time — for example, when wood burns, when soap cleans out stains, or when we cook meals. Every single occurrence of such a process validates the theory of chemical reactions.

The formation of molecules

The Miller-Urey ExperimentCC-BY-SA YassineMrabet

The current theory is that, when the Earth was born, volcanic eruptions released large amounts of carbon dioxide (CO₂), nitrogen (N₂), hydrogen sulfide (H₂S), and sulfur dioxide (SO₂) into the atmosphere, forming a kind of “primordial soup”36. Lightening released heat energy, leading to chemical reactions that randomly assembled molecules. Some molecules would immediately dissolve thereafter, others would chemically react with other molecules, and again others would stay.

This theory can be experimentally verified, as American scientists Stanley Miller and Harold Urey showed in 1953: They simulated the early atmosphere of Earth by a gas mixture of methane (CH₄), ammonia (NH₂), and hydrogen (H₂). They simulated the water vapor from the early oceans by pumping steam into this mixture. The steam was then allowed to condense back into water, the water was heated again to steam, pumped into the gas, and so on. Within a day, the mixture had turned pink. Miller and Urey showed that various forms of molecules had been created, many of which are basic components of living beings.37 Later analyses of the original experimental material showed that even more molecules had formed than those reported by Urey and Miller.38

The Miller-Urey experiment gives us a testable theory: Whenever a certain gas mixture is exposed to lightning, certain molecules form. This means that, if the early Earth had this gas mixture plus lightning, then it is likely that the very same molecules formed.

Nucleotides

The Miller-Urey Experiment produced a variety of larger molecules. Later variants of the experiment were able to produce, in particular, molecules called nucleobases (also called nitrogenous bases)39. There are 5 such bases, called adenine (A), guanine (G), thymine (T), cytosine (C), and uracil (U). Two of them are shown here:

Each of these nucleobases can connect by chemical reactions to a five-carbon sugar and to a phosphate group. This yields a molecule called a nucleotide40. The nucleotides for adenine and cytosine are shown here:

Two nucleotides can connect together by chemical bonds. This chemical reaction releases water, as shown here:

Other nucleotides can bind to the free ends of this connection, so that we obtain a chain of nucleotides. Such a chain is called a nucleic acid40. Often, the nucleotides are denoted by their initial letters, so that a nucleic acid could be, for example, GGGAUUGUUCAA. In reality, the backbone of such a chain is not straight. This is because some nucleobases are complementary, meaning that they can pair. For example, guanine (G) can pair with cytosine (C). When complementary bases at different points on the chain connect to each other, the molecule forms loops (like shown in the figure). This gives the molecules a complex 3-dimensional structure.

There are two main types of nucleic acids that are important for living beings: ribonucleic acids (RNA) and deoxyribonucleic acids (DNA). We will first focus on RNA strands — single-stranded nucleic acids that do not contain thymine (T). Such RNA strands can be assembled in the laboratory41. This gives us a theory, which says that if nucleotides are brought together (with the necessary catalysts), they form an RNA strand. This theory is testable, and has indeed been validated experimentally. We therefore assume that such strands formed on the early Earth.

Chance

Only few RNA sequences have biological functions (the others are just random sequences). Now how likely is it that one particular RNA sequence got assembled by chance on the early Earth?

There are several such calculations on the Web42 43, but many of the variables in this game are just unknown. Therefore, we shall merely show (with rather arbitrary quantities) how such calculations usually proceed and which factors are usually taken into account.

Let’s say that we want to grow one particular RNA sequence, which contains 50 bases (50 is a reasonable number for a short RNA sequence, but in the end it is an arbitrary choice). We start with one base. At each point in time, a new base attaches. There are 4 different bases for RNA. However, there are also other, competing molecules that can attach to our sequence, thus spoiling the entire thing. Let’s say that in total there are 10 types of molecules that can attach to our chain, and only one of them is the right one (again, 10 is an arbitrary choice). Then this gives us a chance of 1 in 10⁵⁰ of assembling that RNA sequence. This is a huge number. It is roughly the total number of atoms on Earth. So is a chance of 1 in 10⁵⁰ too small to be ever met?

Several factors come into play here. First, there would not only be one RNA sequence growing, but billions of them in parallel. For comparison, one liter of water contains 10²⁵ molecules of water44. All water on, in, and above the Earth has a volume of roughly 10²¹ liters of water45. This means we had (and have) 10⁴⁶ molecules of water available on Earth. Assume that we have 1 base molecule per million water molecules (this is again an arbitrary assumption, based on some references42). Then this gives us 10⁴⁰ chains that could start in parallel. So we have a chance of 1 in 10¹⁰ that one of them is the one we’re looking for. 10¹⁰ is still a huge number. However, we also have a large amount of time: If we assume it takes (let’s say) a day to grow such a chain, then it would take 27 million years for the chain we want to appear sometime during that time span. In comparison, life (in the form of RNA chains that inhabit a cell) started roughly 500 million years after the formation of the Earth.

Real RNA strands, as they appear in today’s living beings, are longer than the ones we have assembled here (with around 100 or even more than 1000 bases). Chains may also be destroyed while they grow. At the same time, several additional factors come into play: Conditions may change during these millions of years, making it harder or easier to assemble the chains. For example, the presence of clay can speed up the formation of RNA molecules significantly46 47. Another factor is that additional molecules may form over time, and these can hamper or speed up the process. Furthermore, there may be several RNA molecules that are different from the one we want to assemble, but which have the same functions. Then it is sufficient to assemble any of them. Note also that the experiment was not constrained to Earth. There are 10²² stars in the visible universe alone. If only 1 in a million has an Earth-like planet (which is again an arbitrary guess), then this gives us 10¹⁶ places in the Universe to assemble RNA chains.

These calculations do not prove anything, because they are based on arbitrary numbers. They serve just to illustrate the magnitudes of the values involved. They also serve to illustrate that new data points may actually make the chances of life much bigger than we thought (like the example of clay).

RNA self-replication

How early RNA replication might have worked48

We have seen that RNA molecules can assemble by chance. It is assumed that some of these RNA molecules had the ability to replicate. The figure shows how this could have worked: Complementary bases bind together and thus form an “inverted copy” of the original. This copy gives rise to another “inverted copy”, which is equivalent to the original. Such a process does not happen spontaneously, but needs energy and catalysts.

Indeed, scientists have found ways to create self-replicating RNAs in the laboratory49. Such molecules can produce copies of themselves, and can thus be considered variants of the early ancestors of life.

Protocells

So far, we have discussed how RNA molecules form, and how they possibly replicated. Now let us see how the first cells might have formed. A cell has a membrane, which separates the inside from the outside. This membrane usually consists of molecules whose head is hydrophilic, i.e., it is chemically attracted to water. The tail of the molecule is hydrophobic, i.e., it is chemically pushed away from water. When large quantities of such molecules are poured into water, they spontaneously form bubbles, because this is one of the ways in which all heads face the water and all tails are protected from water50. Such a structure is called a vesicle, or liposome (shown in the figure).

There are several molecules that have this property, and they are called lipids. One particular subclass of lipids are fatty acids. These are molecules that have a rather long tail. As other lipids, they spontaneously form vesicles when poured into water. When combined with clay (or, more precisely, montmorillonite), the process occurs even more quickly. Some of the vesicles form around the clay molecules. Since RNA attaches to the clay molecules, it is sufficient to mix fatty acids, clay, and RNA in order to get RNA chains inside vesicles. This means that we have vesicles that contain RNA chains51. The theory is that these constellations would have formed the first protocells.

Vesicles are relatively stable in their shape, but the individual fatty acids that compose them move around a lot. This entails that the vesicle walls are permeable to certain molecules. Depending on their size, some molecules are able to pass through the wall. This gives us a structure that protects the RNA from larger molecules and from physical impact but allows other molecules to float in and out.

Protocell division

On the early Earth, storms, water movements, heat turbulences, and volcano eruptions would have mixed the elements. In that process some RNA strands ended up in vesicles, thus creating the first protocells. The protocell walls are permeable to certain molecules, and so nucleotides can enter and exit the protocell. Some RNA strands are able to replicate themselves. They wait until the right molecule floats into the protocell, and add it to the copy of themselves that they are currently assembling. When the copy is ready, it splits off.

At the same time, other vesicles would be floating around in the water. Experiments in the laboratory show that vesicles attract these vesicles, and integrate them into their body. In this way, vesicles grow continuously when they come in contact with other vesicles or “single” fatty acids. When the protocells grow, their surface area increases, but their volume does not. This is because the membrane does not let water in. Hence, the protocell gets longer (as shown in the figure), and becomes unstable. Eventually, it will break into two pieces. Now remember that we had an RNA strand and its copy floating around in the protocell. If the two RNA strands happen to be in the same part of the splitting protocell, then they will continue sharing that protocell. However, if the protocell keeps splitting, then it is likely that at some point the strands will eventually end up in two different protocells. We have thus witnessed protocell replication and division.52 53

At this point in evolution, the life cycle of a protocell is governed mainly by random fluctuation and random chemical reactions. Only a small fraction of the protocells would actually be functional. Large numbers of protocells would be empty, mutilated, or destroyed by other chemical or physical interactions. It is even possible that the entire protocell population was destroyed at some point in time, and then re-formed through the same processes.

Mutation

We have seen that protocells can form and replicate. The protocells contain RNA strands, and these can interact with other molecules in several ways. For example, we can imagine that a certain RNA strand has a subsequence of nucleotides that binds to fatty acids. Then this RNA strand would attach to the protocell wall. When this RNA strand replicates, all of its copies would also attach to the wall.

We can also imagine that an RNA strand has a sequence that binds to certain molecules. When such molecules float into the protocell, the RNA strand would accumulate them. These molecules, in turn, can interact with the other attracted molecules, the RNA strand, or the protocell wall. For example, some molecules could turn out to fortify the protocell wall. If the RNA strand attracts such molecules, then the protocell will behave very differently from other protocells. Whenever the RNA strand replicates, it will copy this behavior to its clones.

Now we might wonder how such different behaviors come about when there was initially just one type of RNA strand that was able to replicate. The answer is that the copy mechanism of RNAs does not work 100% correctly. When one RNA assembles another RNA, it may occasionally introduce additional nucleotides or leave out others. Thus, each copy is usually slightly different from the others.

This process is called mutation. A mutation can destroy the behavior of the RNA. For example, a mutation can destroy the self-replication ability of the RNA. Then this particular copy will not continue to replicate. However, the mutation can also introduce new behaviors — simply because new subsequences may appear.

Early life

At this point of our discussion, we have seen how molecules form, how RNA strands form and mutate, and how protocells form and divide. All of these processes happen purely by chemical reactions. Many of these processes can be replicated in the laboratory, giving us testable theories about them.

We have now arrived at little cells that replicate themselves, and we may discuss whether to call this “life”. Whether you want to call this “life” or not depends on how you prefer to use this word. However, the organisms that we have seen have all the ingredients that we usually require for life:

a membrane that distinguishes the individual from the environment;
the ability to “ingest” certain molecules while blocking or ignoring other molecules; and
the ability to replicate, transmitting hereditary information with mutations.

Darwinism

We have now arrived at a point where we can introduce the principle of Darwinism, named after English biologist Charles Darwin. This principle says:

If there is an organism that can replicate with mutations, and if this replication continues for a long time, then those mutations that ensure the most successful replication will prevail.

Let us take an example. Let’s suppose that we have one RNA strand that curls up, and another RNA strand that takes the form of a long string. When the cell divides, the division cuts the cell space into two random compartments. While the “curls” will most likely end up in one compartment, the “strings” may be cut in two. Now let’s say you take 100 cells with curls and 100 cells with strings. Let’s say they all replicate, so that each cell contains two of them. When the cells divide, the curls will end up unharmed. However, let’s say that half of the strings are cut in two by the cell division and destroyed as a result. Thus, we have 200 curls and 100 strings. Now the RNAs replicate again, giving us 400 curls and 200 strings. Again, all 400 curls survive, but only 100 strings survive. We see where this is going: While the curls will become more numerous, the strings will stay at 100 individuals. Now let us say that 10% of the cells suffer random destruction by mutation, chemical reactions, and physical impact in each cycle. Then the curls will double in each cycle, and then lose 10% of their individuals. The strings, in contrast, will be reduced in 50 steps to 0 individuals. Thus, the curls prevailed, and the strings died out.

If you think about it, the principle of Darwinism is trivial: Whatever works best prevails. Whatever else there is dies out. Technically, the principle of Darwinism is a rule: Given a certain population of individuals, and given knowledge about which mutations ensure that the copies will survive, the rule predicts which population will prevail.

Protein synthesis

A ribosome producing a proteinCC-BY Bensaccount

At this stage of the early Earth, we have a number of structures that divide randomly and that copy their RNA. Through the process of mutation, the cells form variants. Some variants would be crushed by the elements in the exterior environment, while others would prove more stable. This process would favor variants that are more resistant to the environment and faster in their replication cycle.

One crucial element in this process are amino acids. Amino acids are molecules that popped out of the Miller-Urey Experiment, and thus likely existed on the early Earth. These amino acids can plug together to form chains. A protein, then, is a long chain of amino acids with a 3-dimensional structure, which performs certain functions54. For example, proteins can attach to each other through chemical bonds, alter their composition upon reacting with another molecule, decompose into smaller pieces, or aggregate to even larger molecules.

Eventually, one mutation would create a ribosome — a macro-molecule composed of special proteins and nucleic acids. The interesting thing about ribosomes is that they can assemble new proteins (they are like a “factory of proteins”). They assemble the proteins that are dictated by a special type of RNA strands called messenger RNA strands. The ribosome maps each sequence of 3 nucleotides in the RNA strand to one amino acid in the protein, in a process called translation.55

A messenger RNA can encode (and the ribosome can then create) almost arbitrary proteins with various chemical properties and functions. This allows the cell to build up complex structures. It is as if the cell owned a 3D printer.

The evolution of cells

The cell wall of an escherichia coli bacterium, coloredCC-BY David Goodsell

Ribosomes allow cells to produce any proteins as dictated by the messenger RNA. It is clear that RNA strands that could team up with ribosomes had an evolutionary advantage, as they could produce proteins that fortify cell walls, catalyze RNA replication, or accelerate chemical reactions. Over time, they would replace the strands that did not have this capability.

Deoxyribonucleic acids (DNA) evolved along similar lines as RNA, and consist of adenine (A), cytosine (C), guanine (G), and thymine (T) bases. Over time, the DNA strands came to replace RNA strands as support for genetic information. This is because DNA strands are more stable: They consist of two linked strands that wind around each other to resemble a twisted ladder — a shape known as a double helix.56

In this manner cells evolved into prokaryotes — simple single-celled beings. Prokaryotes continue to exist to this day. In fact, prokaryotes are one of the most abundant groups of organisms on Earth and inhabit practically all environments: They are found in water, soil, air, animals’ gastrointestinal tracts, hot springs, and even the Antarctic ice shield.57

Prokaryotes include bacteria, which can be seen under the microscope. They are a reasonably well-understood form of life, and are proof that life can go on just by chemical reactions. The oldest known prokaryotes are cyanobacteria (which we have briefly discussed already). Eukaryotic cells, in contrast, are more complex cells. They are a thousand times bigger, are surrounded by plasma membranes, and contain a nucleus. It might be surprising to see the complexity contained in a single cell. But the process of cell evolution did not happen overnight. Eukaryotic cells evolved over 2 billion years of time50. This means that nearly half of the time of the existence of Earth was needed just to get complex cells up and running.

Locomotion

A bacterium is a complex unicellular organism. The flagellum is a string of proteins that comes out of bacterium like a tail. The flagellum is built up from the stem. New proteins are produced, and these assemble at the tip of the stem, thus prolonging the tail until it becomes a full flagellum58. It rotates. This rotation is powered by a chemical reaction: There is a concentration gradient in protons (not: proteins) between the interior and the exterior of the cell. This causes a constant flow of protons across the cell membrane. This flow, in turn, rotates the flagellum. The flagellum can rotate up to 300 times per second.59

This process moves the bacterium forward. A run lasts about one second and moves the bacterium 10-20 times its length before it stops. The direction of the rotation is controlled by a protein at the stem. When the flagellum turns counter-clockwise, the bacterium moves in one direction. When it turns clockwise, the bacterium just tumbles in place. The swimming of a bacterium is a sequence of tumble moments and swimming moments.59

Bacteria use this process to find glucose — a molecule that they use to produce energy, and that we can think of as their food. A bacterium has a glucose receptor on the side opposite to the flagellum. Whenever a glucose molecule attaches, the bacterium switches to “swim” mode. Since the receptor is at the opposite side of the flagellum, the swimming happens in the direction of the glucose60. After some time, the glucose molecule detaches, and the bacterium switches back to “tumble” mode. It tumbles and changes direction until a new glucose molecule attaches. Thus, when it swims in the direction of increasing glucose concentration, it will swim more often and tumble less. If it swims in the other direction, it will swim less and tumble more. This leads to a random walk, which is slightly biased towards the direction of higher glucose levels. If this process is repeated, the bacterium will eventually swim to the source of the glucose59 . Those bacteria that managed to do this saw their chemical processes accelerated, and thus reproduced faster than those that did not have this capability. Therefore, they eventually prevailed.

Today, the mechanism of locomotion in bacteria is reasonably well understood, down to the level of proteins, molecules, and atoms. In fact, the exact proteins involved in this process have been cataloged completely61.

It might seem close to unbelievable how such a complex mechanism evolved. However, remember that DNA can encode (and ribosomes can then produce) nearly arbitrary proteins. Through mutation, the cells would “try out” different proteins. Any design that gives a bacterium just the slightest advantage over other designs would have dominated the others62. All in all, the evolution of bacteria took 1 billion years63 — 3 thousand times longer than humans exist.

Intention

We have seen how a bacterium moves towards higher concentrations of glucose. The process seems kind of intelligent, because the bacterium manages to swim towards the glucose even though it has only limited steering capacity. Hence, we have a tendency to say that the bacterium “wants” to move towards the glucose. We are thus ascribing an intention to the bacterium. What we mean by intention here is a non-permanent internal state, often triggered by external input, that conducts the bacterium to show a certain behavior. The word “intention” is just a convenient shorthand (an auxiliary notion in the terms of this book) for this phenomenon.

Interestingly, the process of the bacterium moving towards the glucose is entirely chemical. It would be easy to build a robot that shows the same behavior, and moves (say) towards the light. It is all just a purely mechanical procedure. We will later argue that human behavior, too, is entirely driven by chemical processes. While it is vastly more complex than the behavior of a bacterium , it is not of a different nature. In both cases, a system exhibits a certain behavior as the result of a non-permanent internal state.

Multicellular organisms

We have seen how cells evolved and how they became complex enough to become autonomous and self-moving organisms. We will now see how cells team up into multicellular beings.

Multicellularity evolved several times independently in several different organism species. One way in which multicellularity evolves is as follows: By random permutations, it can happen that some cells of the same species start clinging together. It can then turn out that this allegiance grants them some evolutionary advantage. For example, it can be shown that collections of cells can perform chemotaxis more efficiently than single cells64. These “social cells” then reproduce more frequently than their solo cousins, and the offspring of the social cells inherits the tendency to cling together. Over time, the cells specialize: Some cells lose multi-functionality and concentrate on one particular functionality instead. Indeed, individual cells can be induced to collaborate and form multicellular organisms in the laboratory solely through evolutionary pressure, resulting in a division of labor among the cells65.

This process can be observed in dictyostelids (also known as dictyosteliomycetes, cellular slime molds, or dictyostelia). Dictyostelids are amoebae, i.e., unicellular organisms. When food is readily available, they are individual amoebae, which feed and divide normally. However, when the food supply is exhausted, each individual amoeba gets stressed and sends out a Cyclic adenosine monophosphate molecule. When another amoeba detects this molecule, it moves towards the concentration of this molecule. Each attracted amoeba also starts sending out such molecules, thus calling even more amoebae. Eventually, these amoebae form a multicellular assembly, called a pseudoplasmodium or slug. This composite organism has the ability to move — and uses it to emigrate to areas of higher food concentration. Different cells take different roles in this process, thus giving rise to a truly multicellular organism.66 67

Evolution

We have seen how multicellular organisms evolved from simple molecules. The theory of Evolution says that this process continued, and that all living beings evolved from these basic beings. This hypothesis was first formulated by Charles Darwin in his 1859 book On the Origin of Species68. In the form of a rule, it goes as follows:

For any species (contemporary or ancient, down to simple vesicles), there is a previous species from which this species evolved through gradual mutation.

This theory says that we can trace the path from all contemporary species back down to simple vesicles. Vice versa, the theory predicts that simple beings evolved into more complex beings and later into the plants and animals that we know today.

The principle that drives this process, according to Darwin, is natural selection. It is the idea that a species evolves collectively because less well adapted mutations are constantly weeded out in favor of better adapted mutations. Let us look at some traits that can evolve this way:

Speed: If one individual can move faster than another individual, and if both are chased by a predator, then the slower individual will more likely be caught and killed while the faster is more likely to survive. The faster one therefore has a higher chance of passing its genes on to the next generation, and the next generation will, on average, be a tiny bit faster as a result. Then the same thing can happen for individuals in the next generation, leading to their survival, and so on.
Adaptation: If one individual is slightly better adapted to its environment than another individual (say it has slightly longer fingers and can cling slightly better to tree branches, or it has a bit more fur and is protected better against the cold), then this individual will fare slightly better in life. It will have more chances to find food and/or escape predators, and therefore have a slightly greater chance of passing on its genes — meaning that the next generation will also have its traits that led to its higher chance of survival. If this process is iterated for millions of individuals and for millions of years, these traits will eventually prevail.
Resistance to illnesses: If one individual happens to have a mutation that makes it resistant against a certain fatal virus, then this individual has a higher chance of survival than those individuals without this mutation. The following generation is more likely to inherit this particular mutation, and hence enjoy a better chance of survival as well. A given individual with a disadvantageous mutation may still have more reproductive success than an individual with a better trait. However, if the process is repeated over millions of individuals and millions of years, then the advantageous traits will prevail. (As a side note, this applies only to illnesses that appear before mating. Illnesses of age, such as Alzheimer’s, will not be eradicated in this way because they do not influence the reproductive success of the individual.)

One way to envision this process is to imagine that two teams play soccer on a field where the ground is slightly sloped towards one of the goals. The net effect of the tilt favors the team whose goal is on the up-slope. Of course the other team can still win, but when the teams play dozens of matches, it is more likely that the team whose goal is uphill wins a bit more often. Evolution actually adds an interesting twist to this image since if a species is better adapted, it reproduces more frequently. In the analogy with the soccer game, this means that with every match that the uphill team wins, the slope becomes just a tiny bit steeper for the opposing team, leading to even more losses on average over time, and accelerating the process overall. The more the up-slope team wins, the steeper the slope will become, and the easier it will be to win again. In the end, the soccer pitch will be vertical, and the downhill team has no chance whatsoever to win. Evolution is analogous to this outcome: The advantageous traits first become only slightly more frequent, but then with the passage of time overtake the entire population.

Why should we believe this theory of Evolution? We shall now see several arguments.

The fossil record

Fossil of a Kainops invius, around 400 million years agoCC-BY-SA Moussa Direct Ltd.

A fossil is a trace of an animal or plant of a past geologic age that has been preserved in Earth’s crust70. Fossilization is a rare occurrence. The conditions must be just right in order for an organism that dies to become fossilized, and then for somebody to find it later. The theory of Evolution does not say that we will find fossils of all species that preceded today’s species. Nobody can force a fossil to appear or a scientist to find it. Instead, the theory of Evolution says that if we do find fossils, and if we arrange them chronologically, then we will see a gradual change between the fossils of the same species, with the newer ones resembling today’s species more.

This is indeed what we find. For many species, alive or extinct, we have found fossils or other remains. These include traces of multicellular organisms in stone, imprints of plants, insects enclosed in amber, tracks or feces, and even skeletons. Over time, scientists have found literally hundreds of thousands of fossils (Wikipedia maintains a list71). These include animal fossils, plant fossils, and also fossils of more basic life forms. To determine how old a fossil is, we can use radiometric dating: We date the rock layers above and below the fossil and thus estimate its age.

So far, we have found no fossil that would break the principle of Evolution. On the contrary, the theory of Evolution correctly predicts the properties of the fossils that we find. The theory has thus been validated in thousands of cases.

Fossils tell us a lot about the organism in question. From the skeleton of an animal, we can tell whether it moved on two legs or four legs. From the shape of the feet, we can tell whether the animal lived in trees. From the teeth, we can tell what the animal ate. From the size of the skull, we can tell the brain size. From the shape of the joints, we can determine the possible movements that the animal could perform. From the size of the bones, we can determine the kinds of muscles that the animal had. The more fossils we find, the more they complete our picture of the entire process of the development of life — from the first single-celled beings up to the predecessors of humans.

Paleogenetics

Fossils can be studied not just by their physical appearance, but also by their DNA. A DNA is a sequence of nucleotides, and DNA sequencing is the process of identifying these nucleotides. The DNA of a human contains 3 billion nucleotides, and with advances in science, a human’s DNA can now be sequenced in about 5 hours72. The DNA of hundreds of other species have been completely sequenced as well (Wikipedia maintains a list73). This matters, because a DNA sequence contains genes, i.e., segments of nucleotides that control which proteins will be built. With this, they control the physical development and behavior of the organism. Genes are hereditary, and are passed down to the descendants74.

Paleogenetics is the study of genes in fossils. Since every cell of a living being carries its entire DNA75, it can be recovered from a large variety of biological materials, of different origin, state of preservation and age, such as bones, teeth, feces, mummified tissues, and hairs. However, since fossils are usually tens of thousands of years old, the material has typically degraded and been invaded by bacteria and other microorganisms. As a result, of the DNA that is recovered from a fossil, only a small proportion is actually usable. Nevertheless, by overlaying parts of recovered DNA from different fossils, scientists can reconstruct larger parts of the DNA sequence76. For example, the DNA of Neanderthals was sequenced in 201077.

Once the DNA of two individuals has been sequenced, their DNA can be compared. For example, any two humans differ in roughly 1 out of 2500 genes78. A human and a chimpanzee differ in roughly 1 out of 100 genes79, and so on. Since we often know which parts of the DNA are responsible for which part of the body, by looking at the genes we can often tell how two species differ physically.

DNA sequencing can tell us not only how similar two species are but also when two species became distinct. By looking at the number of mutations needed so that one DNA would match the other (a technique known as the molecular clock) and a sense of how frequently mutations occur, we can estimate the time at which the species parted ways 80.

The DNA of individuals contains copies of part of the DNA from the father and part from the mother. This tells us not just something about the physical traits of the father and the mother, but also how similar they were as well. This sheds light on the social structure of the species, by telling us whether individuals of the species mated within family clans.

Interestingly, every discovery that we have made so far using paleogenetics validates the theory of Evolution. We have found no fossil so far where the paleogenetic analysis has contradicted the theory. We will therefore assume the theory of Evolution to be true in what follows. We discuss the falsifiablity and other formal properties of the theory further down .

The timeline of Evolution

Evolution is very powerful: Over time, organisms of successive generations can grow wings, develop fur, gain more brain mass, learn certain behaviors, or adapt to certain climates as a result of natural selection. This does not mean that the entire population of living beings evolves in the same way: It can happen that one population of beings becomes so different from another that they do not reproduce with them any more. Then they make up what is called a species. Each species evolves on its own, and can also give rise again to new species. Some species die out (the giant dinosaurs are examples). Others are superseded by new species. Again others make it into the present. These are the living beings we see today.

Based on evidence from fossils and paleogenetics, we can trace Evolution back in time. We find that the first species lived in water. Some species stayed there and evolved there. Others set out to conquer the land. Gradually, more and more complex beings evolved, including fish, insects, dinosaurs, birds, and mammals. The figure below shows when major evolutionary events occurred.

Ineed, the process of evolution, adaptation, and creation of new species continues to this day — and it will likely continue while life exists. Every newborn animal has some slight mutations in its genes when compared to its parents. Animals become resistant to viruses, develop capabilities to compete with newly arriving competitor species, or change their physical traits to adapt to the environment.

The Tree of Life

Based on fossils, similarities in DNA, and paleogenetics, we can establish when species parted ways in the past. We can thus reconstruct the branches of historical species, and this yields what is called the phylogenetic tree or simply the tree of life (shown in the picture). The inner branches of this tree show the early evolution of species from a common ancestor in the past. The outermost branches show the species of today.

We might be tempted to believe that the root branches of the tree are birds, mammals, and plants. That is, however, not the case. The root branches are rather bacteria (blue in the diagram), archaea (green), and eukaryota (pink). Eukaryota then split into animals, plants and fungi, and the animals include us humans (second from the right in the pink part). Thus, as you can see (or can’t see), humans are only a tiny fraction of the natural world of living creatures.

The picture is not much different for the total biomass on Earth: The sum of all biomass on Earth is around 550 gigatons. Of these, around 80% are plants, 10% to 15% are bacteria, and the remainder are fungi, archaea, protists, animals, and viruses81. Humans make up around 0.01% of the total (see diagram).

Extinction

A Spinophorosaurus, 160 million years old, 13 meters long, in Agadez, NigerCC-BY Universidad Nacional de Educación a Distancia

Over the past 4 billion years, thousands of species have evolved only to become extinct a few million years later. As predicted by the theory of Evolution, these species never re-appear. The most prominent example are maybe dinosaurs: They are species that evolved over time but then died off. Another example are the Neanderthals, a branch of humans that lived 250,000 years ago. They died out 200,000 years later. Indeed, 90% of all species that ever lived have become extinct82.

Hundreds of other species have disappeared due to human intervention. They were hunted to extinction or their life environment was altered so much that they collectively died off. The International Union for the Conservation of Nature (IUCN) has identified hundreds of species that are currently at the edge of extinction83.

Some species are pushed to the edge of extinction but then recover. For example, hundreds of years ago, tens of millions of American Bisons roamed the American prairies. Humans hunted them down, and by the late 19th century, only a few hundred of each subspecies remained in the wild. Yet, aided by conservation efforts, the population has recovered to several hundred thousand today84. Similarly, the population of the northern elephant seal fell to only 10-20 individuals in the 1890s, but the population has since rebounded85. Whenever a population goes through such a bottleneck, the genetic diversity of the species is severely reduced, and the remaining animals are more similar among each other.

Oddities of evolution

Evolution is not a goal-oriented process. Mammals didn’t acquire feet so that they could run. Rather, those animals that had any means of propulsion (pushing themselves forward, curling their body, etc.) were more successful than those that did not. Ultimately, the ones with more efficient means of propulsion (i.e., legs) prevailed.

To exemplify this, we can look at mammals that have legs but do not use them: whales.

Whales live in the sea but evolved from land-based mammals that had developed legs. Then they started feeding in the sea and eventually moved fully back to the oceans. In this process, natural selection gradually removed their legs. However, to this day, whales having pelvic bones that testify to their heritage. This process can be traced back through the fossil record, as we have found fossils of all intermediate stages86.

Such seemingly superfluous structures are common in nature. They are called vestigial structures. The blind mole rat, for example, has eyes that are completely covered by a layer of skin. This means that the animal cannot see87 . The animal developed eyes when it lived above ground, and then when it proved advantageous to cover them, natural selection did just that.

We discuss more such oddities later.

Artificial selection

We have seen that natural selection filters out disadvantageous traits from a population of individuals. This process can also be induced artificially. Consider dogs. Imagine that we would like to breed a species of large dog that runs fast so that it can help herd sheep. Then all we have to do is take any population of dogs, select the dogs that run fastest, and breed them. The offspring of these dogs will then have the fast-running genes of their parents. Among these offspring, we select again those that run fastest and breed them. Eventually, we will generate a population of dogs that run fast.

This may sound like a very disrespectful way to treat nature. However, it is what humans have done since time immemorial with plants and animals. There are large dogs that have been bred with the explicit purpose to herd sheep (the German shepherd dog). There are aggressive dogs that have been bred to protect their owners (bulldogs). And there are dogs that have been bred to be cute and cuddly (poodles). In this way humans have actively used the principle of selection and evolution to produce the species they want. These species did not exist before. Thus, the theory of Evolution is testable, in the sense that we can actually put it into action.

Artificial selection has been at work in some less obvious places, too. Have a look at the fruit in the picture. It is ball-shaped, yellow, and has big grains in it. Can you guess what it is?

It’s actually a wild banana — as bananas used to be before humans bred them. Over centuries, humans selected the bananas with fewer seeds, with better taste, and with longer shape, and bred them. This has led to the banana as we know it today: long, seedless, and yellow88. Thus, several of the animals and plants around us are actually results of targeted evolution and “human” selection.

Humans

The evolution of humans

We have seen how plants, bacteria, and animals evolved. We will now look into one particular branch of ancient animals: those that evolved into humans. Humans stem from the branch of the great apes, together with orangutans, gorillas, and chimpanzees. The fossil record and genetic analyses tell us humans became distinct from the predecessors of chimpanzees 5 to 7 million years ago89.

What this means is that both humans and chimpanzees have a common ancestor. This setting is comparable to the development of the ancient Celtic people: They originally lived in the Alps, but eventually spread out all over Europe. Some of them became French people while others became English people90. This does not mean that one is “better” than the other. Nor does it mean that they are equal in all aspects. (On the contrary, the French have developed a cuisine that is considered vastly superior to the English one.) Furthermore, the common ancestry does not mean that there cannot be any more English people just because there are now French people. It just means they have a common ancestor. And it is the same with apes and humans. We know today that there must have been a single female in the past who had two daughters — one that became the ancestor of humanity, and the other the ancestor of chimpanzees91.

If God created humans from dust, why is there still dust?
Checkmate, Christians!
Anonymous

Humans

We have seen that humans and apes share a common ancestor. From what we know, the evolution of humans was not a linear process. On the contrary, nature tried out different branches of humanoid beings. This is evidenced by fossils of different human-like species across time. We show the current understanding of human evolution here:

A reconstruction of the Sahelanthropus tchadensis, quite possibly the last common ancestor of humans and chimpanzees
in the Smithsonian Museum of Natural History

For every humanoid fossil, scientists determine its age, and its similarity to other fossils. Based on this, they conclude either that the fossil belongs to the same species as other fossils, or that it is so different that it qualifies as a different species. This is not a clear-cut process: The definition and the understanding of a species evolves continuously as more fossils are found. Based on the similarity and geographical distribution of fossils, scientists hypothesize which species evolved into which other species. For example, it is assumed that Ardipethecus ramidus evolved into its successor, Australopithecus anamensis. This means that the two species blend into each other, with Ramidus individuals increasingly resembling Anamensis individuals as time progressed, until the latter finally became sufficiently different that we apply a new name to them.

One species usually occupies a time range of hundreds of thousands of years, corresponding to tens of thousands of generations. It is not yet always known which species gave rise to which other species, which species interbred, and which fossils can be considered a new species. This uncertainty is shown as light blue areas in the diagram. Interestingly, some of the species overlapped geographically and temporally, meaning that different species of humanoids coexisted. We can imagine this like different species of dogs living at the same time: While they are all dogs, they are all different, and some of them are so different that they do not interbreed.

In general, the following things happened throughout the evolution of the humanoids:

the brain became larger;
bipedalism became the norm;
the amount of hair was reduced; and
tools were invented and used.

Over time one branch of this evolutionary process came to dominate all other branches. This is the species to which we belong: Homo Sapiens.

People are just fish plus time.
Dilbert in Scott Adams' comic strip Dilbert

Ardipithecus ramidus (“Ardi”)

The skeleton of Ardi. Note the feet.CC-BY-SA Tobias Fluegel.

Ardipithecus ramidus (called simply “Ardi”) is an ancient species that is assumed to be one of the earliest ancestors of humanity. Fossils of around 35 individuals of this species have been found. The Ardis lived around 4.4 million years ago in Africa. They had a grasping big toe adapted for locomotion in trees. However, the skeletons suggest that the species lacked the adaptations of living apes for climbing vertically, hanging from branches, and walking on their knuckles. Instead, Ardis were “careful climbers” in the trees, and supported their weight on the palms of their hands while using the divergent big toe for grasping. At the same time, the feet, pelvis, legs, and hands are adapted also for bipedal locomotion, suggesting that Ardis were bipeds on the ground. The large flaring bones of the upper pelvis were positioned so that Ardis could walk on two legs without lurching from side to side like a chimp. But the lower pelvis was built like an ape’s, to accommodate huge hind limb muscles used in climbing. Ardis stood about 1.20 meters tall and weighed about 50 kilograms. Wear patterns and isotopes in the teeth suggest a diet that included fruits, nuts, and other forest foods. They had reduced canine teeth, i.e., two diamond-shaped teeth at the front edges of the mouth. These were smaller than those of a dog, but larger than those of a human. Ardi had about 25% of the brain size of a modern human, at 300 to 350 milliliters.92 93 94

Ardi brought several evolutionary novelties: First, Ardi was habitually bipedal (as evidenced by the fossils). Second, Ardi abandoned the large, pointed upper canine teeth that keep getting sharpened by rubbing against the lower teeth. Both characteristics distinguish Ardi from the chimpanzees.95 Therefore, it is assumed that Ardi was among the first species to branch off from the grand apes and start the journey to become human.

Australopithecus afarensis (“Lucy”)

A reconstruction of Lucy
in the Smithsonian National Museum of Natural History

Australopithecus afarensis is an extinct species that is assumed to be the successor of Ardi and one of the ancestors of humans. One of its prominent skeleton findings was named Lucy. The species lived between 3.9 and 2.8 million years ago in Africa. Like Ardi, members of Lucy’s species had reduced canine teeth, although they were still relatively larger than in modern humans. They also had a relatively small brain size (430 milliliters) and a prognathic face (i.e., a face with forward projecting jaws). The curvature of the finger and toe bones approaches that of modern-day apes, and suggests that Australopithecus afarensis was able to climb trees. On the other hand, the loss of an abductable great toe suggests that Lucy’s species was not able to grasp trees with her feet. It is currently debated to what degree members of the species were able to walk like a human, but it is undisputed that they could walk on two legs. Females grew to only around 1.10 meters in height, and males were much larger at about 1.50 meters. If observations on the relationship between sexual differences and social group structure from modern great apes are applied to Australopithecus afarensis, then we can deduce that these creatures most likely lived in small social groups containing a mixture of males and females, children and adults. Quite possibly, the species were the first to use stone tools.96 97

The Lucy species later evolved into (or co-existed with) the Australopithecus africanus, which had a greater brain volume of about 480 milliliters. Males may have been on average 1.35 meters in height, and females 1.10 meters. These species were already biped, but were not specialized for a striding gait.98

Homo habilis

Homo habilis is most likely a descendant of the Australopithecus species. Homo habilis lived between 2.3 and 1.5 million years ago in Africa. The species had a brain size of around 610 milliliters — roughly half that of a modern human. The species were smaller than modern humans, on average standing no more than 1.30 meters. The hole for the spinal cord in was located in the centre of the skull base, showing that this species walked on two legs. Walking on two legs allowed the species to carry items or babies while moving. It would also reduce exposure to Sun heat. Bipedalism allows the hands to take over other functions. The finger bone proportions of Homo habilis suggest the human-like ability to form a precision grip, thus allowing the species to take and hold an item. Chemical analysis suggests that this species was mainly vegetarian but did include some meat in their diet.99.

Homo habilis remains are often accompanied by primitive stone tools. As opposed to Australopithecus afarensis’s unshaped tools, these stone tools were intentionally shaped. Homo habilis used one stone to split a flint stone in two pieces, so that the flint stone had a sharp edge. These are the so-called Oldowan (or Mode 1) tools — a crucial departure from previous species, and the reason for the name of the species (Homo habilis means “handy man”).99

Homo erectus

Around 2 to 1 million years ago, branches of Homo habilis gave rise to a humanoid species called Homo erectus (literally: “the upright man”). This species was about 1.45 to 1.85 meters tall, and had a brain size of around 1 liter100. Their weight ranged from 40 to 68 kilograms. Early African Homo erectus fossils are the oldest known early humans to have possessed modern human-like body proportions with relatively elongated legs and shorter arms compared to the size of the torso. These features are considered adaptations to a life lived on the ground, indicating the loss of earlier tree-climbing adaptations, with the ability to walk and possibly run long distances101. The loss of body hair took place in parallel with the development of full bipedalism. It is assumed that the naked skin allowed the species to reduce body heat more effectively through sweating. In this way, they could forage safely during midday heat, when most carnivores rest. They could also pursue prey by trekking and endurance running through the hottest hours of the day. The prey animals would eventually overheat, allowing the Homo erectus to capture them.102

There is fossil evidence that Homo erectus cared for old and weak individuals. The species also made more complex tools than Homo habilis, the so-called Acheulean (Mode 2) tools. These are symmetrically cut flint stones, which can be used as hand axes. Most importantly, Homo erectus was able to control fire, and used it to cook food.101 The earliest evidence for the control of fire that we currently have date to 1 million years ago. These are burned bone and ashed plant remains that were found in the Wonderwerk Cave in South Africa103. We do not know when the species were first able to make fire at will. Early humans probably captured natural fires and kept them alight for as long as they could.104 In any case, the use of fire was an important milestone in human evolution, granting Homo erectus access to light, warmth, protection from predators and the ability to heat food.

It is generally assumed that Homo erectus was the first humanoid species to leave Africa, migrating to Asia. The Asian branch of the species is sometimes called Homo erectus sensu stricto (“Homo erectus in the strict sense of the word”). It is currently debated whether this branch qualifies as a different species. Fossils of this branch have been found in places as far as China and Indonesia, yet the line seems to have died off shortly before the arrival of humans.105

The African branch of Homo erectus is sometimes called Homo ergaster (literally: “working man”), and we will now follow its evolution.

Homo heidelbergensis

Around 700,000 years ago, the Homo ergaster evolved into a species called Homo heidelbergensis (named after the German city of Heidelberg, where its first fossil was found). The Heidelbergensis face was already more human-like, with a vertical front and a broad frontal bone. The species was about 1.70 meters tall, and had a brain size of about 1.2 liters — a significant increase over previous humanoid species. This species definitively controlled fire, and was the first to build simple shelters. Homo heidelbergensis also developed shafting techniques, attaching stones to shafts to create spears. It was the first early human species to routinely hunt large animals such as wild deer, horses, elephants, hippos, and rhinos. These animals were skillfully hunted, and then butchered in an orderly fashion, suggesting that the hunters were working in co-operative groups.106 107

It is commonly assumed that branches of Homo heidelbergensis emigrated from Africa to Europe. The European branch evolved into Neanderthals. The African branch, sometimes called Homo rhodesiensis, evolved into Homo sapiens.106

Neanderthals

A reconstruction of a Neanderthal man. Note the muscular body.CC-BY-SA Neanderthal-Museum, Mettmann

The European branch of Homo heidelbergensis evolved into the Neanderthals (who lived in Europe and Asia) and the Denisovans (who lived in East Asia; both named after the places in Germany and Russia, respectively, where their fossils were found). The Neanderthals evolved between 500,000 and 70,000 years ago. During this period, the North of Europe and Asia were under the influence of advancing and retreating ice sheets. As an adaptation to living in cold environments, the Neanderthals' bodies were shorter and stockier than ours, and also more muscular. Neanderthals had an average brain size of 1.5 liters — larger than that of humans. Otherwise Neanderthals were in many aspects very similar to humans: They made and used a diverse set of sophisticated tools, controlled fire, lived in shelters, made and wore clothing, were skilled hunters of large animals and also ate plant foods, and made symbolic or ornamental objects. There is evidence that Neanderthals deliberately buried their dead and occasionally even marked their graves with offerings, such as flowers. No other primates, and no earlier human species, had ever practiced this sophisticated and symbolic behavior.108 109 110

Homo sapiens

Around 300,000 years ago, the African branch of Homo heidelbergensis evolved into Homo sapiens, i.e., into us humans111. Homo sapiens have smaller teeth than their predecessors. As a consequence of bipedalism, human females have narrower birth canals. Consequently, childbirth is more difficult and dangerous than in most mammals, especially given the larger head size of human babies compared to other primates. For this reason, human females give birth when the baby is still premature (when compared to other mammal babies). This has two important consequences91: First, humans need to take care of their babies much more than other mammals. This is part of the reason for the complex social structures (families, tribes, societies) that we have built. Second, human brains can still be shaped considerably even after birth — through education and socialization. This education is absorbed, and can be passed down to the next generation — much like genes. This is one of the mechanisms that allowed religions and belief systems to take hold.

Biologically speaking, Homo sapiens generally have a larger fore-brain than their predecessors, so that the brain sits above rather than behind the eyes. The brain volume increased to an average of 1.350 liters — roughly three times the size of the brain of a chimpanzee112. Relative to body mass, brain mass was slightly bigger than in the Neanderthals113. The relatively larger brain with a particularly well-developed neocortex, prefrontal cortex and temporal lobes enabled high levels of abstract reasoning, problem solving, sociality, and culture through social learning. The presence of modern human vocal tracts sometime between 100,000 and 50,000 years ago marked the appearance of fully human speech114.

Around 100,000 years ago, some individuals of Homo sapiens started emigrating from Africa. The successors of these migrants arrived in Asia (70,000 years ago), Australia (60,000 years ago), Europe (45,000 years ago), and the Americas (15,000 years ago)115. In this process, they encountered the other descendants of their ancestors: the Neanderthals. The humans were thus confronted with other humanoids that were stronger than themselves. We do not know whether the species fought, lived alongside each other, or mixed in other ways. We do know, however, that humans and Neanderthals interbred: Up to 2% of human genetic material outside of Africa is from the Neanderthals. After this encounter, only the Homo sapiens prevailed.110

How Homo sapiens spread out of AfricaCC0 NordNordWest, adapted

Paintings in the Chauvet Cave in FranceCC-BY-SA Thomas T.

Items of personal adornment such as beads and pendants emerged starting from 90,000 years ago — evidence that humans had progressed from merely trying to survive and were now concerned with their appearance. Cave art began to be produced about 40,000 years ago in Europe and Australia. Most of the art depicts animals (shown in the picture), but potentially also spiritual beings. Portable artwork, such as carved statuettes, first appeared about 35,000 to 40,000 years ago in Europe. The first evidence of clothing appears around 30,000 years ago in the form of needles and buttons. Musical instruments such as flutes and whistles dating to 30,000 years ago have been found in Europe. Shelters were constructed starting from 20,000 years ago. At that time, clans consisted of between 25 and 100 members. Around 11,000 years ago humans began to domesticate plants and animals — although wild foods still remained important in the diet.116 The species also controlled fire and started cooking their food. Cooking food maked it more easily digestible, thus allowing humans to spend less time chewing the food. It may also have contributed to shorter intestinal tracts, and thus to less energy consumption in that organ91.

From 3,000 BCE on, the first states developed in Mesopotamia, Egypt’s Nile Valley, the Indus Valley, China, and the East African Highlands117. Military forces were formed for protection, and government bureaucracies for administration. Writing was developed independently around 3,200 BCE in Mesopotamia and Egypt, around 1,200 BCE in China and around 400 BCE in Mesoamerica118. States cooperated and competed for resources — in some cases waging wars. Around 1,000 BCE, some states, such as Persia, India, China, Rome, and Greece, developed through conquest into the first expansive empires.

Influential religions, such as Judaism, originating in West Asia, and Hinduism, originating in South Asia, also rose to prominence at this time. Later, inventions such as the press, and advances in astronomy, mathematics, philosophy, and metallurgy helped shape daily life. The Scientific Revolution in the 17th century, the Enlightenment in the 18th century, and the Industrial Revolution in the 18th and 19th centuries promoted major innovations in science, government, and technology. With the advent of the Information Age at the end of the 20th century, modern humans live in a world that has become increasingly globalized and interconnected. The life expectancy has grown from around 30 years to around 80 years in some countries. Today, there are 8 billion individuals of the species Homo sapiens — this is us humans.

That said, the evolution of humans continues to this day. For example, Europeans have evolved a tolerance for dairy products into adulthood, whereas people in China and much of Africa generally have not119. Skin color evolves, too: People in warm climates are often dark skinned, because dark skin is less volatile to sunburn. Light skin pigmentation, in contrast, protects against depletion of vitamin D, which requires sunlight to make.120 To this day, mutations cause degenerations and disabilities. Illnesses develop and sometimes die out as humans develop resistance to them. In this way, humans are not actually the crown of creation, but rather one of the many species that evolved and that continue to evolve.

Complexity

Emergence

We now leave the topic of Evolution behind us and focus on the natural world as it is now. We observe that nature offers a stunning range of shapes, patterns, regularities, and organization — and often these are very beautiful. Where do these shapes and patterns come from; how did nature “organize herself”? In many instances, the process behind these patterns is emergence. Emergence is the development of particular patterns, properties, or behaviors in parts of complex systems that happen only when the parts of the system interact, and that the parts do not have on their own121. Interestingly, emergence does not require central coordination. We look at two examples here.

Our first example are snowflakes. How come they are so very regular, symmetric, and beautiful structures (see picture)? It turns out that every snowflake begins with a tiny heart of ice, created when a droplet of water in a cloud freezes around a microscopic dust particle. Next, the seed crystal starts to capture molecules of water vapor that are floating near it. They freeze onto the crystal and cause it to grow. This growth is shaped by two processes, faceting and branching. Faceting is the uniform growth all around the current structure. In this phase, each water molecule grabs on to as many other molecules as possible. This results in six smooth facets. (If you start laying coins on a table, each touching as many other coins as possible, you will end up with a similar hexagon-shaped pattern.) Depending on the temperature and the humidity, the snowflake can then switch to branching mode. In this mode, water vapor accumulates on each of the six corners instead. What starts out as a small bump on each corner soon becomes a larger bump, and then the beginning of an entire branch of ice. Each snowflake is the result of repeated switching back and forth between faceting and branching.

How does each new crystal element “know” whether it is in branching mode or faceting mode? The answer is that the same physical and chemical conditions apply simultaneously at all points of the snowflake. If the snowflake is in a certain temperature, then each arm will grow in branching mode. This is not because one arm would talk to the other, but simply because this temperature is the same at all points of the snowflake. When the snowflake is in another temperature, the entire flake will be in faceting mode.

Now if the physical and chemical conditions lead to symmetrical snowflakes, why is each individual snowflake different from the rest? The answer is that, in its journey to the ground, a snowflake will pass through different heights at different temperatures. The snowflake may also be blown up again into higher areas, so that temperature is not necessarily monotonously increasing. Each temperature dictates whether the snowflake is in branching mode or in faceting mode. In this way, the sequence of temperatures and the time that the snowflake spends in each temperature determines the shape of the flake.122

Other crystals grow in a comparable manner. All of these processes are driven by purely local reactions: An individual crystal does not “know” how the others attach. It just attaches to its neighbor. There is also no central authority that tells each crystal where to attach. Each crystal just attaches where the chemical properties allow it to. Thus, we have a phenomenon where local behavior without central coordination leads to the growth of complex, symmetric, and beautiful structures.

Shapes generated by L-SystemsCC0 SolKoll

Plants grow in a similar way. Each plant cell “sees” only its immediate neighbors. Depending on where these neighbors are, the cell replicates in a particular manner. If every cell does this, and all the new cells do this again, the resulting structure becomes symmetric and ordered. This process can be described by L-Systems. An L-System can be seen as a rule that says how to grow a single point into a small shape. This rule is applied to an initial point, and then to all points of the resulting shape, and so on. In the biological world, cells can follow such a rule. This single local rule is applied over and over again, and finally yields a global shape. L-systems can generate many plant forms of nature (see picture). Again, a very simple local mechanism gives rise to a complex global structure.123

Anything can happen, and it usually does.
Amy Winehouse

Simulating emergence

A cellular automaton with the rule “Color a cell if exactly one of the three cells above is colored”.

Emergence is the rise of complex patterns from simple components. We can also simulate the emergence of structure on a computer. This is often done by cellular automata. A cellular automaton looks like a checker board (shown in the illustration). In the basic version, each cell can be either colored or white, and initially all fields are white. We start at the top of the checkboard, and color some random cells in the first row (in the figure, this is just one cell). Then, we proceed to the second row. A set of rules tells us how to color the second row. A rule can for example say: If exactly one of the three cells above are colored, then the cell shall be colored, too (shown in red). Such rules can depend only on the neighboring cells in the previous row. This is a very simple mechanism, which we can imagine happening also in nature: One protein can do one particular thing depending on what its neighbors do, or one ant does one particular thing depending on what its colleagues do. This process is then iterated (always with the same rules) down the checkboard.124

Shapes generated by cellular automata. Note the plant shapes at the top in the middle, and the snowflakes in the middle.CC-BY-SA Steven Wolfram

The surprising thing is now that, depending on the choice of rules, very complex and beautiful patterns emerge (shown in the illustration). With very simple rules, we can create the patterns of the fur of a tiger124, the shape of a fern plant, the shape of a snowflake (if we start from the center), the currents of fluids, the form of snakes, the shape of leaves, or the pigmentation of animals. In each case, the rule is very simple: It is just an instruction to color one single cell depending on its neighbors. There are only finitely many of these rules, and we can even enumerate all possible sets of rules. The results, however, can be highly complex and beautiful. This shows that the application of local rules, where every cell looks just at its neighbors, can lead to global patterns.

Complex behavior

We have seen that a local process can lead to global organization. So far, we have looked only at static shapes. We will now look at dynamic behavior that emerges from the behavior of smaller units.

In the animal world, one example of such dynamic behavior is how ants find the shortest path to a food source. Initially, the ants just stroll randomly around their nest. When one ant finds food, it brings a piece of this food back to the nest. While doing so, it leaves a trail of pheromones, i.e., chemical substances. Other ants that find these pheromones will follow them, and thus also find the food. Different ants will take different paths to and from the nest. However, an ant will generally prefer to walk where it can smell the pheromones. The pheromones also become weaker with time. Now something very interesting happens: If there are two paths to the food, a shorter and a longer one, and each is followed by the same number of ants, then the ants on the shorter path will bring back the food much faster. Thus, their pheromone trail will be much fresher. This means that other ants are more likely to choose this path. Since these ants also leave a trail of pheromones, the shorter path will accumulate even more pheromones. Thus, even more ants will follow it. In the end, all ants wind up following the shortest path to the food. Here, a complex global problem (finding the shortest path between two points) was solved optimally by simple local behavior.125 In a similar way, ants use pheromones during house hunting, for recruitment to battlegrounds, to guide the building of tunnels, to inform individuals about their travel direction, and to measure the size of potential nest cavities126.

Crucially, these procedures do not require central coordination. The queen ant does not give orders or tell the ants what to do. Instead, each ant reacts to stimuli in the form of chemical scent from larvae, other ants, intruders, food and buildup of waste, and leaves behind a chemical trail. The trail in turn provides a stimulus to other ants. Each ant is an autonomous unit that reacts depending only on its local environment and the genetically encoded rules for its variety of ant. Ants are extremely simple organisms, with limited memory or intelligence, and yet collectively engage in seemingly intelligent behavior without the need for any planning, control, or even direct communication between them.127

Another example of complex behavior in the animal world is swarming. Swarming is the collective movement of similar organisms in a larger structure. Birds, for example, form swarms, as do fish and insects. From an evolutionary perspective, swarming has several benefits for the participating organisms. First, it can be more efficient to move in a swarm than to move alone. For example, drones that swarm conserve up to 70% of the energy they would need to fly alone128. Second, a swarm makes it harder for a predator to single out an individual prey. Any swarm member that stands out in appearance will be preferentially targeted by predators.129 Hence, fish prefer to swarm with individuals that resemble them (or, more precisely: Those fish that did not have such a preference were eliminated and could not pass on their habit).

Now how do swarms form? It turns out that swarming can be simulated by 3 simple rules130 :

move in the same direction as your neighbors;
remain close to your neighbors; and
avoid collisions with your neighbors.

If every individual organism just follows these three principles, swarming behavior emerges. It has been shown that the organisms often consider only the closest 6 to 8 neighboring organisms131 132. Thus, the complex macro process of swarming is governed by very local principles.

Simulating complex behavior

Just like elementary processes can give rise to complex patterns, they can also give rise to complex behavior. Such behavior can also be simulated by cellular automata. If we allow the rules for cellular automata to recolor a cell that has already been colored before, then the checkboard becomes dynamic.

An example of Conway’s Game of Life

One of the most famous examples of a dynamic cellular automaton is Conway’s Game of Life, a system devised by British mathematician John Horton Conway 133. In this automaton, every cell is either alive (i.e., black) or dead (white). In the beginning, we initialize the cells randomly as either alive or dead. Each cell interacts with the eight neighbors that surround it. At each step in time, the following transitions occur:

Any live cell with fewer than two live neighbors dies, as if caused by under-population.
Any live cell with two or three live neighbors lives on to the next generation.
Any live cell with more than three live neighbours dies, as if by overcrowding.
Any dead cell with exactly three live neighbours becomes a live cell, as if by reproduction.

If this process is iterated, very complex dynamics occur. Depending on the initial configuration, we can generate reproduction, static behavior, oscillations (where the same shape periodically reappears), and complex interactions, where one shape moves to disrupt another shape. All of this happens only based on local behavior. Each cell just lives or dies depending on its neighbors — it does not “know” that it is part of a complex periodic system. This shows again that local simple behavior can lead to complex global behavior.

American computer scientist Edward Fredkin developed a variation of Conway’s Game of Life that has an interesting property: It can reproduce any given shape. For this to work, the checkerboard is first initialized with the shape that we want to reproduce. Then, the automaton applies a simple rule: A cell is alive if and only if an odd number of its neighbors are alive. When we run this rule, it will recreate the initial shape after a few iterations — whatever it was. Once the shape has been duplicated, we can continue applying the rule, and the shape will be duplicated again, and so forth. Thus, even if each cell is “aware” of only its immediate surroundings, the cells can still accomplish a complex task such as the replication of an arbitrary shape.134

Predictability

We have seen that local processes can lead to global patterns and organized behavior. Each of these processes is deterministic. If nature just proceeds by small deterministic steps, does that mean that the result is predictable? In particular, if humans really consist just of cells that follow simple processes, are human actions predictable?

These are difficult questions to answer. We first observe that organized local behavior does not always lead to organized global behavior. It can also lead to very chaotic global behavior. To see this, consider again the cellular automata. These automata can draw very beautiful patterns on the checkboard, but they can also create entirely “random” chaotic patterns that show no regularity or organization whatsoever. They are just arbitrary dots of black and white. Thus, local organization does not necessarily lead to global organization124.

Second, since a rule can generate very random-looking patterns, it is not always easy to say whether any given pattern is actually randomly generated (without a rule) or whether it is the result of a rule that produces random looking results. Truly random patterns and organized patterns often look indistinguishable124. Thus, given any phenomenon of the real world, it may be hard or even impossible to say whether it was generated by a local process or not.

Finally, some processes are so complicated that it is impossible to describe them by a mathematical function. That is, there is no method that determines the outcome of the process after n steps upfront, without actually executing these n steps. The only way to discover what happens after the 100,000th step is to run all steps from 1 to 100,000 and to see what happens. In the language of nature, this means that the only way to find out what happens in the future is to simulate the local processes of nature into the future. Since nature is very complex, such a simulation would likely not be able to run much faster than nature itself. Thus, the only way to find out what will happen in the future may be to wait and see what will happen. In this sense, nature is unpredictable — and this includes human actions.

Who can say where the road goes?
Where the day flows?
Only time...
And who can say if your love grows
As your heart chose?
Only time...
Enya in “Only Time”

The unpredictable future

The white triangle seems to be disappearing as we go down in the process. Will it die out completely, or will it re-appear? CC-BY-SA Steven Wolfram in “A New Kind of Science”

We have seen that we can construct cases where the only way to predict an event is to wait until it happens. Yet even if we have the time to just wait and see, we may still be unable to solve some of the grand mysteries of life. Consider again a cellular automaton. When its rule is applied to color each successive line of the checkerboard, some shapes may occur repeatedly (for example, the white triangle shown in the figure occurs in several places). These shapes may re-occur in later steps, or they may never occur again. In the picture, the white triangle appears several times at the top of the figure, but then disappears. Now consider the question whether the triangle has died out, i.e., will never occur again. To answer this question, we could run the automaton and see whether the pattern returns. But even if we did not see the pattern return, that would not prove that it disappeared forever. It could reappear at any future step. The only way to find out whether the triangle ever returns is to run the automaton forever. In fact we can prove mathematically that certain questions are undecidable, i.e., it is impossible to make a decision without running the automaton forever. Translated to the case of nature, this means that even if we know the processes that govern nature, and even if we have enough time to observe what happens, we may still be unable to decide whether a given event will ever happen or not. If quantum physics has it right, then there may even be a factor of true randomness in nature, in the sense that identical physical circumstances can lead, at least in principle, to different outcomes. So the bottom line is that there are things that we cannot predict.

A simple example makes this clear. Assume that it were possible to predict that there will be a revolution in a certain country. Then the government of that country would likely do everything to prevent that revolution from happening (hand out cash to its citizens, reinforce the security services, or call elections). As a result, the revolution would most likely not happen. Thus, the prediction would turn out to be wrong. This is an example of a level-two chaotic system, where the predictions that we make about a state can actually alter that state91. It is therefore impossible to predict all events of the future.

Nobody knows what I'm going to do.
American President Donald Trump, referring presumably also to himself

Free will

We have seen that humans are just a collection of cells that have evolved from simpler life forms. If everything is just atoms, then human actions, as well as human thinking, is determined by chemical reactions in the brain and in the body . How then can humans have free will — in the sense of the power to make decisions that are not determined by the laws of nature?

This is a difficult and hotly debated question in the philosophical and scientific communities. One possible interpretation is that free will in the sense of “the ability to take decisions that are not determined by the laws of nature” does not exist. There is no little man, no “homunculus”, in the brain that is the real arbiter of our decisions, and that lights up the neurons correspondingly. There is just the neurons, and these work according to the laws of nature. Thus, free will, as we ordinarily understand it, is probably an illusion135. This is a position known as hard determinism. Whatever humans do or think is the consequence of the chemical reactions in their brain, and they are bound by these reactions. To see this, take the next thought that comes to your mind — any thought. Did you consciously take the decision to think that thought? Certainly not. This thought just came91.

This is a scary insight: It implies that we do not actually control our life in the way we think we do. Everything is determined by physical and chemical processes. Thus, it seems that it is not the self that is making decisions, but that human action is merely the consequence of chemical processes. The self is just left to watch (and imagine it is controlling that action). However, this is probably the wrong way to look at it. It might be more accurate to say that the self is identical to these processes. Thus, the self “makes decisions” — but does so according to the laws of nature.

What does this mean for everyday life? Interestingly, not much. No matter the absence of free will, we still have fears and desires. As we will argue later , we were selected by Evolution to fear death, and to desire food, warmth, safety, human contact, avoidance of suffering for ourselves and for others, and some form of recognition by other people. We were also selected to use our brain (consciously or not) to act towards these desires. Put these two together, and you get a being that acts to achieve certain things — a human.

Does this mean that we can predict what a human will think or want? Interestingly, that is not the case. We have seen that there are things that we can provably not predict, and there are other things that are so complex to predict that predicting them would amount to waiting until they happen. Human thinking is likely one of them124. In other words: Even if human thought and action is determined by local processes, it may still be impossible to predict what a human will think or do. This is why it remains useful to think of humans as if they had free will. We discuss this perspective in detail in the Chapter on the Meaning of Life and the Chapter on Morality.

There is the worry that to reject free will is to render all of life pointless: Why would you bother with anything if it has all long since been determined? The answer is that you will bother because you are a human, and that is what humans do. Even if you decide, as part of a little intellectual exercise, that you are going to sit around and do nothing because you have concluded that you have no free will, you are eventually going to get up and make yourself a sandwich. And if you don’t, you’ve got bigger problems than philosophy can fix.
Joshua Greene and Jonathan Cohen

Consciousness

This chapter has argued that humans are just complex machines that consist of chemical and physical components. This hypothesis has given rise to a problem known as the hard problem of consciousness: If humans consist just of inanimate matter, how can they have subjective experiences (called qualia in the philosophical jargon). Assume for example that we build a robot that resembles a human in every aspect, down to the level of neurons (what is known as a zombie in the branch of philosophy that studies the mind). Then would that robot feel pain and joy in the same way as humans do?

In the view of this book, the answer is that it probably would. There is no reason why a system that is physically identical to a human should be in any way different from a human. From all we can tell, qualia are not unique to humans: Dogs, for example, clearly feel pain and joy as well. Qualia can also be present to different degrees. A human, for example, has around 100 billion neurons. A dog has just 2 billion. Hence, a dog cannot feel the satisfaction of a scientific discovery as a human can, but there is some evidence that it can, for example, appreciate music136. A frog has just 16 million neurons, and it probably cannot appreciate music, while it clearly feels pain. A pond snail has just 11,000 neurons, and yet it also shows signs of distress when it is hurt. A roundworm has just 302 neurons, and its entire brain has been mapped 137. With these 302 neurons, the worm feeds, finds a mate, and reproduces. To what degree it experiences pleasure in these activities is anyone’s guess, but these data points suggest that qualia are a phenomenon that appears gradually with more brain power. Human embryos, too, seem to develop qualia gradually: While a fertilized human egg certainly does not have feelings, the fetus develops more and more sensory capabilities over the course of the pregnancy and becomes a baby that is perfectly capable of feelings and subjective experiences. In this light, qualia seem of the same nature as other emerged phenomena.

The question is then what makes us conscious beings -– as opposed to pond snails and dogs. The answer offered in these pages is that it probably comes again from the considerable complexity of the human brain. 100 billion neurons are enough not just to process sensory input, but also to build abstract concepts from them. Based on what we perceive, we build concepts such as “dogs”, “music”, “cuteness”, or “pleasure”. In the terminology of this book, these concepts are auxiliary notions. In the terminology of the Predictive Processing Model (a particular way to model the human brain in cognitive and computational neuroscience, which bears close resemblance to the theory of truth of this book), these concepts correspond to latent variables. These are intermediate representations that the brain builds in order to better predict sensory impressions. The human brain now has access not just to the sensory impressions themselves, but also to the latent variables that it has built on top of them. It is this capacity to build such variables, to reflect on them, and to perceive this reflection which we commonly call consciousness. And yet, not all that happens in the brain is accessible in the form of latent variables. Much of what happens in the brain is merely the low-level processing of signals. It could well be that this opaque combination of low-level processing and consciously accessible latent variables leads humans to infer that they are home to puzzling “qualitative states”138.

Questions

What has all of this to do with atheism?

This chapter has described how the Universe and life came about from a scientific point of view. Now how does this relate to atheism?

Atheism is the disbelief in supernatural beings. As such, atheism excludes the belief that the Earth and life were created by gods. Atheism does not tell us, however, what atheists believe about the formation of life and the Universe. Atheism is just disbelief in gods and does not preclude or prescribe any other belief about the Universe (or about anything else, for that matter). Different atheists will have different views on this topic.

However, a popular view among atheists is that science is the best method to answer the questions of life and the Universe. This is also the stance of Humanism, the particular brand of atheism advocated in this book. What science says on these questions is what this chapter outlined in the preceding sections. Thus, the preceding sections will likely appeal to a large number of atheists as a reasonable view on the formation and operation of the Universe.

How can you believe in science?

Looking for a proof of evolution? You're sitting on it! CC-BY-SA BodyParts3D

Humanists believe that science is the best way to gather knowledge about the physical world. However, most Humanists do not even know all the theories of science (and maybe no single person does). So, how can this belief in science be justified?

Humanists do not believe every single theory of science. They do not incorporate the entire scientific literature in their belief system. Nobody can do that. They just believe that that science is the best method to learn about the physical world. Now why is that? It is because scientific theories have a number of properties:

They are grounded in observations, i.e., they always predict perceptions from perceptions. Since they are grounded, they are falsifiable.
They are systematically subjected to attempts to prove them wrong. Theories that produce false predictions are rejected, leaving only those that make true predictions.
They have to make a large number of true predictions before they are accepted into the scientific literature. Thus, scientific theories are validated, and usually even testable.

Thus, science is basically a systematic search for theories that make true predictions. In the terms of this book, science is thus tantamount to a systematic search for the truth. Of course, science cannot guarantee that a theory will make true predictions in eternity, i.e., it cannot prove that a theory is part of the truth. However, it aims for the best possible approximation of the truth. This holds regardless of the actual content of a particular theory: If a theory has been tested, verified, re-tested, and always found to make correct predictions, then the theory is a good approximation of truth no matter what it is about. Since science does exactly this, Humanists believe that science discovers the truth.

Many people object to the scientific method. And yet, even these people use the fruits of science in their everyday life. For example, people use plastic every day. It would be impossible to produce plastic the way we do if the theory of chemical reactions were false. And it is this theory of chemical reactions that gives us not just plastic, but also our understanding of the early Universe. Likewise, it would be impossible to produce aspirin, acetaminophen, and ibuprofen if the theories of molecular biology were wrong. And these theories explain not just how these medications work, but also how proteins are constructed from DNA. Or consider Einstein’s theory of relativity: This theory is needed to make GPS satellites work — and we use GPS satellites every day for the navigation systems of our cars and the geo-location on our mobile phones. Thus, we validate Einstein’s theory every minute of our lives. And it is the very same theory that informs us about the size of the Universe.

Science is not the truth.
It is a way to find the truth.
The Candid Atheist

Science has not answered everything!

This book has elaborated on several aspects of life and the Universe that science can explain. However, there are numerous holes in the story. There are species we have not discovered, stars that we do not know about, and proteins that we have not mapped. On the metaphysical side, we do not know what was before the Big Bang (if anything), we do not know where the Universe is going, and we do not know how the human brain and mind work. Since all these questions are unsolved, why do people still put so much faith in science?

The first answer is that, while science has not discovered everything, what it has discovered is validated and useful. Thus, even though science may have treated only tiny bits of the big questions, these bits are at least safe to believe in. One can know something without knowing everything.

Second, even if science has not discovered everything, it has at least separated what we know from what we don’t know. It has established that certain questions do not yet have answers. This too is helpful, because it can prevent us from believing in answers that have been made up. We elaborate on this in the Chapter on the God of Gaps.

Finally, the parts that we know are growing at breakneck speed. Until 1000 years ago, we had not the slightest idea how the Universe was shaped, how life evolved, or how cells work. Until 300 years ago, we did not know about cells, proteins, bacteria, the galaxies, and Evolution. Until 10 years ago, we had a pretty good understanding of life and the Universe, but crucial bits were still missing. Today, we can trace nearly the entire history of the Universe from the first nano-seconds after the Big Bang until today. Ever new bits and pieces are added as this book is being written. Thus, even though the picture science offers may never be complete, it gets more and more complete with every year that passes.

That one thing is missing shall not prevent us from enjoying the others.
Jane Austin

Science cannot answer everything!

We can argue that a focus on scientific explanations is in fact a reduction of the scope of human thinking, because there are things that are inherently outside science.

This book subscribes to a notion of truth that is based on perceptions. Anything that explains or predicts perceptions is recognized as valuable. These can be perceptions in the physical sense (such as what you see or hear), but they can also be psychological perceptions such as feelings, desires, and states of mind. Anything that can predict these perceptions is welcome. Thus, the theory of truth presented in this book goes beyond physics and biology, and extends to other sciences such as sociology and psychology, and even to simple commonsense reasoning. For example, we know that sincere appreciation makes people happy, that fear makes people irrational, and that a person who prays will feel calmer. These are validated theories, and hence a step towards the truth. They are just as valuable as the theories that explain life and the Universe.

Then there are theories that have never predicted any human perceptions. These are the material of stories and myths. They can provide inspiration or entertainment, and thus they have a role in human culture . However, they should not be confused with truth.

It is those who know so little about science who so positively assert that this or that problem will never be solved by it.
Charles Darwin, rephrased

How do you explain the paranormal?

Many people are convinced that paranormal activities are happening all around us: levitation, miraculous healing, or communication with the dead. How do we explain these activities in a purely atheist world view?

On an atheist view, paranormal activities do not exist. This is because, despite ubiquitous recording devices, worldwide communication, and extremely well-developed scientific processes, no single credible, confirmable evidence has ever been put forth of all these paranormal activities. All we get are blurry photographs, doctored images, and unreliable testimonies. These are not enough to convince an atheist of the paranormal. We discuss this stance in detail in the Chapter on Proofs for God.

Now contrast this with the miracles that science produces:

One such miracle are methods that provably cure and even eliminate illnesses. For exampe, smallpox was once considered an invincible illness — and yet science eradicated it. Science offered a cure not just for one particular patient in one remote corner of civilization but for all of humankind. That can be considered a real miracle.
Another miracle are magical rituals that let you do telepathy with a loved one. This telepathy works not only for a specially trained magician, but for everybody. All that is needed is a small magical tool called a mobile phone.
Finally, science offer miraculous techniques for levitation. In religious or mystical world views, levitation (or walking on water) works only for the prophets or gurus of one particular religion, and only under specific circumstances. The levitation that science delivers, in contrast, works for everybody, and allows arbitrary people to cover huge distances across the surface of the Earth in just hours. All that is needed is a special vehicle called a plane.

Different from the religious or mystical miracles, these miracles are out there for everybody to see. They actually continuously make our lives better. That is more than we can say of any religious miracle. Thus, if miracles convince you to believe in something, then you have all the more reason to believe in science.

Science is like magic, but for real.
Anonymous

Are humans just apes?

Fossils of humans in their different stages of evolutionary development
in the Melbourne Museum of Science, Australia

The idea that humans are just more developed primitive apes is not a very flattering one to some, and as a result the idea is continuously being challenged. Is it really believable that we evolved from apes?

It turns out that we do not have much choice in our answer. If we look at the fossil record, we see fossils of different types of apes. These fossils exist –- we cannot just say that they don’t (see picture). These fossils can be dated. They have belonged to a species. Once you have established that the fossils belong to a species, you have essentially conceded the point: There existed different species, which resemble humans more and more as time progressed. The most recent fossils belong to our species.

If different experiments give you the same result,
it is no longer subject to your opinion.
Neil de Grasse Tyson

Are some species better than others?

Some fish have developed human-like hands, and walk on the sea ground rather than swim.CC-BY Rick Stuart-Smith / Reef Life Survey

The theory of Evolution says that species evolve, and that those that fit the environment better will outnumber those that don’t. This makes it sound as if some species were “generally better” than others. In particular, it sounds as if humans were “better” than other species

In fact, the theory of Evolution makes no such claim. It just says that those species who are better adapted will outnumber the others. Here, “better adapted” can mean anything that increases the likelihood of survival: being faster, smarter, or larger — but also smaller or more resilient. Pigeons, for example, are perfectly adapted to the environment of modern cities: They are extremely resilient to pollution, can eat almost everything, and reproduce very actively. In this respect, they are much better adapted to life in the cities than humans. It may well be that humans will one day exterminate themselves through pollution or war, while pigeons, ants, cockroaches, and rats survive. Thus, humans are not “generally better” than pigeons. On the contrary, the theory of Evolution says that humans are a species just like all the others. It was religion that came up with the theory that humans would be special.

Which came first, the chicken or the egg? The answer is the egg, but it was not from a chicken.
David Fastovsky and David Weishampel

Is Evolution falsifiable?

This book makes much out of the concept of falsifiability. So the question arises whether the theory of Evolution can be falsified.

It turns out that it can. All it would take to falsify Evolution is to find any fossil that does not fit into the Tree of Life. As British-born scientist John Burdon Sanderson Haldane observed, fossil rabbits in the Precambrian would disprove Evolution 139. So far, however, we have never found a fossil that would break the principle of Evolution.

The theory of Evolution also says that gene mutations are passed on through the generations of species. This means that any of the following would prove the theory of Evolution wrong140:

If it could be shown that organisms with identical DNA have different genetic traits.
If it could be shown that when mutations do occur, they are not passed down through the generations.
If it could be shown that although mutations are passed down, no mutation could produce the sort of phenotypic changes that drive natural selection.
If it could be shown that selection or environmental pressures do not favor the reproductive success of better adapted individuals.
If it could be shown that even though selection or environmental pressures favor the reproductive success of better adapted individuals, “better adapted individuals” (at any one time) are not shown to change into other species.

However, we have found none of these counter-indications so far.

Evolution is just a theory!

The theory of Evolution is called a “theory”. Doesn’t this already show that it’s not a fact?

Scientists use the word “theory” much in the sense that this book uses it: A theory is a set of rules that explain and predict the phenomena of nature. The theory is assumed to be true if (1) it is falsifiable, (2) it is applicable, and (3) it makes only true predictions. It is an even better theory if (4) it is testable and (5) it compresses information. As it so happens, all of this is the case for the theory of Evolution:

The theory is falsifiable.
The theory has made individual predictions already.
The theory is validated through the fossil record, paleogenetics, and the oddities of evolution.
The theory is testable.
The theory is compressive, because it explains properties of the entire fossil record with a single rule.

In fact, the theory accurately explains what we observe, and predicts what we will observe. This is more than any religious theory can say of itself. Thus, we have every reason to believe that the theory of Evolution is true.

For this, it does not matter whether we call Evolution a “theory” or a “hobblenock”. What matters is that it accurately describes reality.

Now scientists still call it a “theory” and not a “fact”. This is because they are ready to abandon it if it ever makes a false prediction. Again, this is more than any religious system can say of itself. In fact, all generalizations in science are mere theories. For example, the theory of gravity is almost certainly true, but still called a theory. This is because it could one day make a wrong prediction. It’s just that it never has. And it is the same with the theory of Evolution.

The difference between a miracle and a fact is exactly the difference between a mermaid and a seal.
Mark Twain

God did it!

One alternative explanation for the genesis of the Universe, the Earth, and life is a supernatural one: “If something exists, then God created it”.

We discuss this explanation in detail in the Chapter on the God of Gaps. Here, we just note that this theory cannot be a true in the sense of this book for the following reasons:

It cannot be falsified. There is nothing that a believer would accept as a proof that God did not create a particular thing. This means that we can come up with arbitrarily many contradictory supernatural theories, which also explain the birth of the Universe. This is indeed what people do.
The theory is not applicable, because it does not make any perceptible predictions whatsoever. It is for this reason that theologians have never ever come up with a correct prediction about this world that could not have been made by science.
The theory makes assumptions (such as the existence of God) for which there is no evidence.

Apart from that, the theory does not compress information. All that the supernatural explanation can say about this world is “It is like that because God made it that way”. This, however, does not tell us anything more than what we knew anyway. Therefore, the theory has no explanatory power.

You cannot see Evolution!

Opponents of the theory of Evolution can argue that the theory is too abstract and hypothesizes only about the past. They hold that we have never witnessed Evolution during our lifetime.

However, we can actually see the effects of Evolution also in our lifetime. British evolutionary biologists Peter and Rosemary Grant have studied how the body and beak size of Galápagos finches changes in response to changes in the food supply, driven by natural selection. This happened over several decades — slowly, for sure, but fast enough to study it in real time.141

The claim that different species may come into existence is harder to observe. And yet we can see this happening as well142:

Populations of periwinkles are evolving elaborate and different penises, which prevents them mating with other populations of snail, isolating them into different species.
The Mimulus peregrinus flower is one of the youngest recorded, appearing less than 140 years ago.
In the mid-1900s another new flower, Senecio cambrensis, naturally speciated in North Wales in the United Kingdom, while around the same time two species of flower, Tragopogon mirus and Tragopogon miscellus, appeared in Washington State in the United States.
In the latter part of the 20th Century, the flower species Cardamine schulzii appeared in Switzerland.
The Senecio eboracensis flower evolved into a new species in the past 40 to 50 years.

Thus, as predicted by the theory of Evolution, new species do in fact appear.

You can criticize Evolution for making strange predictions about the real world.
Note, though, that religion has yet to make any at all.
The Candid Atheist

God created the Universe to look old

Science tells us that the Universe is 14 billion years old. Certain interpretations of the Bible tell us that the Universe is 6000 years old. One proposed solution to this contradiction is that God created the Universe 6000 years ago, but that he made everything look as if it were 14 billion years old.

The attentive reader will have noticed that any hypothesis about faked evidence is unfalsifiable: We would never be able to show that the evidence we see was faked. This means that the hypothesis is meaningless: If we assume that the evidence was faked, we cannot draw any conclusion from it. We are as wise as before. Furthermore, we can come up with arbitrary other theories of faked evidence which contradict the first theory. It is just as possible as that the Universe was created 10 minutes ago, but we are all under the illusion it is much older. None of these theories can be proven wrong. This all just confirms that unfalsifiable theories are not admissible in rational discourse.

The Atheist Bible, next chapter: Morality

The Universe

The Earth

The Sun

The Universe

The Big Bang

Before the Big Bang

The birth of the Sun and the Earth

The age of the Earth

Life

Life

Chemical reactions

The formation of molecules

Nucleotides

Chance

RNA self-replication

Protocells

Protocell division

Mutation

Early life

Darwinism

Protein synthesis

The evolution of cells

Locomotion

Intention

Multicellular organisms

Evolution

Evolution

The fossil record

Paleogenetics

The timeline of Evolution

The Tree of Life

Extinction

Oddities of evolution

Artificial selection

Humans

The evolution of humans

Humans

Ardipithecus ramidus (“Ardi”)

Australopithecus afarensis (“Lucy”)

Homo habilis

Homo erectus

Homo heidelbergensis

Neanderthals

Homo sapiens

Complexity

Emergence

Simulating emergence

Complex behavior

Simulating complex behavior

Predictability

The unpredictable future

Free will

Consciousness

Questions

What has all of this to do with atheism?

How can you believe in science?

Science has not answered everything!

Science cannot answer everything!

How do you explain the paranormal?

Are humans just apes?

Are some species better than others?

Is Evolution falsifiable?

Evolution is just a theory!

God did it!

You cannot see Evolution!

God created the Universe to look old

References