CC-BY Fabian M. Suchanek

The Universe

The Earth

The Earth is spherical CC0 NASA
We call “the Earth” the planet on which humans reside (i.e., on which we perceive ourselves). The Earth is spherical, taking the form of a huge ball. Evidence for this claim is as follows:
  1. The Earth appears as a disc on photographs taken from space regardless of the vantage point. Also, the shadow of the Earth on the Moon during a lunar eclipse is always a circle.
  2. When we move away from the surface of the Earth, we can see more and more of the sky. The rate of change as altitude increases is the same in all directions and at all locations on the Earth.
  3. It is possible to circumnavigate the world – that is, to travel around the world and return to where you started.
These statements provide evidence for the hypothesis that the Earth is round. This hypothesis can then explain the following facts:
  1. The sun is lower in the sky as you travel towards the poles. For example, when traveling northward, stars such as Polaris, the north star, are higher in the sky, whereas other bright stars such as Canopus, visible in Egypt, disappear from the sky.
  2. The length of daylight varies more between summer and winter the farther you are from the equator.
  3. The times reported for lunar eclipses (which are seen simultaneously) are many hours later in places like India than Europe. Local times are confirmed later by travel using chronometers and telegraphic communication.
  4. North of the Tropic of the Cancer, the shadow of the Sun never points South. South of the Tropic of Capricorn, the shadow never points North.
We have thus found evidence for a spherical Earth. We have also found that the hypothesis of the spherical Earth makes correct predictions. Hence we assume that the Earth is spherical.
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.

The Sun

We observe that there are other things in space than just Earth. We can for example see the Sun and the Moon. We have the theory that if we can see something, then this something has physical existence, and hence we assume that the Sun and the Moon exist physically.

Mars traces a loop in the sky © Tunç Tezel, with permission
People first believed that the Sun revolved around the Earth. This theory, however, predicted certain things that do not coincide with our 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 contradicts the geocentric theory. It was one of the factors that prompted Galileo Galilei to doubt that theory. .

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. This can 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. Thus, one of the predictions of the heliocentric theory turned out true. In fact, all predictions of that theory have turned out true to date, including solar eclipses, lunar eclipses, and the shape of the moon at different times of the month. The theory was thus validated, and we assume it to be true.
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 Spinning Earth

The Earth revolves around the Sun with one turn per year. It also spins around its own axis, with one turn per day.
We have come to the conclusion that the Earth revolves around its own axis. This is why we have day and night: When our part of the Earth faces the Sun, we have daylight, but when we turn away from the Sun, we enter into the night. The axis of the Earth is slightly tilted with respect to the axis of the movement around the Sun. In summer, the northern hemisphere is tilted towards the Sun. Hence, it spends longer in the illuminated half of the ball, and the days are longer. In Winter, the northern hemisphere is tilted away, and it spends more time during night. The opposite is true for the southern hemisphere. At the poles, the story is different. In June, the northern pole is entirely in the illuminated part of the ball, and hence the Sun never sets, while the southern pole is in long darkness. In December, the opposite is true.

In summer, the northern hemisphere is tilted towards the Sun. Hence, the Sun rays arrive almost vertically. This is why the Sun appears high in the sky during the summer months in the northern hemisphere, and why it is so warm – because it receives much more energy per square meter. In winter, the northern hemisphere is tilted away from the Sun and the Sun appears low in the sky. During the winter months the northern hemisphere is colder because receives less energy per square meter due to the surface being at an angle to the Sun rays. At the Equator, the effects are minimal, because the Sun rays arrive nearly vertically throughout the year. Hence, there is nothing like the equivalent of winter at the Equator. Thus, this theory offers not just true predictions, but also a useful compression of different natural phenomena.

You might wonder why we do not feel the spinning of the Earth. This is because the atmosphere moves with us. When you are in an airplane and you close your eyes, you do not feel that you are moving at 1000 km per hour. You do not even feel when the plane flies in a curve. The same is true for our journey on Earth.

There is however one way to measure the effect of the spin: At the equator the centrifugal force caused by the Earth spinning is greater than at the poles. Hence, we are just a tiny bit heavier at the poles. Since gravity remains the dominant force, this change is small (a difference in 0.3% of your weight). But it is still measurable.

The Sun, with all the planets revolving around it, can still ripen a bunch of grapes — as if it had nothing else in the Universe to do.
Galileo Galilei (ascribed)

The Universe

There are not just the Earth and the Sun in the Universe. There are other planets and stars. These objects emit or reflect light that we can see. We can even estimate their distance to our planet. This can be calculated 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,” i.e. within 300 light years of the Earth).

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 spectra 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. 2

In recent times, additional technology has become available: We can emit radio waves and measure how they are reflected by celestial bodies. We can launch satellites and have them send back data. We can even send people to space and have them take pictures.

These techniques have led to the following conclusions: the Earth orbits the Sun at a distance of 150 million kilometers. The light of the Sun needs 8 minutes to reach us. We know that there are more planets orbiting the Sun than just Earth. The farthest objects orbiting the Sun are around 50 times farther from the Sun than Earth. To reach these objects orbiting in what is known as the Kuiper belt (Pluto is located there), the light from the Sun needs around 7 hours to travel. The Sun’s field of gravity reaches even farther than the Kuiper belt, giving way to that of surrounding stars around 2 light years from the Sun. This area makes up the Solar System.

The Solar System is just one of many such systems. Each system revolves around a star. The Solar System and its neighboring systems span a few hundred light years. This neighborhood is embedded in the Milky Way — our galaxy. A galaxy is a collection of star systems like the Solar System. The Milky Way spans a gigantic distance of 100,000 light years. This means that even if we could travel at the speed of light, we would need half the time that humans have existed on the planet Earth to cross it. The Milky Way has between 200 and 400 billion stars like our Sun, so there are roughly 50 stars for every person on Earth.

The Milky Way is located in the “Local Group”, which spans some 10 million light years. This group lives in the Virgo Supercluster, which spans 100 million light years. The observable universe is made up of many such superclusters. It is around 100 billion light years across. This means that if a star at the fringes of the observable universe dies, it would take 50 billion years to notice 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

The Doppler effect
We all have experienced the Doppler effect: 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 (known as red shift). Since light travels extremely fast, these effects are only visible when the light-emitting body moves away from us at an extremely high speed. We know roughly what the color of stars should be, because we know which color the nuclear reactions in them produce to emit the light. Now here is the surprise: All stars are slightly more red than they should be. This means that they are all moving away from Earth at the speed of billions of kilometers per hour. This holds no matter where we look in the universe.

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 Edwin Hubble and his colleagues made this observation, the hypothesis of the expanding universe has been confirmed by a large number of other observations. Among them include 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 point or compressed ball of matter. If this is true, then this single point must have been very dense. This theory is commonly known as the “Big Bang theory”. Based on how fast the stars are moving away from us, the “big bang” must have been roughly 14 billion years ago. 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 they have come up with theories to explain the composition of quarks, electrons, atoms, and molecules. These theories are continuously being developed, confirmed, rejected, and adjusted, as is usual in science. We can even replicate the conditions near the beginning of the expansion of the universe in large particle accelerators. Therefore, the theory of the Big Bang is currently accepted as the best theory we have about the birth of the universe — although this may change as more evidence comes to light.

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, parallel universes, or the halt of time.

The pausing of time is not completely illogical. To see this, consider Albert Einstein’s relativity theory. This theory is a set of rules that 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 it. Their clocks have to be continuously adjusted in order to be in sync with the clocks on Earth. 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 have entailed that time did not move at all. Then the question of “before” would not make any sense.

Still, this leaves open the question of “why” the Big Bang happened. The problem with science is that it can only propose 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.

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 (paraphrased)

Birth of the Sun and the Earth

The current scientific hypothesis is that the Big Bang produced a large amount of 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 Sun. The resulting compression heated the center, and this caused the start of nuclear fusion. This is a process in which two hydrogen atoms are forced so close together that their nuclei meet. The nuclei resist being forced together because they are all charged positively. If they do meet, they fuse together into a helium nucleus, releasing a large amount of energy in the form of heat. Fusion like this can be repeated in the laboratory, as Mark Oliphant showed in 1932. It is also the same principle that hydrogen bombs use. The Sun fuses 620m tons of hydrogen each second.

How the early Earth might have looked CC BY 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. Still, the Earth was very hot – so hot that the metals in the debris melted and fell to the center of the Earth. Over time the outer layer cooled down and formed a crust. This process gave the Earth its layered structure. The inner core of the Earth is solid. It consists primarily of an iron-nickel alloy and is approximately 5000 °C. Its size is roughly 70% of the moon . The inner core is wrapped in the outer core, a liquid mix of iron and nickel with a temperature of about 4000 °C. The outer core is not under enough pressure to become a solid. The outer layers of the Earth are cooler, and hence again solid.

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 to water and formed the oceans. 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.

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, 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: see 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). 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 8000 years ago. Thus, the Earth must have existed at least 8000 years ago.

Scientists have also developed much more sophisticated methods of dating objects. The most common is so-called radiometric dating: Many 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 1.25 billion years. Aragon 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 Aragon, it must have come from radioactive decay. The ratio of Aragon to Potassium can then be used to estimate the age of the mineral. By using these radioactive “clocks”, the oldest rock yet found on Earth (from western Greenland) is dated at 3.9 billion years old. Some moon rock samples brought back to earth by astronauts have been dated at 4.5 billion years. Analysis of these along with other geologic and astronomical evidence led scientists to conclude that the solar system was formed about 4.6 billion years ago. Thus, the scientific estimate of the age of the Earth is larger than the one given by the Bible by a factor of a million. 2

Life

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, and exchange substances with the environment. This applies both to complex life forms (such as mammals and humans) and to more simple ones (such as bacteria, algae, 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 forms of life that we can still see are fossils of some microorganisms on a sandstone discovered in Western Australia. These are 3.5 billion years old. These organisms consisted of only a few cells . These evolved into multicellular organisms, into algae, then into plants, fish, land animals, and finally into humans. Humans have been around for a relatively short amount of time. For comparison: The time it took for life to start is 1000 times longer than the time that humanity has existed.

We will now trace the process by which evolution lead to the creation of humanity 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 attract each other by their electrical charge, connecting and forming a molecule of two hydrogens. 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 sometimes abbreviated as “H2”, because it consists of 2 hydrogen atoms.

The chemical reaction that forms water
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 on the right.

In general, any process that transforms molecules or atoms into other molecules or atoms is called a chemical reaction . The 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 can also require the presence of other molecules (so-called catalyzers or reagents) to proceed .

For this book, a chemical reaction is a theory that says that if certain chemical substances are brought together, and if energy and reagents or catalyzers are present as required, then a new chemical substance will form. These theories have validated themselves zillions of times and are widely testable, i.e., they can be reproduced in the laboratory. Chemical reactions also happen in real life all around us (for example, when wood burns, when soap cleans out stains, or when we cook meals).

Molecules

The Miller Urey Experiment CC-BY-SA YassineMrabet
We have seen that atoms can plug together to form molecules. 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. Lightening released heat energy, leading to many chemical reactions. Molecules were randomly assembled by chemical reactions out of the primordial atomic soup. 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 Stanley Miller and Harold Urey showed in 1953. For this purpose, they simulated the early atmosphere of Earth by a gas mixture of methane (Ch3), 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 over 20 different forms of molecules had been created, many of which are basic components of living beings. Later analyses of the original experimental material showed that even more molecules had formed than those reported by Urey and Miller. Today, we know that the circumstances of the early Earth were probably different from what Urey and Miller assumed. If this experiment is repeated with gas mixtures that resemble more what we think was the original atmosphere of the Earth, then even more diverse molecules would be produced.

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 the very same molecules formed. Interestingly, such molecules have since also been found on a comet 3.

Proteins

An Amino Acid
The Milley Urey Experiment produced a variety of molecules. Among these were amino acids. Amino acids are molecules that consist of one amine (-NH2) and one carboxylic acid (-COOH), along with a side‐chain of atoms that is specific to each amino acid. The figure on the right shows the generic form of an amino acid, where the side‐chain is abbreviated by “R”.

These molecules can plug together to form peptides . This works through a chemical reaction that creates a bond between the carboxyl group of one amino acid and the amino group of another by shedding atoms from either the amine or carboxylic acid that come together to form H2O (water) as shown here:

Connecting two amino acids to a (small) peptide CC0 V8rik

Longer peptides are called proteins. Both peptides and proteins can perform a number of functions, if put together with other peptides, proteins, or molecules. For example, they 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. All of this happens through chemical reactions. We will describe a few of these in what follows.

RNA

The Milley Urey Experiment produced a variety of larger molecules. Some of these molecules were amino acids, which can give rise to proteins. Later variants of the experiment were able to produce nucleobases (also called nitrogenous bases). These are molecules that make up our DNA. There are 5 nucleous 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 nucleotide. 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:

An RNA Molecule
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 Ribonucleic acid molecule (RNA). Often, the nucleotides are denoted by their initial letters, so that an RNA molecule could be, e.g., GGGAUUGUUCAA. In reality, the backbone of an RNA molecule is not straight. Bases at different points on the chain attract each other, so that the RNA forms loops (like that shown on the right). This gives RNA molecules a complex 3-dimensional structure.

RNA chains can be assembled in the laboratory. This gives us a theory, which says that if nucleotides are brought together, they form an RNA chain. This theory is testable, and has indeed been validated in the laboratory.

Chance

We have seen that certain molecules can come together to form RNA chains — the precursor of DNA. However, only certain RNA sequences have biological functions (the others are just random sequences). Now the question is how likely it is that one particular RNA sequence got assembled by chance on the early Earth.

There are several such calculations on the Web (e.g., 4, 5, or the ), but I could not find one that I would find convincing. Many of the variables in the game are just unknown. I can just show how such calculations usually proceed and which factors are usually taken into account (for this purpose, I am using rather arbitrary quantities).

Let’s say that we want to grow one particular RNA sequence, which contains 50 bases (50 is a reasonable number for an 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 (DNA uses thymine instead of RNA’s uracil). 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 10^50 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 10^50 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 10^25 molecules of water. Today’s oceans have a volume of roughly 10^21 litres of water. This means we had (and have) 10^46 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 references in 4). Then this gives us 10^40 chains that could start in parallel. So we have a chance of 1 in 10^10 that one of them is the one we’re looking for. 10^10 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.

Several additional factors come into play: Chains may be destroyed while they grow. Conditions may change during these millions of years, making it harder or easier to assemble the chains. For example, clay can speed up the formation of RNA molecules significantly 6. The charged clay surface attracts the nucleotides and the increased local concentration of nucleotides leads to more chemical reactions 7. 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 10^22 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 10^16 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).

Be that as it may, we do know that we can build chains of amino acids. Experiments in the laboratory show that we can build chains of 55 amino acids in 1-2 weeks 4 to form peptides. This gives us a testable theory for amino acids. Experiments show that RNA chains of up to 50 nucleotides can indeed be assembled in a very similar way.

Replication

How RNA replication might work according to 8
We have seen that RNA molecules can assemble by chance. It is assumed that some of these RNA molecules have the ability to replicate themselves. The figure on the right shows how this could work.

Thus, there could be RNA chains that are able to reproduce themselves. This is just one hypothesis. There are several laboratories in the world that work on self-replicating RNA chains, but as of now, none has succeeded in creating an RNA molecule that can replicate itself from individual nucleobases. As of 2016, the state of the art is:

Cells

A liposome CC0 LadyofHats
So far, we have discussed how RNA molecules form. It is assumed that some of them are able to replicate. 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 hydrophile, i.e., it is chemically attracted to water. The tail of the molecule is hydrophobe, 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 water. Such a structure is called a vesicle, or liposome (shown on the right).

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 liposomes that contain RNA chains 6. The theory is that these constellations would have formed the first protocells .

Liposomes are relatively stable in their shape, but the individual fatty acids that compose them move around a lot. This entails that the liposome walls are permeable to certain molecules. Depending on their size, some peptides 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.

Cell 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. Such a vesicle is called a cell. This process can likewise be replicated in the laboratory. The cell walls are permeable to certain molecules, and so nucleotides can enter and exit the cell. Some RNA strands are able to replicate themselves. They wait until the right molecule floats into the cell, and add it to the copy of themselves that they are currently assembling. When the copy is ready, it splits off.

Cell division.
In red: vesicles.
In blue: RNA strands.
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 its cell body. In this way, vesicles grow continuously when they come in contact with other vesicles or “single” fatty acids. When cells grow, their surface area increases, but their volume does not. This gives the cell a prolate shape (as shown in the figure on the right), and makes it unstable. Eventually, it will break apart into two pieces. Now remember that we had an RNA strand and its copy floating around in the cell. If the two RNA strands happen to be in the same part of the splitting cell, then they will continue sharing that cell. However, if the cell keeps splitting, then it is likely that at some point the strands will eventually end up in two different cells. We have witnessed cell replication and division.

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

Mutation

We have seen that cells can form and replicate. The cells contain RNA strands, and these can interact with the cell wall and with other molecules or peptides 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 cell wall. When this RNA strand replicates, all of its copies would also attach to the cell wall.

We can also imagine that an RNA strand has a sequence that binds to certain peptides. When such peptides float into the cell, the RNA strand would accumulate them. Certain types of peptides can bind to other types of peptides, so that one particular RNA strand can end up creating peptide structures in its cell. Certain peptides can interact with the wall of the cell, and either fortify it or disrupt it. If the RNA strand attracts such peptides, then the cell will behave very differently from other cells. 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, if the mutation fails to maintain the subsequence that attaches to the cell wall, then the copy will lose this behavior. A mutation can also 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 peptides form, how RNA strands form, how cells form, and how cells divide and mutate. 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 to call something “life”:

Darwinism

We have now arrived at a point where we can introduce the principle of Darwinism. This principle says:
If there is an organism that can replicate with mutations, and if this process continues for a long time, then those mutations that ensure the most successful replication will prevail.
Let us take an example. Let’s suppose we have one RNA strand that curls up, and another RNA strand that takes the form of a long string (this example is made up). 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 its individuals. The strings, in contrast, will be reduced in 50 steps to 0 individuals. Thus, the curls prevailed. After 50 steps, there will be only curls.

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 evolution 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. The process of a changing and thereby surviving population is called evolution.

Darwinism was first developed by the British scientist Charles Darwinism in his 1859 book “On the Origin of Species” .

Ribosomes

At this stage of the early Earth, we have a number of cells 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.

Over time, cells would become more complex. Some cells would start interacting with proteins. Some RNA strands would attach certain proteins to their cell wall, others would collect certain proteins in the interior of the cell, and again others would use proteins to shape the cell. Thus, the population of cells with proteins would become much more varied. Eventually, one random mutation would create a protein called a ribosome . Ribosomes can assemble other proteins from RNA strands. The ribosome maps each sequence of 3 nucleotides in the RNA strand to one amino acid in the protein. Thus, the RNA can essentially dictate which proteins to create .

RNAs with a ribosome are able to create almost arbitrary proteins with arbitrary chemical properties and functions. These proteins can be free-floating or they can attach to each other. They can also be built so that they attach exactly to one particular other protein. This allows the cell to build up complex structures. It is as if the cell owned a 3D printer. The RNA encodes which proteins to produce and thus any copy of the RNA will build the same proteins. A sequence of nucleotides in a strand of RNA that fulfils such a function is called a gene. Genes determine the build-up and the operations of a cell.

From now on, we will no longer speak in terms of atoms or molecules, but in terms of proteins. The proteins in real cells consist of hundreds of amino acids. They take complex 3-dimensional forms, and they can have complex, yet well-defined interactions with other proteins. RNA strands can also be selectively modified in the laboratory so that cells produce certain proteins or inhibit others 13.

Evolution of cells

The cell wall of an e. coli baterium, colored CC-BY David Goodsell
Simple cells are just a vesicle plus an RNA. Later, ribosomes allowed cells to produce almost arbitrary proteins. 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, support RNA replication, or accelerate chemical reactions. Over time, they would replace the strands that did not have this capability. DNA strands evolved along similar lines as RNA. They fulfill similar functions as RNA strands, but are more stable and reproduce much more reliably. Hence, they eventually prevailed over RNA strands.

In this manner cells evolved into prokaryotes — simple single-celled beings. Prokaryotes continue to exist today. In fact, prokaryotes are the most diverse and abundant group of organisms on Earth and inhabit practically all environments where the temperature is below +140 °C. They are found in water, soil, air, animals’ gastrointestinal tracts, hot springs and even deep beneath the Earth’s crust in rocks. Practically all surfaces that have not been specially sterilized are covered by prokaryotes. The number of prokaryotes on Earth is estimated to be around five million trillion trillion, or 5×10^30, accounting for at least half the biomass on Earth.

Prokaryotes include bacteria, which can be seen under the microscope. They are a reasonably well-understood form of life. Many of the proteins in bacterium have been identified . They are proof that life can go on just by chemical reactions. Other types of single-celled life include fungi and algae. All of these are just collections of molecules that continuously react with each other. These continuous reactions are what is called “life”.

It might be surprising to see the complexity contained in a single cell. But the process of cell evolution did not happen overnight. Cells evolved over 2 billion years of time. This means that half of the time of the existence of Earth was needed just to get complex cells up and running.

Locomotion

Chemotaxis
A bacterium is a complex cell. 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 flagellum. 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 10,000 times per minute.

This process moves the bacterium forward — up to a speed of 17cm per hour. This does not seem like much but is 60 times the length of the cell per second. The speed of the process can be regulated by changing the concentration gradient and thus the flow of protons. 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.

Bacteria need glucose (a molecule) to power these motions. This is their food. Bacterium swim in liquids in which glucose is dissolved. The higher the concentration of glucose, the faster the chemical processes inside the bacterium can work. This means that bacteria with an ample supply of glucose can reproduce faster. The bacterium finds glucose as follows: It 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 glucose 13. 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 glucose . 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. The exact proteins involved in this process are catalogued here: 14.

It might seem close to unbelievable how such a complex mechanism evolved. However, remember that the DNA can encode and 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 others 15. All in all, the evolution from cells to bacteria took 1 billion years — 5 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. And yet the process 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 with no kind of thinking involved.

And yet we have a tendency to say that the bacterium “wants” to move towards the glucose. What we mean is: Moving towards the glucose is beneficial for the reproduction of the bacteria. Therefore, those bacteria that moved towards the glucose prevailed over those that did not. Hence, any bacterium that we see today is hardwired to show this behavior. The behavior is no more voluntary than water flowing down a river: Both processes are entirely driven by laws (one chemical and the other physical) and are predictable. Still, we have a tendency to say that the water “wants” to flow downhill.

Multicellular organisms

We have seen how cells evolved and how they became complex enough to become autonomous and self-moving organisms. The more complex organisms that we know consist of several cells. In particular, multicellular organisms consist of several types of cells, which each fulfill a particular function. The question is now how these came about.

Science has not yet found a conclusive answer to this question. All we know is that multicellularity evolved several times independently in several different organism species. Not all of these evolutionary paths led to functional organisms. There are several hypotheses as to how cells first started grouping together . The one that is considered most plausible is that multicellularity evolved from several cells of the same species that cling together. This may happen either because the cells fail to separate, or because separate cells of the same species attach to each other. Over time, the cells specialize: Some cells lose multi-functionality and “concentrate” on one particular functionality instead.

This process can be observed in dictyostelids. Dictyostelids are amoeba, 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, they aggregate to form a multicellular assembly, called a pseudoplasmodium, grex, or slug. The slug has a definite anterior and posterior, responds to light and temperature gradients, and has the ability to migrate . This composite organism then moves towards areas of higher food concentration. Different cells take different roles in this process, and so we have a truly multicellular organism.

The question is now how this multicellular organism reproduces. For this to happen, the organism must duplicate and ensure that all the different cells are formed in their respective places. The amoeba does this as follows: Under the correct circumstances, the slug matures and forms a sporocarp (fruiting body) with a stalk supporting one or more sori (balls of spores). These spores are inactive cells protected by resistant cell walls, and become new amoebae once food is available . In other words, the multicellular organism serves as a host for baby amoeba. These baby amoeba are independent unicellular beings. However, when they are released, they may cling together and form again a multicellular being, in which they specialize to take one particular function. Thus, the amoeba by themselves are a kind of “stem” cells for the multicellular organism.

Life cycle of a Dictyostelid CC-BY Hideshi, font-size adapted
This process is entirely chemical, which has been discovered and analyzed. When an amoeba is stressed, it sends out a Cyclic adenosine monophosphate (cAMP) molecule. When another amoeba detects this molecule, it moves towards the concentration of this molecule. This leads to an aggregation of amoeba. Each of these also starts sending out cAMP molecules, thus calling even more amoebas. The entire DNA of the dictyostelid amoeba has been mapped and published. It contains around 12,500 genes. The entire process of how this multicellular being replicates has been catalogued.

Evolution

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. In the form of a rule, the theory of evolution states:
For any species (contemporary or ancient, simple vesicles excluded), there is a previous species from which this species evolved through gradual mutation.
The 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. Living beings first evolved in water and later conquered the land. Gradually, the beings became more complex: fish, insects, dinosaurs, birds, and mammals all emerged. The figure below is a timeline that traces when major evolutionary events occurred.

The timeline of life CC0 LadyofHats

But how does evolution occur? The principle that governs this process is natural selection.

Natural Selection

According to natural selection, given a species that reproduces with mutations, the most beneficial mutations will prevail. This principle applies not just to cells but to any species. The following traits can play a role in the survival and evolution of a species:
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 his 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 evolution is when two teams play soccer on a field where the ground is slightly sloped towards one of the goals, with the net effect of the tilt favoring the team whose goal is on the upslope. 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 downslope 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.

This process is called natural selection. It is powerful enough to result in changes to an organism completely. A species can grow wings, develop fur, gain more brain mass, learn certain behaviors, or adapt to certain climates as a result of natural selection. This is the process of evolution.

The Tree of Life

The tree of life CC0 LadyofHats
The theory of evolution says that all beings evolved by gradual change from previous beings. This does not mean that there would be only one type of being, which gradually evolves as time passes. Instead, a group of individuals can evolve into a separate species of its own, leaving other groups to evolve differently. This occurs when one population becomes so different from another that they do not reproduce with them any more. When this process is mapped it yields a tree-like structure, in which a branch evolves and then splits into several branches. These branches in turn evolve and eventually split up again. This structure is called the “phylogenetic tree” or simply the “tree of life”.

The major branches (in terms of number of species) are not birds, mammals, and plants, but rather bacteria, archaea, and eucaryota. These life forms, which are mostly invisible to the naked eye, are highly diverse and extremely numerous. Indeed, it is estimated that bacteria and related life forms alone make up half of the biomass on our planet. This makes sense when you look at the timeline, as bacteria has had much more time to evolve than mammals, who are relative newcomers. Where there are divisions in branches, say between humans and birds, both species evolved independently of the other. The fact that they coexist today means that they are both equally well adapted to the environment of today.

Animals are in the branch of Eucaryota. In this branch, we find birds, insects, and mammals. Further up the branch of mammals we find humans. In the figure on the right, the root of the tree is in the middle. The branch of Eucaryota is on upper left (in pink), and humans are the second from the right. As you can (or can’t) see, humans are only a tiny fraction of the natural world of living creatures.

Evolution continues to this day and likely never will end. 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. Humans continue to evolve as well. For example, Europeans have evolved a tolerance for dairy products into adulthood, whereas people in China and most of Africa have not.

The fossil record

Fossil of a Kainops invius, around 400m years ago CC-BY-SA Moussa Direct Ltd.
The theory of evolution says that all living beings evolved gradually from previous beings. Why should we believe this theory? For the same reason we believe any theory: because it has made only true predictions so far. 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, and even skeletons. Fossils can also consist of the marks left by an organism, such as tracks or feces. Over time, scientists have found literally hundreds of thousands of fossils17. These include animal fossils, plant fossils, and also fossils of more basic life forms.

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. Fossils can also be dated, which allows us to determine how old they are. One of the techniques used to date fossils is radiometric dating. We date the rock layers above and below the fossil and thus estimate its age. We can also use nearby fossils with a known age to estimate its age.

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 actually say that we will find fossils of all species (some have not been found yet). It just says that if we do, its age will fall between less and more evolved species. This is a falsifiable and therefore testable theory. J.B.S. Haldane famously stated that “fossil rabbits in the Precambrian” would disprove evolution. So far, we have not found a fossil that would break the principle. This is a strong performance: we have discovered hundreds of thousands of fossils, which span 4 billion years. Not one has been found that contradicts the theory. 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, and scientists therefore assume the theory of evolution to be true. The more fossils that are found, 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

DNA is a sequence of nucleotides that determine the genetic behavior of an organism. DNA sequencing is the process of identifying these nucleotides. The DNA of a human contains 3 billion nucleotides, but with advances in science a human’s DNA as of 2021 can be sequenced in about 24 hours. The DNA of hundreds of other species have been completely sequenced, including all the species in the tree of life, meaning that we know exactly which genes these beings possess18.

Paleogenetics is the study of genes (DNA) in fossils. Since every cell of a living being carries its DNA, it can be recovered even from tiny fossil parts. However, since fossils are usually millions 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 around 5% is actually useable. Nevertheless, by overlaying parts of recovered DNA from different fossils, scientists can reconstruct larger parts of the DNA sequence. For example, the genome of Neandertal humans was sequenced in 2010.

Once the DNA of two individuals has been sequenced, their DNA can be compared. The closer the two individuals are on the tree of life, the more DNA they share. For example, a human baby and their mother differ only in roughly 1 out of 60 million genes. Any two humans differ in 1 out of 1000 genes. A human and a chimpanzee differ in 1 out of 100 genes, and so on. Since we often know which parts of the genome 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 their branching occurred in the tree of life .

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 not found a single fossil so far where the paleogenetic analysis has contradicted the theory of evolution.

Extinction

A Spinophorosaurus, 160 million years old, 13 meters long, in Agadez/Niger CC-BY Universidad Nacional de Educación a Distancia
The tree of life traces which species evolved from which other species. This does not mean that all species are still around. Some species have died out. Over the past 4 billion years, thousands of species have evolved only to become extinct a few million years later. The most prominent example are dinosaurs: they are species that evolved over time but then died off. In fact, 90% of all species that ever lived have became extinct 19.

Hundreds of other species have become extinct 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 extinction 20.

Other species became extinct before modern humans. The Neanderthals, for example, were a branch of humans that lived 250,000 years ago. They died out 200,000 years later. As predicted by the theory of evolution, a species that became extinct never re-appears.

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 the bison down, and in 1890 only 750 individuals remained. Yet the population recovered to several hundred thousand today. Similarly, the population of the northern elephant seal fell to about 30 individuals in the 1890s, but the population has since rebounded. 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

Given any population of species, the ones with beneficial traits have more success in finding food, surviving, and mating. They prevail and give their traits to their offspring, which over time leads to the species as a whole developing this trait.

It’s important to recognize that evolution is not a goal-oriented process. Mammals didn’t acquire feet so that they could run. Rather, it was the case that 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 prove this, we can look at mammals that have legs but do not use them: whales.

The evolution of whales
Whales live in the sea but evolved from land-based mammals that had developed legs. Then they started grazing in the sea and eventually moved fully to the oceans. But while they obviously no longer used their legs they kept them, though the process of evolution led to modern-day whales having small leg bones that do not protrude from the body (and thus provide no disadvantage). This process can be traced back through the fossil record, as we have found fossils of the intermediate stages.

Such structures are common in nature. They are called vestigial structures. The mole rat, for example, has eyes that are completely covered by a layer of skin. This means that the animal is blind . 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 this way, in the sense that we can actually put it into action.

In classroom settings there is not enough time to breed dogs and see evolution work, but it is possible to experiment with drosophila flies (search “drosophila evolution” on the Web). Drosophila are tiny flies that live on fruit and mature and reproduce very quickly. It is also easy to induce mutations by exposing them to radiation from a television screen. If individuals that develop abnormalities are selected to reproduce, very quickly a population of mutated flies can develop with more than 6 legs, with no wings, with 3 eyes, and so on. In this accelerated scenario the theory of evolution makes verifiable and testable predictions.

What is this? CC-BY-SA Warut Roonguthai
Artificial selection has been at work in some less obvious places, too. Have a look at the fruit seen on the right. 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 yellow. Why did this banana not evolve naturally? Because the human banana is unable to survive in the wild. It requires so much water that it can grow only in plantations. 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 around 5 million years ago.

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 Frenchmen while others became Englishmen. 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 Englishmen just because there are now Frenchmen. 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 chimpanzees 21.

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:
For every humanoid fossil, scientists determine its age, and its similarity to other fossils. Based on this, they either conclude 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:

Over time one branch of this evolutionary process came to dominate all other branches. This is the species to which we belong: Homo Sapiens.
Molecular evidence suggests that our common ancestor with chimpanzees lived, in Africa, between five and seven million years ago, say half a million generations ago. This is not long by evolutionary standards ... in your left hand you hold the right hand of your mother. In turn she holds the hand of her mother, your grandmother. Your grandmother holds her mother’s hand, and so on ... How far do we have to go until we reach our common ancestor with the chimpanzees? It is a surprisingly short way. Allowing one yard per person, we arrive at the ancestor we share with chimpanzees in under 500 kilometers. (That is the distance from Los Angeles to San Francisco, or from Paris to Amsterdam.)
Richard Dawkins in “Gaps in the Mind”

Ardipithecus ramidus (“Ardi”)

The skeleton of Ardi. Note the feet. CC-BY-SA Tobias Fluegel.
Ardipithecus ramidus (“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 4.4m 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 120 centimeters 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 20% of the brain size of a modern human, at 300 cm³ to 350 cm³. 22

Ardi cannot be a common ancestor of chimpanzees and humans. Chimpanzees’ feet are specialised for grasping trees. Ardi’s feet are better suited for walking because the middle of the foot is more stable, while a chimpanzee’s foot is more flexible . Thus, 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

A reconstruction of Lucy in the Smithsonian Museum of Natural History. CC-BY-SA Tim Evanson
The Australopithecus afarensis is an extinct species that is assumed to be the successor of Ardi and one of the ancestors of humans. The species lived between 3.9 and 2.9 million years ago in Africa. Like Ardi, members of Lucy’s species had reduced canine teeth, although they are still relatively larger than in modern humans. They also had a relatively small brain size (380cm³ - 430 cm³) 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 she could walk on two legs. Males of the species were most likely larger than females. 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 family groups, consisting of a single dominant male and a number of breeding females. Quite possibly, the species were the first to use stone tools.

The Lucy species later evolved into (or co-existed with) the Australopithecus africanus, which had a greater brain volume of about 420-510 cm³. Males may have been on average 140 cm in height and 40 kg in weight, and females 125 cm and 30 kg. These species were already biped, but could walk less efficiently than humans .

Homo habilis

How Homo habilis could have looked. GFDL Lillyundfreya.
Homo habilis is most likely a descendant of the Australopithecus species. Homo habilis lived around 2 million years ago in Africa. The species had a brain size of 550 cm³ to 687 cm³ — roughly half that of a modern human. These hominins were smaller than modern humans, on average standing no more than 1.3m, and weighting 32 kg. 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 23. The loss of body hair took place between 3 and 2 million years ago, in parallel with the development of full bipedalism.

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 . This is a crucial departure from previous species.

Homo Erectus

A reconstruction of Homo erectus (Homo ergaster) at the Sterkfontein Caves exhibition CC-BY flowcomm.
Around 2 million years ago, branches of Homo habilis gave rise to a humanoid species called Homo erectus. This species was about 145 - 185 cm tall, and had a brain size of 500-1200 cm³. Their weight ranged from 40-68 kg. 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 distances 24.

There is fossil evidence that this species cared for old and weak individuals. The species also made more complex tools than Homo habilis, the so-called Mode 2 (Acheulean) tools. These are symmetrically cut flint stones, which can be used as hand axes. Most importantly, Homo erectus was probably able to control fire. The species used hearths (campfires) for cooking food. It is currently unclear when the species started using fire, with the oldest undisputed evidence being traces of a campfire at Gesher Benot Ya’aqov in Israel, dated to about 700,000 years ago. Homo erectus was probably not able to make fire. Rather, they probably used the hot ashes or burning wood from a forest or grass fire, and then kept the fire or coals going for as long as possible by adding more wood and plant materials many times each day. Natural sources of animal fats and petrochemicals that burn could also have been used to keep and maintain fires. Fire would have helped the species to defend themselves against animals and to produce heat and light. .

It is generally assumed that Homo erectus was the first humanoid species to leave Africa, migrating to Asia. Fossils of Homo erectus have been found in places as far as China and Indonesia. (The African line of Homo erectus is sometimes called Homo ergaster, while the Asian line is sometimes called Homo erectus sensu stricto. It is currently debated whether the emigration led to the formation of two different species. (An emigration can take place in a few thousand years, while the evolution into a new species generally takes more than a hundred thousand years.)

The Asian line of Homo erectus came to colonize large parts of Asia, yet it seemed to have ceased to exist shortly before or after the arrival of humans. The last known population of Homo erectus is from the Indonesian island of Java around 100,000 years ago.

Homo Heidelbergensis

A reconstruction of Homo heidelbergensis at the Smithsonian Museum of Natural HistoryCC-BY-SA Tim Evanson.
The African line of Homo erectus, the Homo ergaster, evolved into a species called Homo heidelbergensis around 700,000 years ago. The Heidelbergensis face was already more human-like, with a vertical front and a broad frontal bone. The species was about 170 cm tall, and had a brain size of about 1200 cm³ — a significant increase over previous humanoid species. The species built dwellings out of wood and rock. Fire likely became an integral part of daily life around 400,000 years ago. 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. Remains of animals such as wild deer, horses, elephants, hippos, and rhinos with butchery marks on their bones have been found together at sites with Homo heidelbergensis fossils. The species may have been able to carry out coordinated hunting strategies, and similarly they seem to have had a higher dependence on meat 25.

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.

Neandertals

A reconstruction of a Neanderthal man in Neanderthal-Museum. Note the more 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). The Neanderthals evolved around 200,000 years ago. At this time, the North of Europe and Asia was covered with ice. It is estimated that there were about 70,000 Neanderthals at the peak of the population size. The fossils of about 500 individuals have been found. Neanderthals and modern humans share about 99.5% of their DNA.

Neanderthals had an average brain size of 1600 cm³ — larger than that of humans. They were also much stronger than humans. Otherwise Neanderthals were in many aspects very similar to humans. They developed tools and art and buried their dead. Stone tools discovered on the southern Ionian Greek islands suggest that Neanderthals were sailing the Mediterranean Sea as early as 110,000 years ago. An analysis of Neanderthal teeth found traces of cooked vegetable matter, meaning that the species controlled fire.

Homo sapiens

The African branch of Homo heidelbergensis evolved into Homo sapiens, i.e., into us humans. Homo sapiens have smaller teeth than their predecessors. They are also the only ape in which the female is fertile year-round, and in which no special signals of fertility are produced by the body, meaning that it is not possible for a male to determine when a female is in her fertile period. 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 consequences21: 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 babies 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 1350 cm³ — over twice the size of the brain of a chimpanzee or gorilla. The relatively larger brain with a particularly well-developed neocortex, prefrontal cortex and temporal lobes enables high levels of abstract reasoning, language, problem solving, sociality, and culture through social learning. The larynx and hyoid bone descended in the species, thus making speech possible.

There is evidence that Homo sapiens started wearing clothing roughly 100,000 years ago. Around that time, some individuals of Homo sapiens emigrated from Africa. The successors of these migrants arrived in Asia (70,000 years ago), Europe (40,000 years ago), and the Americas (15,000 years ago). 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 and yet probably possessed more primitive tools. 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.

How Homo sapiens spread out of AfricaCC0 NordNordWest
Paintings in the Chauvet Cave in France CC-BY-SA Thomas T.
Homo sapiens developed elements such as language, music and other cultural universals roughly 50,000 years ago. The species also started developing arts and manufacture. The first artifacts (little figurines) are dated around 40,000 years ago. The first cave paintings appeared 30,000 years ago (shown right). The species also controlled fire and started cooking their food. Cooking food makes 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 organ 21.

Until 10,000 years ago, Homo sapiens lived as hunter-gatherers. At this time, they started agriculture, domesticating plants and animals, and thus allowing for the growth of civilization. They also used metal tools. About 6,000 years ago, the first proto-states developed in Mesopotamia, Egypt’s Nile Valley and the Indus Valley. Military forces were formed for protection, and government bureaucracies for administration. Writing was developed around 5,000 years ago by the Sumerians. States cooperated and competed for resources – in some cases waging wars. Around 2,000 - 3,000 years ago, 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. Inventions such as the press, and advances in astronomy, mathematics, philosophy, and metallurgy helped shape daily life. The Scientific Revolution in the 17th century and the Industrial Revolution in the 18th-19th centuries promoted major innovations in transport, such as the railway and automobile; energy development, such as coal and electricity; and government, such as representative democracy and Communism. 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 7 billion individuals of the species Homo sapiens — this is us humans.

The evolution of humans continues today. For example, some branches of humans have developed the genes that allow adult humans to digest lactose (milk), while others did not. Illnesses develop and sometimes die out as humans develop resistance to them. Mutations cause degenerations and disabilities. Skin color evolves, as does genetic predisposition to particular weights and heights. People in warm climates are often relatively slender, tall and dark skinned, because dark skin is less volatile to sunburn. Light skin pigmentation protects against depletion of vitamin D, which requires sunlight to make. Due to practices of group endogamy (i.e., mating within the same group), similarities cluster locally around kin groups and lineages, or by national, ethnic, cultural and linguistic boundaries.

People are just fish plus time.

Complexity

Emergence

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 rise of complex structures from interactions between smaller entities that themselves do not exhibit these properties. Interestingly, emergence does not require central coordination. We look at two examples here.

A snowflake CC-BY-SA Alexey Kljatov
Our first example are snowflakes. How come they are so very regular, symmetric, and beautiful structures? As it turns out, snowflakes form from water dust roughly 3km above the ground. When the water dust freezes, it forms ice crystals. When other water dust particles collide with this ice crystal, they will also become ice and stick to the initial cluster. Due to the form of the water molecules, individual crystals can only stick together in very specific angles. This constraint makes any water crystal grow in hexagonal shapes, entailing that snowflakes have 6 arms, and every one of these 6 arms has again small arms that grow off at the same angle. The length of an arm is determined by an equilibrium of energy. For a certain surrounding temperature, there is a certain optimal length. When this length is reached, the arm splits in two smaller arms. As more crystals join, the snowflake grows accordingly in a symmetrical fashion.

How does each new crystal element “know” what shape the other crystals at the other arms chose? 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 to the specified length. 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. Add in that the crystals can only attach in one specific angle, and you get an identical process and hence an identical symmetrical shape at all points of the flake.

Now if the physical and chemical conditions lead to symmetrical snowflakes, why is each individual snowflake different from the rest? The answer again goes back to those conditions. Since snowflakes have higher density than air, they fall to the ground. In this journey, a snowflake will pass through different heights at different temperatures. The snowflake may also be blown up again into higher areas, so that the sequence of temperatures is not necessarily monotonously increasing. Each temperature entails a different optimal arm length for the crystal growth. Thus, if a snowflake falls through temperatures A, B, C, B, C, D, it will first form 6 arms of the length given by temperature A, then each arm will split into 2 arms of the length given by temperature B, then the arms split into arms of length C, length B again, length C, and length D. The sequence of temperatures and the time that the snowflake spends in each temperature determines the shape of the flake.

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-Systems CC0 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 we can see how a very simple local mechanism gives rise to a complex global structure.

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 on the right). 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 (see the illustration on the right 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.

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 in “A New Kind of Science”
The surprising thing is how, depending on the choice of rules, very complex and beautiful patterns emerge (shown on the right). With very simple rules, we can create the patterns of the fur of a tiger 26, 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 quite beautiful. This shows that the application of local rules, where every cell looks just at its neighbors, can lead to global patterns.

It is relatively simple to come up with a cellular automaton that is able to reproduce a given shape. This cellular automaton consists of a fixed set of rules for how to color the cells. When we draw any black-and-white shape on the checkboard and run these rules, the rules will then create a shape — whatever it is. Once the shape has been duplicated, we can continue applying the rules, 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 complex tasks such as the replication of an arbitrary shape.

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 dynamic behavior that emerges from local 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. Other ants that find these pheromones will follow them, and thus also find the food. Several ants will take several 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. In a similar way, ants routinely find the maximum distance from all colony entrances to dispose of dead bodies. With such mechanisms, a colony of ants achieves complex tasks such as constructing nests, taking care of their young, building bridges, and foraging for food.

Crucially, the solution to these problems does not require central coordination. The queen ant does not give direct orders and does not 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, which lack any memory or intelligence, and yet collectively engage in seemingly intelligent behavior without the need for any planning, control, or even direct communication between the agents. .

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, as a peloton of professional bicyclists illustrate, it is more efficient to move in a swarm than to move alone. For example, geese in a V-formation conserve between 12-20% of the energy they would need to fly alone. 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. Hence, fish prefer to swarm with individuals that resemble them. Swarms also improve the chances of an individual to find a mating partner.

Now how do swarms form? Researchers have studied this question through a variety of techniques. For example, they can film swarm behavior and try to model it by rules, they can modify an individual organism’s scope of vision, or they can introduce small robots that resemble the swarming organisms and observe the changes in behavior. It turns out that swarming is governed by 3 simple rules :

  1. Move in the same direction as your neighbors
  2. Remain close to your neighbors
  3. Avoid collisions with your neighbors
By every individual organism following just these three principles, swarming behavior emerges. It has been shown that the organisms often consider only around 6 neighboring organisms. 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 the British mathematician John Horton Conway. In this instance, every cell is either alive (= black) or dead (= white). In the beginning, we initialize the cells randomly as either alive or dead. Each cell interacts with its eight neighbors, which are just the cells that surround it. At each step in time, the following transitions occur: 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.

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 organization 26.

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 indistinguishable 26. 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.

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 and to extrapolate them to 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. Human actions are unpredictable in this sense as well.

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 the cellular automaton. When the rule is applied to color each successive line of the checkerboard, some shapes may occur repeatedly (e.g., the white triangle shown on the right 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 that would not prove that it disappears forever. It could reappear. The only way to find out whether the triangle ever returns is to run the automaton forever. In fact we can prove mathematically that it is impossible in certain cases to make a decision without running the automaton forever. The question is actually undecidable (in the information-theoretic sense of the word). This means that there cannot be a systematic way to find out in finite time whether a given pattern will die out or not. 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, 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 at the time the predicted revolution was on the horizon 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 state 21. It is therefore impossible to predict all events of the future.

This does not mean that it would be impossible in general to make any predictions. There are still lots of other cases where we can make a prediction. For example, we can imagine a very simple cellular automaton that just draws everything in black. Of course we can predict the future of this automaton. Or imagine that we throw a stone in the air. We can predict that this stone will fall back on Earth no matter all the theoretical results of undecidability.

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. Free will, as we ordinarily understand it, is probably an illusion 27. 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 came 21.

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. In this way, the activity of the brain gives rise to the actions of the human, which in turn impact her or his environment. There is thus no need for fatalism.

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 them 26. 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 27

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 (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, e.g., clearly feel pain and joy as well. Qualia can also be present to different degrees. A human, e.g., has 86 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, e.g., appreciate music. 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. 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. Human embryos, too, appear 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. 86 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 built 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” 28.

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 what you don’t know?

Looking for a proof of evolution? You're sitting on it! CC-BY-SA BodyParts3D
The theories about the universe and life in this book are quite complicated. Most atheists will not even know these theories. One might ask then why these theories are presented as an atheist view point?

First, not all atheists believe in science. The only thing that unites atheists is their disbelief in the supernatural. However, it is fair to say that probably a majority of those who are explicit about their atheism see science as the primary method to gain knowledge about this world. Humanists, in particular, see science as the best method to learn about the world.

However, this does not mean that these atheists incorporate the entire scientific literature in their belief system. Nobody can do that. It just means that they believe that science is the best method to learn about the physical world. You can believe in the utility of science without knowing all scientific theories.

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

How can you believe in science?

The theories about the universe and life in this book are quite complicated. Most atheists will not even know these theories. So why do people still believe in science? How can this belief be justified?

Scientific theories have a number of properties:

  1. Scientific theories are grounded in observations. Since they are grounded, they are falsifiable.
  2. Scientific theories are systematically subjected to attempts to prove them wrong. A theory that produces a false prediction is rejected.
  3. Scientific theories have to make a large number of true predictions before they are accepted into the scientific literature. Thus, scientific theories are applicable and validated. They are usually even testable and are verified in extensive experiments.
In short, science is actually tantamount to a systematic search for the truth as defined in this book: science searches for theories that make true predictions. 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, it would be impossible to produce plastic the way we do if the theory of chemical reactions were false. We use plastic every day. And it is this theory of chemical reactions that not just gives us plastic, but is also behind our understanding of the early universe. Likewise, the very same theory that explains how proteins are constructed from DNA also gives us modern medical drugs. Aspirin, acetaminophen, and ibuprofen are the fruit of molecular biology. In the same way, the theory that predicts the dilatation of time is not only at the heart of the theory about the size of the universe but also how GPS satellites work. They guide the navigation systems of our cars, locate us on a map on our mobile phones, and geotag the pictures we take with our digital camera. It is not possible to make use of such a satellite if (1) one does not know this theory or (2) the theory is false. This shows that the scientific method works. And it is the very same scientific method, and in large parts even the very same scientific theories, that explain life and the universe.

There’s nothing magical about science. It is simply a systematic way for carefully and thoroughly observing nature and using consistent logic to evaluate results. Which part of that exactly do you disagree with? Do you disagree with being thorough? Using careful observation? Being systematic? Or using consistent logic?
Steven Novella

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 science has not discovered everything, but 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.

Third, the parts that we know are growing at breakneck speed. Until 1000 years ago, people had not the slightest idea how the universe was shaped, how life evolved, or how cells work. 100 years ago, people knew about cells, proteins, bacteria, the galaxies, and evolution. 10 years ago, people 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. We can also trace the story of evolution from the atoms to humans. Many of the things that this book contains were not known at the turn of the millennium. New bits and pieces are added as this book is written. Thus, even though the picture science offers may never be complete, it gets more and more complete with every day that passes.
It is those who know little about science who so positively assert that this or that problem will never be solved by it.
Charles Darwin, paraphrased

Science cannot answer everything!

This book bases its explanations of life and the universe on science. We can argue that this focus 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. For example, feelings, desires, and states of mind are all perceptions. Anything that can predict these perceptions is welcome. Thus, the theory of truth presented in this book goes beyond physics and biology. It also extends to other sciences such as sociology and psychology, or 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. They are the material of stories and myths. These can provide inspiration or entertainment, and thus they have a role in human culture. However, they should not be confused with truth.

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 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. These are:

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

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. It is commonly pointed out that Evolution is nothing more than a theory, and that it is just one possible way to see things. Is it really believable that we evolved from apes?

It turns out that you do not have much choice. If you look at the fossil record, you will see fossils of different types of apes. These fossils exist – we cannot just say that they’re not (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: faster, smarter, 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 just species like all the others. It was religion that came up with the theory that humans would be special.

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 John Burdon Sanderson Haldane observed: Any fossil rabbits in the Precambrian would immediately disprove evolution. So far, we have never found any fossil that would break the principle.

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 wrong 29:

Charles Darwin made the case a little differently when he said, “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.” 29. Indeed, we have not found any 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 (1) it is testable and (2) it compresses information. As it so happens, all of this is the case for the theory of evolution:

  1. The theory is falsifiable.
  2. The theory has made individual predictions already.
  3. The theory is validated through the fossil record, paleogenetics, and the oddities of evolution.
  4. The theory is testable.
  5. The theory is compressive, because it explains the entire fossil record with a single rule.
Thus, we have every reason to believe that the theory of evolution is true. 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.

For this, it does not matter whether you 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 theories. For example, the theory of gravity is a theory. This is because it could be that one day it makes a wrong prediction. It’s just that it doesn’t. And it is the same with the theory of evolution.

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:

  1. 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 all explain the birth of the universe. This is indeed what people do.
  2. 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.
  3. 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. We have never witnessed how new species come into existence during our lifetime.

The theory of evolution makes some verifiable predictions that fall in our lifetime. We rely on them for the breeding of our food and domestic animals. The theory also makes falsifiable predictions on the types of fossils that we find. But perhaps more to the point, Peter and Rosemary Grant have studied how the body and beak size of Galápagos finches changes response to changes in the food supply, driven by natural selection. This happened fast enough in real time to study it .

The claim that different species may come into existence is harder to observe. And yet we can see this happening as well 30:

  1. populations of periwinkles are evolving elaborate and different penises, which prevents them mating with other populations of snail, isolating them into different species.
  2. The Mimulus peregrinus flower is one of the youngest recorded, appearing less than 140 years ago.
  3. In the mid-1900s another new flower, Senecio cambrensis, naturally speciated in North Wales in the UK, while around the same time two species of flower Tragopogon mirus and T. miscellus appeared in Washington State in the US.
  4. in the latter part of the 20th Century, the flower species Cardamine schulzii appeared in Switzerland.
  5. The Senecio eboracensis flower evolved into a new species in the past 40 to 50 years, being discovered in 1979 in York, England.

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 13.5 billion years old. Certain interpretations of the Bible tell us that the Universe is 6000 years old. One proposed solution to this is that God created the Universe 6000 years ago, but that he made everything look as if it were 13.5 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

References

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  2. Paul Tobin: “The Creation Myths”, in Rejection of Pascal’s Wager, 2000
  3. The Guardian: “Rosetta mission lander detects organic molecules on surface of comet”, 2014-11-18
  4. Ian Musgrave: “Lies, Damned Lies, Statistics, and Probability of Abiogenesis Calculations”, 1998
  5. Omnevivumexvivo: “The Truth About Abiogenesis And Probability”, 2011-10-12
  6. Discover Magazine: “What Came Before DNA?”, 2014-06
  7. Exploring Origins.org: “Nucleic Acids”, 2021-07-30
  8. A. R. Hernández and J. A. Piccirilli: “Chemical origins of life, Prebiotic RNA unstuck”, in Nature Chemistry, 2013-04-03
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  10. Holliger Lab: “Ribozyme-catalyzed transcription of an active ribozyme”, in Science, 2011
  11. Royal Society of Chemistry: “Chemists edge closer to recreating early life”, 2009-01-09
  12. Tracey A. Lincoln and Gerald F. Joyce: “Self-sustained Replication of an RNA Enzyme”, in Science, 2009-01-08
  13. Team Heidelberg: “Molecular Cloning”, 2008
  14. Seesandra V. Rajagopala et al: “The protein network of bacterial motility”, in Molecular Systems Biology, 2007
  15. Kathryn Applegate: “Bacterial Flagellum: Irreducibly Complex?”, 2010-07-20
  16. Karl Sims: “Evolving Virtual Creatures”, in SIGGRAPH, 1994
  17. Wikipedia: “List of transitional fossils”, 2021
  18. Wikipedia: “List of sequenced animal genomes”, 2021
  19. Neil deGrasse Tyson: “Intelligent Design is Stupid”, 2009-09-15
  20. IUCN: The IUCN Red List of Endangered Species, 2021-01-01
  21. Yuval Noah Harari: Sapiens: A Brief History of Humankind, 2014
  22. National Geographic: Oldest human skeleton, 2009-10-09
  23. Australian Museum: Homo habilis
  24. Smithsonian National Museum of Natural History: Homo erectus, 2021
  25. Smithsonian National Museum of Natural History: Homo heidelbergensis, 2021
  26. Steven Wolfram: New Kind of Science
  27. Joshua Greene and Jonathan Cohen: “For The Law, Neuroscience Changes Nothing And Everything”, in Oxford Handbook of Neuroethics, 2011
  28. Andy Clark: “Consciousness as Generative Entanglement”, in The Journal of Philosophy, 2019-12
  29. RationalWiki: “Falsifiability of evolution”, 2019-10-14
  30. BBC: Evolution - What the world’s youngest species can teach us, 2012-11-23