The Nature of Consciousness

Piero Scaruffi

(Copyright © 2013 Piero Scaruffi | Legal restrictions )
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These are excerpts and elaborations from my book "The Nature of Consciousness"


Origins: What Was Life?

We often forget that brains are first and foremost alive, and no convincing evidence has been presented so far that dead brains can think. As far as we know, minds are alive. As far as we know, life comes first.  If "thinking life" is a particular case of "life", then the same type of processes which are responsible for life may be responsible also for the mind.  And the mystery of the mind, or at least the mystery of the principle that underlies the mind, may have been solved a century ago by the most unlikely sleuth: the British biologist Charles Darwin.

Darwin never really explained what he wanted to explain (the origin of species), but he probably discovered the "type of process" that is responsible for life. He called it "evolution", today we call it "design without a designer", "emergence", "self-organization" and so forth. What it means is that properties may appear when a system reorganizes itself due to external constraints, due to the fact that it has to live and survive in this world.  This very simple principle may underlie as well the secret of thought. Darwin's theory of evolution is not about "survival of the fittest", Darwin's theory is about "design".

Life is defined by properties that occur in species as different as lions and bacteria. Mind would appear to be a property that differentiates humans from other living beings in a crucial way, but at closer inspection… animals do communicate, although they don't use our language; and animals do reason, although they don't use our logic; and animals do show emotions. What is truly unique about humans, other than the fact that we have developed more effective weapons to kill as many animals as we like?


Life As Maintenance

The British biologist Richard Dawkins gave this definition of life: living beings have to work to keep from eventually merging into their surroundings. That is the whole point of life.

There is a natural tendency towards merging seamlessly with the rest of nature.  We have to work in order to maintain our identity. When we stop working, we die: then we merge with our surroundings.

A living being is characterized by different values for all fundamental quantities, whether temperature or density, than its surroundings.

The living being has to perform work in order to maintain that "differential" that is ultimately the essence and the meaning of life.

When the living being dies, the differential rapidly disappears and the dead being slowly dissolves, as all quantities (temperature, density, electricity, etc) become those of the surroundings.

Our habits of eating and drinking are merely a way of working to sustain that differential, in terms of energy and matter.

Living beings are never in equilibrium with their surroundings, unless they are dead.

On the contrary, nonliving things, that cannot defend themselves from the forces of nature, that cannot work "against" nature, are condemned to live in a state of equilibrium with their surroundings.

There is no border for a mountain or a sea: they flow seamlessly into a plain or a beach, whereas there is a clear border between an animal and the forest or the river it inhabits.


The Dynamics of Life

What “being alive” means is easily characterized, as we have plenty of specimens to study: life is about growing and reproducing. A living organism is capable of using the environment (sun, water, minerals, other living organisms) in order to change its own shape and size, and it is capable of creating offspring of a similar kind. In technical terms, life has two aspects: metabolism and replication. Metabolism is the interaction with the environment that results in growth. Replication is the copying of information that results in reproduction. Metabolism affects proteins, replication affects nucleid acids.

The statement that "life is growing and reproducing" is convenient for studying life on this planet, life as we know it. But certainly it would be confusing if we met aliens who speak and feel emotions but do not need to eat or go to the restrooms, and never change shape. They are born adults and they die adults. They do not even reproduce: they are born out of a mineral. Their cells do not contain genetic material. They do not make children. Would that still be “life”?

Also, that definition is not what folk psychology uses to recognize a living thing. What is an animal? Very few people would reply "something that grows and reproduces". Most people would answer "something that moves spontaneously". The "folk" definition is interesting, because it already implies a mind.

At the same time, the folk definition does not discriminate in a crisp manner between animate and inanimate matter. A rock can also move. True, it requires a "force" to move it. But so is the case with animals: they also require a force, although it is a chemical rather than a mechanical force. Animals eat and process their food to produce the chemical force that makes them move. The difference between the stone and the animal is the kind of force and where it comes from.


The Laws Of Nature Revisited

How biology relates to the rest of the universe is less clear.

This universe exhibits an impressive spectrum of natural phenomena, some of which undergo spectacular mutations over macro or micro-time (long periods of time, or short periods of time). Life deserves a special status among them for the sheer quantity and quality of physical and chemical transformations that are involved. Nonetheless, ultimately life has to be just one of them.

Indirectly, it was Charles Darwin who started this train of thought, when he identified simple rules that Nature follows in determining how life proceeds over macro-time. While those “rules” greatly differ from the laws of Physics that (we think) govern the universe, they are natural laws of equal importance to the laws of electromagnetism or gravitation.

Why they differ so much from the others is a matter of debate. It could be that Darwin’s laws are gross approximations of laws that, when discovered, will bear striking resemblance to the laws of Physics; or, conversely, maybe the laws of Physics are gross approximations of laws that, when discovered, will bear striking resemblance to the laws of evolution; or maybe they are just two different levels of explanation, one set of laws applying only to the micro-world, the other set applying to the macro-world.

A key aspect of life is that all living systems are made of the same fundamental constituents, molecules that are capable of catalyzing (speeding up) chemical reactions. But these molecules cannot move and cannot grow. Still, when they are combined in systems, they grow and move. New properties emerge. The first new property is the ability to self-assemble, to join other molecules and form new structures which are in turn able to self-assemble, triggering a cycle that leads to cells, tissues, organs, bodies, and possibly, societies and ecosystems.

In order to approach the subject of “life” in a scientific manner, we first need to discriminate among the various meanings of that term. What we normally call “life” is actually three separate phenomena. Precisely, in nature we observe three levels of organization: the phylogenetic level, which concerns the evolution over time of the genetic programs within individuals and species (and therefore the evolution of species); the ontogenetic level, which concerns the developmental process (or “growth”) of a single multicellular organism; and the epigenetic level, which concerns the learning processes during an individual organism's lifetime (in particular, the nervous system, but also the immune system).

In other words, life occurs at three levels: organisms evolve into other organisms, each organism changes (or grows) from birth till death, and finally the behavior of each organism changes during its lifetime (the organism “learns”).

There are therefore two aspects to the word "life". Because of the way life evolved and came to be what it is today, life is both reproduction and metabolism: it is both information that survives from one individual to another ("genotype"), and information about the individual ("phenotype"). When we say that "ants are alive" and "I am alive" we mean two different things, even if we use the same word. To unify those two meanings it takes a theory that explains both life as reproduction and life as growth.


Design Without a Designer

In 1859 Darwin published "The Origin Of Species". His claim was simple: all existing organisms are the descendants of simpler ancestors that lived in the distant past, and the main force driving this evolution is natural selection by the environment. This is possible because living organisms reproduce and vary (make children that are slightly different than the parents). Natural selection “selects” the fittest children, and the process continues, generation after generation, causing evolution. Through this process of evolution, organisms acquire characteristics that make them more "fit" to survive in their environment (or better "adapted" to their environment).

Darwin based his theory of evolution on some hard facts. The population of every species can potentially grow exponentially in size. Most populations don't. Resources are limited. Individuals of all species are unique, each one slightly different from the other. Such individual differences are passed on to offspring. His conclusion was that variation (the random production of different individuals) and selection ("survival of the fittest") are two fundamental features of life on this planet and that, together, they can account for the evolution of species.

To visualize what is so special about Darwin's idea, imagine that you are in a quandary and the situation is very complex. You have two options: 1. You can spend days analyzing the situation and trying to find the best strategy to cope with it. Or 2. You can spend only a few minutes listing ten strategies, which are more or less random and all different one from the other. In the former case, you are still thinking. In the latter case, you start applying each of the strategies at the same time.  As you do so, some strategies turn out to be silly, others look promising.  You pursue the ones that are promising. For example, you try ten different (random) variations on each of the promising ones. Again, some will prove themselves just plain silly, but others will look even more promising. And so forth. By trial and error (case 2.), you will always be working with a few promising strategies and possibly with a few excellent ones. After a few days you may have found one or  more strategies that cope perfectly well with the situation.  In case 1., you will be without a strategy for as long as you are thinking. When you finally find the best strategy (assuming that you have enough experience and intelligence to find it at all), it may be too late.

In many situations, "design by trial and error" (case 2.) tends to be more efficient than "design by a designer" (case 1.).

So Darwin opted for "design without a designer": nature builds species which are better and better adapted and the strategy it employs is one of trial and error.

The idea of evolution established a new scientific paradigm that has probably been more influential than even Newton's Mechanics or Einstein's Relativity.

Basically, evolution takes advantage of the uncertainty left in the transmission of genes from one generation to another: the offspring is never an exact copy of the parents, there is room for variation. The environment (e.g., natural selection) indirectly “selects” which variations (and therefore which individuals) survive. And the cycle resumes. After enough generations have elapsed, the traits may have varied to the point that a new species has been created. Nobody programs the changes in the genetic information. Changes occur all the time. There may be algorithms to determine how change is fostered. But there is no algorithm to determine which variation has to survive: the environment will make the selection.

Living organisms are so complex that it seems highly improbable that natural selection alone could produce them. But Darwin's theory of variation and natural selection, spread over millions of years, yields a sequence of infinitesimally graded steps of evolution that eventually produce complexity. Each step embodies information about the environment and how to survive in it. The genetic information of an organism is a massive database of wisdom accrued over the millennia. It contains a detailed description of the ancient world and a list of instructions for surviving in it.

The gorgeous and majestic logical systems of physical sciences are replaced by a completely different, and rather primitive, system of randomness, of chance, of trial and error.

Of course, one could object that natural selection has (short-term) tactics, but no (long-term) strategy: that is why natural selection has never produced a clock or even a wheel.  Tactics, on the other hand, can achieve eyes and brains.  Humans can build clocks, but not eyes. Nature can build eyes, but not clocks.  Whatever humans build, it has to be built within a lifetime through a carefully planned design. Nature builds its artifacts through millions of years of short-term tactics. "Design" refers to two different phenomena when applied to nature or humans. The difference is that human design has a designer.

Darwinism solved the problem of "design without a designer": variation and selection alone can shape the animal world as it is, although variation is undirected and there is no selector for selection. Darwin's greatest intuition was that design (very complex design) can emerge spontaneously via an algorithmic process.

To be fair, Darwin already realized that natural selection alone was not enough to explain the evolution of very complex traits (such as the human brain itself). Thus he later introduced a second kind of selection, that, while not as popular as “natural” selection, could actually account for rapid development of complex organs in primates: sexual selection. Sexual selection is due to the different way males and females of a species behave towards reproduction: males compete for females, females choose males. Thus males and females are under pressure to develop features that not only will improve their chances of surviving in a hostile environment but will also improve their chances of reproducing with a member of the other sex. Primates are under the pressure of both natural selection “and” sexual selection (competition for survival “and” competition for reproduction). Sex is not only a footnote.


The Logic Of Replication

In 1865 the Austrian botanist Gregor Mendel, while studying pea plants, proposed a mechanism for inheritance that was to be rediscovered in 1901. Contrary to the common-sense belief of the time, he realized that traits are inherited as units, not as "blends". Mendel came to believe that each trait is represented by a "unit" of transmission, by a "gene" (a term coined in 1909 by Wilhelm Johanssen). Furthermore, traits are passed on to the offspring in a completely random manner: any offspring can have any combination of the traits of the parents.

Mendel proved that "blending inheritance" is false, that we do not "blend" the inheritances we receive from our parents. There is a unit of inheritance, the gene, and we either inherit a gene or we don't inherit it.  Our eyes are either blue or brown, but not a blend of blue and brown.  We are either male or female, but not a blend of male and female.  (The color of the skin may be intermediate between the colors of the parents, but that is because the color is due to the sum of numerous genetic effects).

The British biologist William Bateson coined the term "genetics" in 1906. The Danish botanist Wilhelm Johannsen coined the term "gene" in 1909. In the 1920s the US biologist Thomas Hunt Morgan discovered that genes are arranged linearly along "chromosomes".

The model of genes provided for a practical basis to express some of Darwin's ideas. For example, Darwinian variation within a phenotype can be explained in terms of genetic "mutations" within a genotype: when copying genes, nature is prone to making typographical errors that yield variation in a population.

 In the 1920s population genetics (as formulated by the US biologist Sewall Wright and the British biologist Ronald Fisher) turned Darwinism into a stochastic theory (i.e., it introduced probabilities). Evolution became a shift in gene frequencies within a population over time. Fisher, in particular, proved that natural selection requires Mendelian inheritance in order to work the way it works. Fisher unified Darwin and Mendel (initially Mendel had even been viewed as anti-Darwin): what changes in evolution is the relative frequency of discrete hereditary units, each of which may or may not appear (more or less randomly) in successive generations. In the 1940s the two theories were merged for good in the so called "modern synthesis". In practice, the synthetic theory of evolution merged a theory of inheritance (Mendel’s genetics) and a theory of species (Darwin’s evolutionary biology).

Since those days, the idea of natural selection has undergone three stages of development, parallel to developments in the physical sciences: the deterministic dynamics of Isaac Newton, the stochastic dynamics of  Clerk Maxwell and Ludwig Boltzmann, and finally the dynamics of self-organizing systems. Originally, Darwin's theory was related to Newton's Physics in that it assumed an external force (natural selection) causing change in living organisms (just like Newton posited an external force, gravity, causing change in the motion of astronomical objects). However, with the formulation of population genetics by Ronald Fisher and others, Darwinism became stochastic (the thermodynamic model of genetic natural selection, in which fitness is maximized like entropy), just what Physics had become with Boltzmann's theory of gases. In the 1990s self-organizing systems provided a new model to think about the organization of life at different levels, from cells to societies.

Darwin had not explained what he set out to explain: the origin of species. The Russian geneticist Theodosius Dobzhansky came closer: what makes a species a species is sex.  Different populations of the same species actually have different genomes, but only some genes need to be compatible for sexual reproduction to occur. If those genes are affected by mutations, then two populations may become incompatible and a new species is born.

In 1944 the Canadian physician Oswald Avery identified the vehicle of inheritance, the substance that genes are made of, the bearer of genetic information: the deoxyribonucleic acid (DNA for short).

In 1953 the British biologist Francis Crick and the US biologist James Watson figured out the double-helix structure of the DNA molecule. It appeared that genetic information is encoded in a rather mathematical form, which was christened “genetic code” because that’s what it is: a code. The “genome” is the repertory of genes of an organism.

In 1957 Crick, by using only logical reasoning, reached the conclusion that information must flow only from the nucleid acids to proteins, never the other way around.

In 1961 the South African biologist Sydney Brenner and the French biologist Francois Jacob discovered that cells of ribonucleic acid (messenger RNA), carry the genetic instructions from the DNA to the ribosomes, the sites within a cell that manufacture proteins.

Also in 1961 Jacob and the French biologist Jacques Monod discovered the mechanism of gene regulation: genes turn each other on and off, i.e. genes are organized in a network. Jacob and Monod also noticed that the interaction among genes might explain cell differentiation (the fact that cells containing the same genetic information end up doing completely different things).

By 1966 the US chemist Marshall Nirenberg had cracked the "genetic code", the code used by DNA to generate proteins. He and the Indian biologist Har Gobind Khorana discovered how the four-letter language of DNA is translated into the twenty-letter language of proteins (the DNA is made of four kinds of nucleotides, proteins are made of twenty types of aminoacids).

In the 1980s we started deciphering the genome of different animals, including our own.


The Logic Of Evolution

Evolution is about a pattern (in particular, a string of DNA, but it could also be some other pattern) and it involves the following steps:

·   Reproduction. Copies are made of the pattern.

·   Variation. Random errors appear in the copies and yield variants.

·   Selection. The environment selects which variants survive.

These simple steps cause continuous mutations of the pattern. Each generation copes better with the environment.

In addition, other factors may accelerate evolution: sex accelerates evolution; learning accelerates evolution.


Universal Selectionism

The thesis of the US psychologist Gary Cziko is that there is a universal process of Darwinian evolution that is responsible for knowledge at all levels, and not only at the biological level.

Cziko relates "knowledge" to the fitness of living beings, to their adaptation to the environment. Knowledge as the product of the interaction with the environment (and as the necessary cause for survival in that environment) implies that all knowledge is created through a Darwinian process of blind variation coupled with environmental selection.

Cziko observes that there are really two kinds of fitness: living beings are adapted to their environment when they are born, and living beings are capable of adapting to changes in their environment during their lifetime. A theory of fitness has to deal with both forms of fitness, the one that has been shaped over the centuries and become part of a species' identity and the other that is shaped over an individual's lifetime and becomes part of the individual's identity ("instinct" and "learning").

The Austrian ethologist Konrad Lorenz saw instinct as having been shaped by blind variation and natural selection: it is "knowledge" acquired over millennia that (in modern terms) is now encoded in the genome of a species. However, the same behavior does not yield the same outcome unless the environment remains exactly the same; which, in general, it doesn't. William James noted that a living being is capable of achieving consistent goals using (slightly) different behaviors. Individuals can "adapt" to circumstances.

Examples of "ontogenetic" adaptation are the muscles that get bigger the more they are used and the immune system, that "learns" what antibodies to make based on which ones are "used" to fight antigens. The immune system is particularly effective in its job. However, it operates on an absolutely blind basis: it creates all the time a lot of different kinds of antibodies hoping that, when attacked, at least one will work against the invader. It is the diversity of its army of soldiers (and the fact that they are permanently available) that makes it effective in fighting the enemy, not a careful training of each soldier and a timely deployment of them. It's diversity and continuity that matter. And they are due to a process of blind variation, not to a process of careful engineering. (Another key feature for the proper functioning of the immune system is, of course, that it produces only antibodies that destroy antigens and no antibodies that destroy body cells; in other words, it is capable of distinguishing self from nonself).

The "blindness" of selectionist processes turns out to be an advantage in other ways as well. There are several examples of "functional shifts", i.e. of parts that evolved for a purpose but then ended up being used for a different purpose, simply because it worked (what the US biologist Stephen Jay Gould termed "exaptation"). The current use of an organ or behavior does not necessarily explain its origin. It may well be that it originated for a different function.

The other major example of "ontogenetic" adaptation is the brain that is shaped not only by the genes but also by experience. Interaction with the environment "selects" which synapses are useful and eliminates the ones that are useless.

Drawing from Konrad Lorenz's evolutionary epistemology of 1941, Cziko views knowledge as adaptation of the brain to the environment. A-priori knowledge (the innate knowledge of entities such as time and space) is the product of the biological evolution of the human brain. During our lifetime the senses provides us with true information about the environment because they have been selected over the millennia based on their usefulness. Therefore the world is not an illusion, and we know it by adapting to what it is.

Cziko observes that "fitness" has to do with "purpose": there is fit when the structure of an organism serves a purposeful function. Animal behavior is purposeful and changes the environment that operates on the animal's behavior. Stimuli influence responses, but responses also influence stimuli. This is William Powers' "perceptual control theory", according to which behavior controls perception as much as perception determines behavior. A control system is as blind as the immune system that creates an army of antibodies. Nonetheless, a control system exhibits a behavior that appears to be "purposeful". It is, in turn, "controlled" by higher-level control systems. An organism is ultimately a hierarchy of control systems, each of which senses something in the environment and tries to control it. Instinctive behavior is the result of the interaction between control systems that have internal goals. Each control system must have survival value if it is still part of an organism. In a sense, there is no learning: there is just the blind functioning of a network of control systems. In another sense, that "is" precisely what we call "learning": a control system at work. When something changes in the environment, the control system senses it and needs to restore its internal goal. It does so by triggering random responses and rewarding the ones that move it closer to its goal. A hierarchy of control systems can create the illusion of learning and of intelligence (as in Valentino Breitenberg's progressively complex robots).

Cziko argues that there is a Darwinian selection not of behaviors but of control systems. Knowledge is the result of a hierarchy of selectionist processes, starting with the biological one studied by Darwin.

"Learning" is necessary because animals need to adapt to changing environments. The brain and the immune system allow animals to find food and to fight lethal viruses. Humans have also developed a higher form of "learning" that consists in cultural knowledge. Cziko shows that it too obeys a process of blind variation and selective retention. Even when we learn something from somebody else we are simply interacting with the environment (the "somebody else") and fine-tuning our knowledge based on that interaction. Both technological and scientific evolution, for example, are due to a number of different "trial and error" processes.

Cziko applies "universal selectionism" to a number of different fields. The most interesting is language. Following the US linguists Elizabeth Bates and Brian MacWhinney ("Competition, variation, and language learning", 1987), Cziko shows that a selectionist approach can well complement Chomsky's nativism to explain how children learn language. There might be innate linguistic skills in the brain (selected over the millennia by evolution) but children learn a language by the same "trial and error" process that Nature employs everywhere. Children try words and sentences and reinforce the ones that "work", just like the brain and the immune system try synapses and antibodies and reinforce the ones that work (or, better, the ones that work are reinforced by the positive outcome).



An organism is a set of cells.  Every cell of an individual (or, better, the nucleus of each cell) contains the DNA molecule for that individual, or its "genome".

"Polymerizing" is the process by which molecules form chains, therefore called "polymers". The polymer of life is formed by molecules of four kinds (four "nucleotides").

A DNA molecule is made of two strings, or "strands", each one the mirror image of the other (in the shape of a "double helix"). Each string is a sequence of "nucleotides" or "bases", which come in four kinds (adenine, guanine, cytosine, thymine). These four bases are paired together (adenine is paired with thymine and cytosine is paired with guanine). Each nucleotide in a string is "mirrored" in a nucleotide of the other string.  Each strand of the helix acts therefore as a template to create the other template. Nucleotides are the elementary unit of the "genetic code". In other words, the genetic code is written in an alphabet of these four chemical units.

Cells split all the time, and each new cell gets one of the two strings of DNA of the original cell, but each string will quickly rebuild its mirror image out of protoplasm. This process is known as "mitosis". Each cell in an individual has almost exactly the same DNA, which means that it carries the same genome.

The genome is made of genes. A gene is a section of the DNA molecule which instructs the cell to manufacture proteins (indirectly, a gene determines a specific trait of the individual). Genes vary in size, from 500 bases long to more than two million bases (long genes tend to have just a very long waste).

The most abused metaphor in biology is that genes represent a program that results in some behavior (the "digital gene" metaphor). In reality, the behavior of genes is not so linear as the digital metaphor imply. Genes tend to work in communities of genes: it is not always clear what a gene does. Some genes are used for more than one chore (the "housekeeping genes"). And some genes do not encode discrete values, but continuous values. Many genes, in other words, are not digital at all. And the genome is not a sequential program, that is executed mechanically one gene after the other. It is more like a network of genes that "regulate" each other. The genetic "program" behaves more like a network of switches.

The DNA is organized into chromosomes (23 pairs in the case of the human race) which are in turn organized into genes. The human genome has 3 billion base pairs of DNA.

This means that each cell contains three billion bases of DNA, which is a string of genes about 2 meters long.  If we multiply for all the cells in the human body, we get a total length of genetic material which is about 16,000 times the distance between the Earth and the Moon.

The way offspring is designed is simple: male sperm and female eggs carry only 23 chromosomes (instead of the 46 that each body cell contains) and when they join they generate a 46-chromosome embryo. The embryo therefore contains some of the chromosomes of the father and some of the chromosomes of the mother.  (As Mendel discovered, the embryo does not contain a "blend" of the mother and the father, but rather some of the mother's attributes and some of the father's attributes).

(Notable among the human chromosomes are the X and Y chromosomes, that are responsible for determining the sex of the offspring. Reptiles do not have genes that decode sex: sex is determined by environmental conditions, mostly the incubation temperature, not by genetic information. The X and Y chromosomes were acquired by mammals much later in evolution. The Y chromosome is only one third  the size of the X chromosome, and the  Y chromosome has disappeared in several mammals. Human males have one X and one Y chromosome, while females have two X chromosomes).

All living organisms use DNA to store hereditary information and they use the exact same code (the "genetic" code) to write such information in DNA: the genome of an individual is written in the genetic code. It is inappropriate (although commonplace) to refer to the "genetic code" of an individual, as all living things on this planet share the same genetic code. The genetic code is a code, just like the Morse code. It specifies how nucleotides (through a "transcription" of the four nucleotides into ribonucleic acid, or RNA, and a translation of RNA into the twenty aminoacids) are mapped into aminoacids, which in turn make up proteins, which in turn make up bodies. Different genomes yield different bodies. But they always employ the same genetic code to carry out this transformation.

 The genetic code is the code used by Nature to express a set of instructions for the growth and behavior of the organism. Each individual is the product of a genome, a specific repertory of genes written in the genetic code. The genome defines the “genotype” of an organism. Genotype is the "genetic makeup" of the organism. The organism itself is the “phenotype”. Phenotype refers to how the genetic makeup is expressed in the body (the physical expression of a gene). The genotype is the repertory of genes of an organism; the phenotype is the physical manifestation of the genotype (the "body").

"Sequencing" the genome refers to the process of identifying the genes.

Humans have about 30,000 genes (out of 3.2 billion DNA units). That is a relatively low number for the complexity of the human body (only six times more than the Escherichia Coli bacterium).

A single gene can often be responsible for important traits. For example, chimpanzees share 98.6% of the human genome, but there is hardly a single trait in common between the two species. 98% of the human genome contains the same DNA found in most other vertebrates. The roundworm has 19,000 genes, just a third less than humans. But a single gene can make a huge difference and very similar genetic programs can differ wildly in phenotypic (bodily) effects. In other words, the relationship between genome and phenotype is nonlinear: the genotypes of humans and chimps differ by only 1.4%, but the difference in the corresponding phenotypes is much more striking than a mere 1.4% (at least from the admittedly biased viewpoint of us humans).  To be fair, the 30,000 genes represent only 1.5% of the genome, the rest being “junk”, i.e. chemicals that don’t seem to encode any instruction.

Some of those genes that humans share with chimps, incidentally, have been around for millions of years, and humans share them with bacteria.  As the British biologist Steven Jones wrote, "everyone is a living fossil".

The smallest genome that is known is the genome of the Mycoplasma Genitalium: 470 genes. One could wonder what is the smallest amount of genes that is required to have life.


The Matter of Life

Life on Earth is based on the element carbon. Carbon can bond with oxygen, hydrogen and nitrogen because of its four valence electrons. Both proteins and nucleic acids (DNA, RNA) are made of carbon, and energy is stored in the form of carbohydrates.

Energy transformations are linked with the dual processes of oxidation and reduction. Oxidation and reduction reactions occur in pairs:  in order for a substance to be reduced another substance must be oxidized. When an atom is oxidized, it loses electrons; and when it is reduced, it gains electrons. Oxidation is a process by which a carbon atom gains bonds to (usually) oxygen.  Reduction is a process by which a carbon atom gains bonds to (usually) hydrogen. Molecules gain oxygen or lose hydrogen in an oxidation reaction; lose oxygen or gain hydrogen in a reduction reaction.

Fritz Lipmann (“The metabolic generation and utilization of phosphate bond energy”, 1941)  discovered that Adenosine Triphosphate (ATP), a high-energy phosphate and therefore a source of readily available energy, and showed that it constitutes the main fuel for many biochemical  processes and, in particular, is the main energy carrier in cells. He had basically found the connection between the metabolism and the physics of biological systems, i.e. the chemical process that makes life possible.

Organic molecules are based on carbon, and energy transactions are based on phosphorus.

Oxidation-reduction energy is pervasive in nature. and (relatively rare) Phosphate-bond energy is relatively rare in nature. Life owes its existence to the fact that at some point the two met.


Genetic Fossils

Genomes have confirmed the theory of evolution.  In the 1950s the Italian biologist Luigi Cavalli-Sforza first had the idea that one could use genetic information to trace the genealogical tree of species. Genomes share common parts and different species are determined by the branching out of the other parts.  The genealogical tree of living beings is carefully reflected in the structure of their genomes. The genome of a species is almost a "memory" of that species' evolutionary journey.  Most human genes, for example, date back to primitive organisms, and they are shared by all modern animals that descend from those organisms. Only a few can be said to be truly "human".

Basically, an organism’s DNA is a record of its evolutionary past. Each living organism “is” a fossil. The same principle helped biologists such as Allan Wilson in the 1980s study the evolution of humans. He focused on mitochondria, the part of the cell that converts sugar into energy. They have their own DNA. This DNA can be used as a “molecular clock” by estimating the number of its mutations.

Because mitochondria are inherited only from the mother, they can only be used to construct a matrilineal genealogical tree. Thus it was derived that all living humans are descendants of one woman who lived about 150,000 years ago. The molecular clock for the patrilineal genealogical tree is a piece of the Y chromosome, which is inherited only by sons from their father. Thus it was derived that all living humans are descendants of a man who lived about 60,000 years ago.



A body is made of cells. Every single cell in the same body contains roughly the same genetic information (barring copying mistakes). However, each cell ends up specializing in a task, depending on where it is located: a heart cell will specialize in heart issues and not, say, liver issues, even though the genetic information describes both sets of issues. A muscle cell is a muscle cell, even though it is identical to a liver cell. This is the phenomenon of "cell differentiation", by which each cell "expresses" only some of the genes in the genome, i.e. only some of the possible proteins are manufactured ("synthesized").

The human body has about 265 different cell types.

Differentiation seems to be regulated by topology: depending on where a cell is, it exchanges energy (which is information) with some cells rather than others. Neighboring cells "self-organize". How cells develop to be what they will be within the body is probably determined by a regulatory mechanism: instead of each cell being "told" by the genes what to become, cells interact among themselves; and the body is the emergent outcome of their interaction. This is an efficient way to produce complex bodies: the genome does not need to specify where each of the 100 trillion cells must go. The difference between humans and chimps is caused by a mere 1.6% of the genome: it is the interactions among cells that greatly amplify that 1.6%. Another advantage is that the body can repair itself: if a cell is damaged, interaction among cells yields a new configuration that makes that damage irrelevant. The price that the organism pays is a long period of "incubation" during which the body “develops” (and it is vulnerable).

A puzzling feature of genomes is that they contain far more useless junk than useful genes. The human genome, in particular, contains about 95% junk, in between genes.



The process of “epigenesis” is the process by which the genotype is turned into the phenotype.

DNA is translated into another kind of polymer, RNA (ribonucleic acid), which is also a four-letter code (adenine, guanine, cytosine, uracil) while RNA, in its turn, is translated into yet another kind of polymer, the protein, whose units are aminoacids. There are twenty kind of aminoacids, so technically a four-letter code is translated into a twenty-letter code.

The way this works is by triplets of DNA units: three DNA units (which can each be of four different kinds, for a total of 4x4x4=64 combinations) is translated into one of the twenty aminoacids (some triplets generate the same aminoacid).

But the translation is more complex as DNA is a one-dimensional structure (a string) whereas a protein is a three-dimensional structure (it's the stuff that our flesh and bone and blood are made of). So the one-dimensional string of instructions of the DNA is used to determine the three-dimensional shape of a protein.

In summary, the DNA is the sequence of instructions for building molecules called proteins, and proteins are manufactured of amino acids, whose order is determined by the DNA. Note that our genome has only 30,000 genes, but our body has 100 trillion cells.

As far as the individual goes, we know that her genome is a synthesis of the genome of the parents plus some random shuffling. But it is not clear yet how much of the final individual is due to the genome and how much to the interaction with the environment. For example, the genome may specify that a muscle must grow between the arm and the trunk, but exercise can make that muscle bigger or smaller. For example, the genome may determine some psychological characteristics of the individual, but study, meditation and peer pressure can alter some of them.  The British biologist William Bateson thought that only the genome mattered: we are machines programmed from birth. The US psychologist John Watson, on the other hand, thought that conditioning could alter at will the personality of an individual: it all depends on experience, the instruction contained in the genome is negligible.

There is also a subtle difference between which genes are in the genome and which genes are actually “expressed”.  For example, the Israeli physician Moshe Szyf (“Maternal Care Effects On The Hippocampal Transcriptome And Anxiety-Mediated Behaviors”, 2005) found evidence that the early experience of the child affects the future psychological life of the child not only because it is stored in memory but also because it determines how some genes will be expressed. Szyf observed physical differences in the hippocampus of rats that account for differences in behavior, and he argued that those differences were caused by the way their mothers raised them. Rats who were raised in similar ways by their mothers tend to have the same kind of hippocampus. He credited this development to the expression of some genes as opposed to others. Maternal care seems to affect the chemistry within the cell that determines if and when those genes are expressed.

The role of RNA is probably underrated. Protein-encoding genes might be in the minority. Many different kinds of RNA exist and some kinds of RNA regulate the life of many protein-encoding genes. The number of protein-encoding genes seems to be mostly the same for all animals, from flies to humans (in the range of 20-30,000). However, the number of genes whose RNA performs other functions vary wildly among species. RNA acts as a simple "messenger" only in simpler organisms. RNA acts more like a “manager” in complex organisms, i.e. its "regulating" activities are much more widespread.


The Cell

The cell itself is the elementary unit of the body (in the case of bacteria, one cell is the whole body), but it has its own structure. Its behavior is driven by the instructions of the DNA, but its function are roughly to transform nutrients into energy (generically, metabolism), to carry out some function thanks to that energy, and to reproduce (mitosis).

Each cell is limited by a membrane and is supported by a skeleton called a “cytoskeleton”. The cytoskeleton is made of a protein called "tubulin", which forms filaments called "microtubules". Most living beings are eukaryotes: their cells contain a nucleus that contains the genetic material (DNA and RNA). The nucleus is the information storage of the cell. It is also the place where DNA is transformed into mRNA. The cell contains many ribosomes, each of which is a machine that manufactures proteins based on the instructions received from the nucleus in the form of mRNA. There is also genetic material in some organelles of the cell called “mitochondria”. Mitochondria are the cell’s "power plant," because they convert nutrients into energy, creating the nucleotide that is the "molecular currency" of intracellular energy. Mitochondria have their own DNA, separate from the cell’s main DNA. Mitochondria are also self-replicating.

Prokaryotes (such as bacteria) are made of simpler cells that do not have a nucleus.


Mutation as Destiny

In reality, the process of copying DNA is not so smooth. When a cell splits, its DNA is copied to the new cells but the copying process (for whatever whim of nature) is prone to "error" (or, at least, to loss of information). In other words, genes mutate all the time inside our bodies. These mutations may cause fatal diseases (such as cancer) and they are responsible for death.

Mutation is what causes aging and death. Millions of cells divide each second and a copy of DNA is likely to carry some mistake, which means that the older we are the more chances that serious mistakes have been made and that our genetic instructions are no longer rational.

Mutation is also the whole point of sex, and this turns out to be the mirror story of death.  Sex is the antidote to the genetic deterioration due to the imperfect copying process. The human race would rapidly degenerate without sex: each individual would pass on genes that have already lost part of their information through so many million internal copies.  Sex is what makes the paradox possible, and almost inevitable: individuals decay, but the race progresses. Because sex recombines the genes of the parents, it can produce both better and worse (genetically speaking) individuals, and natural selection will reward the better ones. The long-term outcome of sex is that it is more likely that better future individuals are produced from the deterioration of present individuals.

Last but not least, mutation is what drives evolution (evolution is variation and natural selection).

Mutation sounds like the god of genetics.

The problem is that mutation is random.  Evolution occurs by accident, by "genetic drift": by chance and time.

Mutation is not everything, though. Mutation requires natural selection in order to yield evolution. 

Inheritance involves genes and environment working together. Diseases which are dormant in our genes, for example, may be sparked off by environmental conditions.  Diet is as important as genes in the development or the prevention of a disease.  And pollution is as important as genes to the development of cancer.  And so forth.

Chance and the environment determine how we evolve. The only party that does not have a saying in this process is… us.


The Origin of Evolution

Fundamental to Gregor Mendel's theory is the distinction between the appearance of an organism (its "phenotype"), which turns out to be a blend of the appearances of its parents, and the physical state of the factors inherited from each parent (the "genotype"), which remain unmixed. The physiology of development fuses, at the level of the whole organism, the information of heredity, which is still kept separated at the genetic level. The two fundamental laws of heredity are that, first, the factors that are passed from parent to offspring (which today we call "genes") maintain their individuality despite their interaction with other genes in the development of the organism, and that, second, gene segregation allows for the reappearance of a variation in later generations of offspring. From these considerations Mendel had the intuition that heredity is based on a discrete (rather than continuous) entity, just like Physics is based on elementary particles. That entity was the gene. What is truly inherited is not the "traits": it is the genes.

(Darwin, incidentally, believed that traits were transmitted from parent to offspring through blood).

Mendel also found that new variation will not be diluted by the process of mating but will always be available for selection, a fact that explains why a population variation is not immediately destroyed by selection itself.  The antithetical properties of heredity and variation are dual aspects of the same process: the actual variation among members of the same generation explains the transmission of similarity across generations.

In our century, population genetics showed that Darwin's theory (that change occurred by the natural selection of many minute variations) and Mendel's theory (that change occurred suddenly, by mutation) were complementary: changes occur in the frequencies of genes.

Modern evolutionary genetics stems from the merging of those two traditions, the Darwinian and the Mendelian, both of which take variation as the crucial aspect of life. The Darwinian view can be summarized as "evolution is the conversion of variation between individuals into variation between species". 

The paradox is that Mendelian theory dictates the frequencies of genotypes as the appropriate genetic description of a population, whereas variation is much more important.  As the US biologist Richard Lewontin put it, "what we can measure is uninteresting and what we are interested in is unmeasurable".


The Steps Of Life

Life evolved through momentous leaps forward.

As the Israeli physicist David Deutsch described it, once replicators were born, they joined forces in self-replicating groups. Such groups are organized in a way that each member contributes to the chemical reactions that allow the whole to replicate itself (with all its members). That was the birth of the first living organism. "Genomes are group of genes that are dependent on each other for replication". The genetic code itself (the way to encode all of this) had to evolve until it reached a point beyond which it did not need to evolve anymore (it hasn't evolved for billions of years) while still allowing for organisms to evolve. The code, that had originally encoded just a single-celled organism, stopped evolving, but it was now powerful enough ("universal") that it could encode a virtually infinite range of (multi-cellular) organisms. That is the power of representation systems when they are universal. They can describe a lot more than what they were originally built for.

First, reproduction occurred: an organism became capable of generating another organism of the same type. Then sexual reproduction occurred, in which it took two organisms to generate an organism of the same type. Then multi-cell organisms appeared, and organisms became complex assemblies of cells. Fourth, some of those cells developed into specialized organs, so that the organism became an entity structured in a multitude of more or less independent parts. Fifth, a central nervous system developed to direct the organs. And, finally, mind and consciousness appeared, probably originating from the same locus that controls the nervous system.


The Origin of Life

Hypotheses abound on how life originated. Most theories analyze the ingredients of life and speculate how they may have been generated by the Earth’s early activity. 

It was in 1952 that a young US physicist, Stanley Miller, working with Harold Urey, advanced the idea that the first molecules of life (including aminoacids, the building blocks of proteins) were formed accidentally by the Earth’s early volcanism and then triggered into reproducing systems by the energy of the sun and lightning strikes. His calculations of how lightning  may have affected the Earth's primitive atmosphere gave rise to the quest for the experiment that would reproduce the birth of life in a laboratory (with hints of Frankenstein and all the rest). One catch remained, though: the product of Miller’s prebiotic chemistry would still be inactive chemicals.

Miller simply revised a theory of chemical formation of life that dates back to the Russian chemist Alexander Oparin, who in 1924 first proposed that life could have been induced in the primeval soup.



Since the pioneering work conducted in the 1960s by the German physicist Manfred Eigen (“Self organization of matter and the evolution of biological macro molecules”, 1971), autocatalysis has been a prime candidate to explain how life could originate from random chemical reactions. Autocatalysis occurs when a substance A catalyzes the formation of a substance B that catalyzes the formation of a substance C that… eventually catalyzes the formation of A again. At the end of the loop there is still enough A to restart it. All the substances in this loop tend to grow, i.e. the loop as a whole tends to grow. Life could have originated precisely from such a loop, in which case the chances that the right combination of chemical reactions occurred at the right time is much higher.

An autocatalytic set is a group of proteins that reproduces itself.

The power of this hypothesis is that "autocatalytic cycles" exhibit properties usually associated with life: metabolism and reproduction. If two such cycles occur in the same "pond", they will compete for resources and natural selection will reward the "best" one.

The German patent lawyer Gunter Waechtershauser ("Before enzymes and templates: theory of surface metabolism", 1988) improved on that model by explaining how the first forms of life could have synthesized their own vital chemicals rather than absorbing them from the environment, i.e. how a metabolic cycle could have started. Unlike Miller, Waechtershauser speculates that prebiotic reactions occurred not in water but on the ground. At high temperatures, chemicals bound to a metallic surface are much more likely to mix and form the complex molecules which are needed for life. Particularly, iron sulfide (a very common mineral on the Earth) could have been a catalyst of chemical reactions that created the biochemistry of living cells. He proved that peptides (short protein chains) could be created out of a few given aminoacids. The next step in the chain would be the emergence of RNA, that he considers a predecessor to DNA. Waechtershauser's emphasis is on "autocatalysis" (in general, as a process that is fast enough for yielding dramatic consequences) and on the ability of minerals in particular to catalyze the right reactions. Life would be but the natural evolution of a primitive chemical cycle that originally arose on an iron-sulfur surface.

The US chemist Melvin Calvin was perhaps the first to suggest that "autocatalytic" processes can make life more likely by speeding up the manufacturing of the basic ingredients.

The US biologist Stuart Kauffman also advanced a theory of how life may have originated from autocatalysis. He refutes the theory that life started simple and became complex in favor of a scenario in which life started complex and whole due to a property of some complex chemical systems, the self-sustaining process of autocatalytic metabolism. When a system of simple chemicals reaches a certain level of complexity, it undergoes a phase transition: the molecules spontaneously combine in an autocatalytic chemical process to yield larger molecules of increasing complexity and catalytic capability. In other words, as the system gets more complex, the chances that it contains a component and its catalyzer increase rapidly. Even if the proteins are chosen randomly, when there are enough of them, there is a chance that some of them form an autocatalytic set.  Self-replication arises out of a simple statistical fact. Life, according to Kauffman,  is but a phase transition that occurs when the system becomes complex enough. 

According to Kauffman, life is vastly more probable than traditionally assumed. And life began complex, not simple, with a metabolic web that was capable of capturing energy sources.

Self-organizing principles are inherent in our universe, and Kauffman views life as a direct consequence of self-organization. Therefore, both the origin of life and its subsequent evolution were inevitable.

The US scientist Michael Conrad ("The Fluctuon Model of Force, Life, and Computation", 1993) developed a unified model of Quantum Physics and General Relativity, the "fluctuon model", according to which Physics is inherently biased towards self-organizing processes. He argued that life-like features stem from Quantum Physics and General Relativity themselves, and that life is therefore a relatively trivial consequence of the evolution of the universe.



Comets are providing another option: that life may have come from other parts of the universe. It was the Greek philosopher Anaxagoras (fifth century BC) who first speculated that life may have been dispersed as seeds in the universe and eventually landed on Earth ("panspermia").

Spanish biochemist John Oro (“Comets and the formation of biochemical compounds on the primitive Earth”, 1961) hypothesized that all building blocks of life were brought to Earth by comets, a theory later popularized by the Belgian astrophysicist Armand Delsemme. Organic material (from water to methyl alcohol, and even forerunners of DNA’s aminoacids) has been found in the galactic clouds that float among the stars of our galaxy. Interstellar matter seems to be rich in molecules that are needed to create life. Trillions of comets wander through the solar system, and they occasionally approach the Earth. They are soaked with the organic dust picked up from the interstellar void. In other words, comets may have their own role in the vast drama of life, sowing the seeds of life on all the planets they intersect. Comets have been found to contain many if not all the ingredients necessary for life to originate. (Incidentally, comets have been found to carry ice, and no theory of the development of the Earth can account yet for the enormous quantity of water contained in the oceans, unless the water came from somewhere else).

Also, left-handed aminoacids (the kind that life uses) were found in the meteorite fragments that showered Australia in 1969 (including some aminoacids unknown on Earth).

If aminoacids are of extraterrestrial origin and Wachtershauser’s mineral-based chemistry can produce biological compounds, the chain that leads from dead matter to living matter would be completed. But life is also capable of reproduction and inheritance. Moreover, Wachtershauser’s model requires high temperatures, whereas  four of the five main components of DNA and RNA (adenine, uracil, guanine, cytosine) are unstable at those temperatures.



The Dutch chemist Anthonie Muller showed that "thermosynthesis" is a viable alternative to explain the origin of life ("Thermoelectric energy conversion could be an energy source of living organisms", 1983). Muller points out that life probably originated in conditions where photosynthesis and chemosynthesis (getting energy from light and food) were unfeasible, simply because there were not enough life and food. If life originated in an underwater volcano covered with ice, neither light nor food were abundant. What was abundant was a temperature difference. This "gradient" of temperature would cause convection currents, that would drag the early forms of life up and down in thermal cycles, from hot to cold and back to hot. The larger the temperature difference, the stronger the convection currents, the faster the thermal cycles, the more efficient the energy production. Heat was therefore the main source of energy, and heat was coming from the environment.

Photosynthesis and chemosynthesis do yield much more power, but thermosynthesis was simply the only feasible form of energy production. The early living cells were basically built around "heat engines". Some of their enzymes or membranes worked essentially as heat engines.

In a steam engine, for example, water is thermally cycled: water is heated until it turns into steam; the steam expands and performs work; the steam loses its energy and returns to liquid form; and the cycle resumes.

In a thermosynthetic cell, a protein is thermally cycled in a similar manner: it is heated until it turns into a more fluid state; this generates work in the form of ATP (the chemical which is the energy source for almost all physiological processes) while the protein returns in its original state; and the cycle resumes.


Life Before Life

Other theories focus on the replication mechanism, which doesn’t necessarily require organic matter to occur.

For example, the British chemist Graham Cairns-Smith argued that the first living beings were not carbon composts but clay crystals, i.e. minerals. He agrees with skeptics who think that the birth of the first cell is just statistically impossible (he calculated the probability of all the events required to create a DNA molecule and concluded that there wasn’t enough matter or time in the universe to achieve it). However, rather than invoking an external force, Cairns-Smith thinks that the most plausible explanation is in the other direction: life is not the towering accomplishment of Nature, but a mere leftover from something bigger that pre-existed. He compares it to some unlikely rock structures that can be found in natural parks: how could chance create such equilibrium-defying structures? They were actually part of a much bigger structure that crumbled to pieces. It was relatively easy for them to be created as part of the bigger structure. Now that the bigger structure is gone, they look surreal and unlikely. Ditto for life: Cairns-Smith believes that life is merely what is left of something that was much more likely to arise than a mouse or a bird. In his opinion, life is the remnant of a mineral process. Life's ancestors were self-replicating patterns of defects in clay crystals. One day those patterns started replicating in a different substance, carbon molecules. In a sense, Cairns-Smith wants to extend evolution to the pre-biotic world, to the world before life was born. (But these molecules are still purely self-replicating entities: it remains unexplained how they started growing bodies...) Basically, Cairns-Smith argued that evolution came first, and life came afterwards, as an accidental side-effect.

Synthetic self-replicating molecules that behave like living organisms have been crafted in the laboratory. The US chemist Julius Rebek ("Self-replicating system”, 1990) recreated artificially the principles of life postulated by the biologist Richard Dawkins: "complementary" molecules (ones that fit into each other by way of spatial structure and chemical bonds) and even self-complementary molecules.

The US chemist Jeffrey Wicken showed that the thermodynamic forces underlying the principles of variation and selection begin to operate in prebiotic evolution and lead to the emergence and development of individual, ecological and socioeconomic life. He treated the prebiosphere (i.e., the Earth before life emerged) as a non-isolated closed system in which energy sources create steady thermodynamic cycles. Some of this energy is captured and dissipated through the formation of ever more complex chemical structures. Soon, autocatalytic systems capable of reproduction appear. Living systems, according to his theory, are but "informed autocatalytic systems".


Life And Heat

Whatever the mechanism that created it, the progenitor of all terrestrial life, four billion yeas ago, was able to tolerate the extreme heat conditions of the time (a few hundred degrees or even a thousand).  As a matter of fact, if we walk backwards up the phylogenetic tree (the tree of species), we find that genetically older organisms can survive at higher and higher temperatures.  Thermophiles (the microbes that live at temperatures of 70-80 degrees) are living relics of the beginnings of life on Earth.

Based on such a phylogenetic tree, the US biologist Carl Woese proposed a classification of living creatures in which thermophiles (or "archaea", first discovered in 1964 by the US biologist Thomas Brock) are different both from eukaryotes (in which DNA is held by a nucleus) and prokaryotes (in which DNA floats free in the cells of bacteria): in thermophiles, DNA floats free (like in prokaryotes) but resembles the DNA of eukaryotes.  Thermophiles can be found underground: some have been retrieved from 3 km beneath earth.  An archaea has about two million base pairs of DNA (a human cell has about three billion).

The Australian physicist Paul Davies retraced the history of life on Earth and concluded that it began inside the Earth, with microbes that lived several kilometers under the crust of the Earth. His reasoning was that the surface of the Earth and the oceans were just too unstable and dangerous for life to appear and survive. Furthermore, the record of genes seems to prove that the ancestor of all life forms lived underneath the Earth’s surface at very high temperatures.

Surprisingly, very little has been made so far of a discovery due to the French chemist Louis Pasteur in the 19th century: that living systems prefer molecules with a certain handedness (all proteins are made of L-aminoacids and genetic material is made of D-sugars). This molecular asymmetry is, actually, the only difference between the chemistry of living and of inanimate matter.


The Origin of Replication

The mystery of the origin of genes is particularly challenging because a gene is such a complicated structure and is unlikely to evolve spontaneously. 

The US biologist Walter Gilbert noted that most of a person's DNA does not code genes but what appears to be gibberish, and even the part that is code is distributed in fragments (or "exons") separated by useless pauses (or "introns").  In his opinion the first genetic material was made of exons, that symbiotically got together and formed new, more complex genetic material. Introns are not random leftovers, but sort of gluing elements from the original material. In a sense, his theory points to the possibility that the gene is not the ultimate unit, but exons are.

Attention has been focusing on RNA since RNA has been shown to be a self-replicating molecule that can act as its own catalyst. DNA cannot make copies of itself, and proteins cannot create themselves. They both depend on each other. But (some kind of) RNA can act as its own enzyme (i.e., its own catalyst). Therefore, RNA is capable of replicating itself without any need for proteins.

Stanley Miller proposed that the first living creatures may have been able to synthesize protein and reproduce without the help of the DNA, depending solely on RNA to catalyze their growth and reproduction. The US chemist Thomas Cech had already proven (in 1982) that RNA molecules alone can induce themselves to split up and splice themselves together in new arrangements. It is also chemically plausible that all four RNA nucleotide bases could have been created in nature by ordinary atmospheric, oceanic and geological processes.  Miller's theory, though, requires that life be born in lukewarm water, not the very high temperatures of thermophiles.

The German physicist Manfred Eigen induced RNA molecules to replicate by themselves, thereby lending credibility to the hypothesis that RNA came before DNA and that the first forms of life employed only RNA. Eigen's experiments with "autocatalytic cycles" involving RNA showed that, under suitable conditions, a solution of nucleotides gives rise spontaneously to a molecule that replicates, mutates and competes with its progeny for survival.  The replication of RNA could then be the fundamental event around which the rest of biology developed. Eigen speculates that the genetic code was created when lengths of RNA interacted with proteins in the "primordial soup". First genes were created, then proteins, then cells. Cells simply provide physical cohesion. Cells first learned to self-replicate and then to surround themselves with protective membranes.

The US physicist Freeman Dyson believes that one cannot consider life only as metabolism or only as replication. Both aspects must be present. Therefore, we must look not for the origin of life, but for the origin of replication and for the origin of metabolism. Since it is unlikely that both metabolism and replication occurred at the same time in one of the primitive organic molecules, Dyson thinks that life must have had a double origin. It is more reasonable to assume that life "began" twice, with organisms capable of reproduction but not of metabolism and with (separate) organisms capable of metabolism but not of reproduction, and only later there arose a mixture of the two by some kind of symbiosis: organisms capable of both reproduction and metabolism.

Dyson's idea is that organisms that could reproduce but not replicate came first. The most elementary form of reproduction is simply a cell division: two cells are created by dividing a cell into two. Replication implies that molecules are copied. Reproduction with replication implies that the new cells "inherit" the molecules of the mother cell. Replication became a parasite over metabolism, meaning that organisms capable of replication needed to use organisms capable of metabolism in order to replicate. First proteins were born and somehow began to metabolize. Then nucleic acids were born and somehow began to replicate using proteins as hosts.

The two organisms became one thanks to a form of symbiosis between host and parasite. Dyson borrows ideas taken from Manfred Eigen (who claims that RNA can appear spontaneously) and Lynn Margulis (who claims that cellular evolution was due to parasites). Basically, his theory is that RNA was the primeval parasite.

The French virologist Patrick Forterre (“A hypothesis for the origin of cellular domain”, 2006), instead, thinks that today’s living beings are descendants of three RNA viruses. These RNA viruses originally evolved the double-stranded DNA molecule to defend their RNA genes, and eventually this “shield” took on a life of its own and became the main mechanism for bacteria, archaea, and eukaryota. It is a fact, that the genes of viruses seem to date back in time to before the birth of cell-based life.

The genetic code is just a code that relates mRNA triples and protein's aminoacids.  The genetic code is the same for every being. It is just a code. It translates the instructions in the genotype into a phenotype. But it is an extremely sophisticated code. Did the genetic code itself evolve from a more primitive code? It is unlikely that the first self-replicating organisms were already using today's genetic code. How did the genetic code arise? And why don't we have any evidence of a pre-existing system of replication? Why is it that today there is only one code, rather than a few competing codes (just like there are a few competing genomes)?



The ultimate meaning of the modern synthesis for the role of humans in nature is open to interpretation. One particular, devastatingly pessimistic, interpretation came from the French biologist Jacques Monod: humans are a mere accident of nature.

To Monod, living beings are characterized by three properties: teleonomy (organisms are endowed with a purpose which is inherent in their structure and determines their behavior); autonomous morphogenesis (the structure of a living organism is due to interactions within the organism itself); and reproductive invariance (the source of information expressed in a living organism is another structurally identical object - it is the information corresponding to its own structure).

A species' teleonomic level is the quantity of information that must be transferred to the next generation in order to assure transmission of the content of reproductive invariance. Invariance precedes teleonomy. Teleonomy is a secondary property stemming from invariance.

All three pose, according to Monod, insurmountable problems.

The birth of teleonomic systems is improbable. The development of the metabolic system is a superlative feat. And the origin of the genetic code and its translation mechanism is an even greater riddle.

Monod concluded that humans are the product of chance, an accident in the universe.

The paradox of DNA is that a mono-dimensional structure like the genome could specify the function of a three-dimensional structure like the body: the function of a protein is under-specified in the code. Therefore it must be the environment that determines a unique interpretation. There is no causal connection between the syntactic (genetic) information and the semantic (phenotypic) information that results from it.

Then the growth of our body, the spontaneous and autonomous morphogenesis, rests upon the properties of proteins.

Monod concluded that life was born by accident. Then Darwin's natural selection made it evolve, and that process too relied on chance. Biological information is inherently determined by chance.

Life is not the consequence of a plan embodied in the laws of nature: it is a mere accident of chance. It can only be understood existentially. Monod reduces "Necessity", i.e. the laws of nature, to natural selection.

In the 19th century the French physicist Pierre Laplace suggested that, known the position and motion of all the particles in the universe, Physics could predict the evolution of the universe into the future.  Laplace formulated the ultimate version of classical determinism: that the behavior of a system depends on the behavior of its parts, and its parts obey the deterministic laws of Physics. Once the initial conditions are known, the whole story of a particle is known. Once all the stories of all the particles are known, the story of the whole system is known. For Laplace, necessity ruled and there was no room for chance. Monod shattered this vision of reality and made it even worse for humans: we are not robots, deterministic products of universal laws, but mere products of chance. In Monod's world, chance plays the role of rationality: chance is the best strategy to play the game of life. Chance is necessary for life to exist and evolve.

Chance alone is the source of all innovation and creation in the biosphere.  The biosphere is a unique occurrence non reducible from first principles.  DNA is a registry of chance.  The universe has no purpose and no meaning.

Monod commented: "Man knows at last that he is alone in the universe's unfeeling immensity out of which he emerged only by chance".

In reality, what Monod highlighted is that the structures and processes on the lower level of an organism do not place any restrictions on higher-level structures and processes. Reality is layered into many levels, and the higher levels are free from determinism from the lower levels. What this means is that high-level processes can be influenced as much from "above" as they are from "below".  Monod's "chance" could simply mean "environment" (which even leaves open the possibility of the super-environment of a god influencing all systems).

The German biophysicist Bernd-Olaf Kuppers thinks that there is nothing special about life: all living phenomena, such as metabolism and inheritance, can be reduced to the interaction of biological macromolecules, i.e. to the laws of Physics and Chemistry. In particular, the living cell originated from the iterative application of the same fundamental rules that preside to all physical and chemical processes. Kuppers favors the hypothesis that the origin of life from inorganic matter is due to emergent processes of self-organization and evolution of macromolecules. But, in the balance between law and chance, only the general direction of evolution is determined by natural law: the detailed path is mainly determined by chance.  Natural law entails biological structures, but does not specify which biological structures.

To contrast Monod’s existential pessimism, Freeman Dyson wrote: "The more I examine the universe and study the details of its architecture, the more evidence I find that the universe in some sense must have known that we were coming."



If Monod thought that life was highly improbable and happened only by chance, the US biologist Harold Morowitz believes that life occurred so early in the history of the planet because it was highly probable.

Based on the chemistry of living matter, Morowitz argued that the simplest living cell that can exhibit growth and replication must be a "bilayer vesicle" made of "amphiphiles" (a class of molecules, that includes, for example, fatty acids). Such a vesicle, thermodynamically speaking, represents a "local minimum" of free energy, and that means that it is a structure that is likely to emerge spontaneously.  The bilayers spontaneously form closed vesicles. The closure (the membrane) led to the physical and chemical separation of the organism from the environment. This is, for Morowitz, the crucial event in the early evolution of life.  Later, these vesicles may have incorporated enzymes as catalysts and all the other machinery of life.  These vesicles are the "protocells" from which modern cells evolved.

In other words, Morowitz believes that first came membranes: first membranes arose, then RNA, DNA or proteins or something else originated life. First of all an organism has a border that differentiates it from the environment, that isolates it thermodynamically, that bestows it an identity, that enables metabolism. The second step is to survive: the membrane's content (the cell) must be able to interact with the environment in such a way that it persists. Then the cell can acquire RNA or DNA or whatever else and reproduce and evolve and so forth.

All of this happened not by chance, but because it was very likely to happen. It was written in the laws of Physics and Chemistry.

Furthermore, Martin Eigen refuted Monod's thesis by showing that natural selection is not blind. Eigen agrees with Monod that information emerges from random fluctuations (from chance), but he thinks that evolution does not act blindly. Evolution is driven by an internal feedback mechanism that searches for the best route to optimal performance.

Eigen found that the distribution of variants is asymmetric, and tends to favor the "best" variants (from a survival point of view). Life seems to know where to look for best variants. As a matter of fact, Eigen discovered a feedback mechanism, inherent in natural selection, that favors (or accelerates the search for) superior variants.  Selection is not blind because it is driven by this internal feedback mechanism. Evolution is inherently biased towards the "best" possible solution to the survival problem, and this creates the illusion of the goal-directedness of evolution.

Evolution is "directed" towards optimization of functional efficiency.

Where Monod thinks that (biological) information arises from non-information by sheer luck, Eigen thinks that a fundamental law drives non-information towards information.


   The Inevitability of Life

Kauffman proved that life is vastly more probable than traditionally assumed.

The US physicist Jeremy England ("Statistical physics of self-replication", 2013) showed that when matter is driven by a strong external source of energy (like the sun) and surrounded by a “heat bath” (like the sea), it tends to restructure itself in order to dissipate increasingly more energy, i.e. to behave like living matter. That “restructuring” can occur in many ways but two are obvious: self-replication and self-organizing. These are two processes that cause (allow?) a system to dissipate increasingly more energy.

The Belgian (but Russian-born) physicist Ilya Prigogine had analyzed the behavior of open systems near equilibrium. The behavior of systems that are far from equilibrium because driven by stronger external sources of energy was studied  by the Australian physicist Denis Evans ("Probability of Second Law Violations in Shearing Steady States", 1993) and by the Polish physicist Chris Jarzynski ("Nonequilibrium Equality for Free Energy Differences", 1997). Then the British chemist Gavin Crooks ("Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences", 2008) discovered a simple law: the probability that atoms will undergo a thermodynamic process divided by the probability of the same atoms undergoing the reverse process (such as reconstituting the original lump of sugar) increases as entropy production increases. In other words, the system’s behavior becomes more and more irreversible. From these observations England derived his theory.

At the same time others showed that self-replication is not a property of living beings alone. Philip Marcus ("Three-Dimensional Vortices Generated by Self-Replication in Stably Stratified Rotating Shear Flows", 2013) and Michael Brenner ("Self-replicating colloidal clusters", 2013) have discovered it in nonliving matter too.


A History of Life

The Belgian biologist Christian de Duve assembled a detailed explanation of how life started and developed, an explanation that is consistent with the data available from Geology, Paleontology and Anthropology.

One of the guiding principles in his search for the origins of life is that the same principle that gave rise to the chemistry of life ("proto-metabolism") must preside over the chemistry of today's life (metabolism).

Life started, in his opinion, with the spontaneous formation of organic molecules that are widely available in the universe.  Organic matter is made of a combination of Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorous and Sulfur (the "CHNOPS" principle).  The prebiotic conditions of the Earth enabled them to grow in a recursive relationship that eventually gave rise to nucleic acids and proteins. Life is this network of mutually binding chemical reactions. Life was bound to rise under the conditions of prebiotic Earth.

In sharp contrast with Monod, life turns out to be a deterministic process that is likely to occur whenever the proper conditions are in place.

DeDuve then analyzes how "base pairing" (the "doubling" in the double helix of DNA) is but a special case of a general mechanism of nature, "molecular complementarity".  This phenomenon opened the "age of information", in which chemistry that had nothing to do with transmitting information gave rise to replication, inheritance and evolution, processes which are based on information.  RNA emerged before proteins did and was responsible for the survival and reproduction of the early forms of life. RNA molecules were the first catalysts of life.  Catalysts sped up the chemical reactions required by life.  Because of the fragility of proto-life forms, the process that led to RNA molecules must have been extremely rapid.

Replication was initiated by single-stranded RNA molecules but soon led to double-stranded nucleid acids.  The mechanism of pairing naturally enables the process of replication, as originally noted by Crick himself (the double works as a negative and a positive, one being the template for the assembly of the other).  RNA molecules made of the four A,G,U and C bases had the advantage that could be replicated, thanks to base pairings.  RNA genes were born. Selection began operating.  Protein synthesis began occurring.

The next quantum leap was the formation of the genetic code and the assembly of a translation apparatus.  Then, the separation of replication and translation gave rise to DNA.

Membranes, i.e. outer defenses, were born because the protocell had to devise efficient ways to derive energy from the environment (transmitting signals from the cell to the environment and viceversa, binding with the environment).  Life became a property of discrete, autonomous units.

At the same time, cell division began to support replication.

Information-based chemistry allowed for the assembly of a cellular structure, which is the one common ancestor to all forms of life on Earth.

Multi-cellular organisms were created over a long period of time (possibly as long as one billion years). Prokaryotes (bacteria) evolved into eukaryotes: the cell grew more complex, the cell became capable of eating other cells, the cell established "endosymbiosis" (permanent symbiosis) with other cells.

The next accelerating factor was sexual reproduction, again due to constrained chance, which led to the biodiversity we are familiar with in our age and to the complex interplay of organisms within the same ecosystem.  The next major step was the development of brains, and the advent of consciousness, which is now reshaping the course of life on Earth. Both life and mind are deterministic consequences of the matter of this universe, not mere chance events.

Each step in the growth of life was providing an incremental selective advantage.

DeDuve believes in one and only one origin of life for the simple reason that life is one: there is only one "life" we are familiar with, the one made of genetic code, metabolism, etc. All "living" creatures share the same "living" processes.

A leitmotiv of the evolution of life is "constrained contingency": mutations occur by chance, but are constrained by physical, chemical and environmental factors.

DeDuve therefore reconciles chance and necessity.


Complexity and Specialization

Darwin himself objected to the idea that there might be a trend towards complexity in nature. Nothing in the laws of evolution implies that life should evolve towards increased complexity. Nevertheless, the facts seem to tell a different story: eukaryotic cells are more complex than prokaryotic ones, animals and plants are more complex than protists, and so on.

The British biologist Ronald Fisher, tried, indirectly, to justify that fact with his fundamental law: the rate of increase in the average fitness of a population equals the genetic variance in fitness. This law is like the second law of Thermodynamics, which implies that entropy can never decrease. Fisher’s law says that the average fitness of a population can never decrease (because variance is never a negative number). 

The British biologist John Maynard-Smith and the Hungarian biologist Eors Szathmary argued against Fisher’s theory and instead proposed that the increase in complexity may originate from very few episodic evolutionary transitions whose goal was not to increase complexity.  Their “major transitions” share a common aspect. Each transition affected  biological units that were capable of independent replication, and each transition turned them into biological units that needed other biological units in order to replicate. For example, independently replicating nucleid acids evolved into chromosomes (assemblies of molecules that must replicate together). Also, sexless life was replaced by species that have male and female members, and that can replicate only if a male and a female “cooperate”.  Ants and bees can only replicate in colonies.

Another side of the same coin is the history of specialization. How this happened is not clear but there must have been a point in time when a set of identical organisms “deteriorated” (or, better, differentiated) into functionally specialized organisms. There was a time when only RNA existed; that world decayed into a world of DNA (that carries out the genetic functions) and proteins (that carry out the function of catalysts). The monolithic cells of prokaryotes evolved into the combination of nucleus, cytoplasm and organelles of the eukaryotes. A world of hermaphrodites morphed into a world of sexual organisms. The members of beehives have specific roles. And so forth.

In these major transitions, sets of identical biological units were replaced by sets of specialized units that needed to cooperate in order to survive and replicate.

Maynard-Smith and Szathmary interpret these transitions also on the basis of information theory: they involve a change in the language that encodes information and a change in the medium that expresses that language. In other words, they are about the way in which  information is stored and transmitted.

Maynard-Smith defined progress in evolution as an increase in information transmitted from one generation to another.

The key to evolution is heredity: the way information is stored, transmitted and translated. Evolution of life as we know it relies on information transmission. And information transmission depends on replication of structures.

Evolution was somewhat accelerated, and changed in character, by and because of dramatic changes in the nature of biological replicators, or in the way that information is transmitted by biological replicators. New kinds of coding methods made possible new kinds of organisms.

Today, replication is achieved via genes that utilize the genetic code.  But this is only the latest episode in a story that started with the most rudimentary replicators.  RNA is capable of playing both the roles of replicator and enzyme, as discovered by the US biophysicist Carl Woese. Thus Maynard-Smith thinks likely that the first replicators were made of RNA.

Szathmary  showed that this would also explain why the genetic alphabet consists of four letters:  four bases are optimal for ribo-organisms. The genetic alphabet evolved when enzymes were ribozymes and organisms with protein enzymes have simply inherited it. At first RNA molecules performed both the job of information management and of constructing the structures specified in that information.

The first major breakthrough in evolution, the first major change in the technique of replication, was the appearance of chromosomes: when one gene is replicated, all are.

A second major change came with the transition from the solitary work of RNA to the dual cooperation of DNA and proteins: it meant the shift from a unitary source of replication to a division of labor: on one hand the nucleic acids that store and transmit information (i.e., the birth of the genetic code as it is today), and on the other hand the proteins that construct the body. Metabolism was born out of that division of labor and was facilitated by the chemical phenomenon of autocatalysis. Autocatalysis allows for self-maintenance, growth and reproduction. Growth is autocatalysis.

Early on, monocellular organisms (prokaryotes) evolved into multicellular organisms (eukaryotes). The new mechanism that arose was gene regulation: the ability to switch on different genes in different cells depending on the stimuli that the cell receives. The code didn't simply provide the instructions to build the organism, but also how cells contributed to the organism.

Asexual cloning was eventually made obsolete by sex, and sex again changed the rules of the game by shuffling the genetic information before transmitting it.  The living world split into animals, plants and fungi that have different information-transmission techniques.

Individuals formed colonies, that developed other means of transmitting information, namely "culture”; and finally social behavior led to language, and language  is a form of information transmission itself.

Each of these steps "invented" a new way of coding, storing and transmitting information.

Maynard Smith does not continue the story to what is truly unique about humans: morality. Over the centuries humans have progressively abandoned or at least decried old habits such as war, torture, slavery, racism, gender discrimination, pollution.

Maynard-Smith also introduced Game Theory into Biology. The premise of game theory is that individuals are rational and self-interested Maynard Smith applied this definition to populations (instead of individuals) and interpreted the two attributes biologically: rationality means that population dynamics tend towards stability, and self-interest means fitness relative to the environment.


Carbon Chauvinism

Life on Earth uses carbon-based molecules and a base-4 genetic code. Is this part of the definition of life? Is it possible for a living being from another planet to be made of something else and be encoded in a different kind of code, or life is possible only for carbon-based molecules and base-4 genetic codes?

There are simple chemical properties that made carbon-based molecules more efficient for creating the kind of life that prospers on Earth. It is, in fact, relatively easy to prove that no other kind of molecules could provide such an effective medium for the creation of evolving, reproducing and growing bodies.

Nonetheless, it is not clear yet if life “has” to be based on carbon, if non-carbon forms of life are possible.

Humans have built robots made mostly of metal and copper that are capable of reproducing, growing, communicating and so forth, i.e. that satisfy the ordinary definitions of life. This is a very simple example of life that does not use Carbon-based molecules and water. If it is possible on Earth itself, it is hard to believe that non-Carbon life is impossible anywhere in the universe.  It is not easy to determine which one is more likely to "spontaneously" arise in nature, an eye or one of these robots.  (The "spontaneously" is in quotes because nothing is truly spontaneous: an eye is the product of natural forces just like a robot is, so far, the product of some human design).

Most calculations of the probabilities of carbon-based life are done by scientists who are biased by the fact that they themselves are made of carbon-based molecules. Earthly scientists (made of carbon-based molecules) do not calculate the odds that a robot (made of steel and copper) or some other form of life could emerge in a different kind of planet or star, where, for example, some odd natural phenomena produce stainless steel and copper wires by the millions.

Most Earthly scientists who talk about "another form of life" end up talking about the Earthly form of life (and therefore proving that carbon-based life is the only one possible).

The truth is that is a bit premature to claim that only carbon-based life is possible in this universe.

Also, it is relatively easy to build purely software systems that exhibit whatever property one ascribes to life. These software systems do not use Carbon-based molecules or water: in fact, they use no chemistry at all.

The real issue is that biologists do not agree on a definition of life. If we don't know what life is, it is hard to discuss... what life is.


The Origin of Adaptation

Living organisms exhibit a striking property: their parts and their behavior are adapted to ensure the survival and the reproduction of their entire body.  Not only the parts: the behavior too. Animals are born knowing what to do to survive.

Adaptation is a fact, not an opinion.  How it came to be is an opinion, not yet a fact.

According to Jean-Baptiste Lamarck, the French botanist of the 19th century who had already claimed in 1802 that animal species are not immutable, acquired characters are inherited: each generation passes on to the following generation what it has learned about adapting to the environment. So far, evidence is against Lamarck: genes do affect proteins, but proteins cannot affect genes. It is a one-way process, from genes to bodies. Once they have been created, bodies cannot change their genes. No matter how much they learn, bodies cannot store it in their genes and pass it on to future generations.

The evidence against Lamarckism is overwhelming. Every generation has to re-learn what previous generations learned. After thousands of years of civilization, children are still born unable to write and to count. Worse: after millions of years, we are still born unable to walk and to speak. According to Lamarck, humans should have already manufactured genes about walking upright and speaking.

We have not found any evidence that a body can purposely alter its own DNA or the DNA it will pass to the offspring. DNA changes only because of random errors in copying. The DNA of a species is manufactured over millions of years by natural selection: the errors that survive become permanent instructions for future generations. But each individual is stuck with the DNA it receives at birth.

Even if he was wrong about the specific mechanism for evolution, Lamarck had powerful insights in the way Nature works on a large scale. In particular, he argued that all of Nature reflects a few general organizing principles. Foremost among them is the effect of use and disuse of organs: muscles atrophy if they are not exercised and bones grow stronger at points where muscles are attached and produce tension.

What Darwin proposed was not "the" theory of evolution (which had already been proposed by many thinkers, including Lamarck himself), but a particular mechanism for evolution: the differential rate of reproduction, under pressure from the environment, of different sorts of individuals within a population; i.e., the differential survival and reproductive success of units of different adaptive efficiency. The key point of Darwin’s theory is that variation and selection are dual aspects of the same problem. Lamarck proposed instead a transformational (rather than variational) mechanism.

Later, Darwin's theory of evolution by selection of that variation was indirectly supported by Mendel's mechanism for the inheritance of variation.

However, the US psychologist James-Mark Baldwin discovered what is now known as the "Baldwin effect" ("A New Factor in Evolution”, 1896): the ability of individuals to learn can guide the evolutionary process, i.e. the ability to learn can affect evolution. Baldwin was interested in the long-term evolutionary effects of environmental changes. For example, organisms that move to a new ecological niche indirectly subject their descendants to selection pressures which are different from the ones experienced by their ancestors; i.e., the selection pressures that generated their own generation are different from the ones that will generate future generations. It is therefore possible that future generations will evolve because of the change in selection pressure due to the new environmental conditions. The ancestors had to “learn” how to behave in the new environment, whereas the descendents will behave by instinct in that same environment. Thus learned behaviors may become instinctive behavior in subsequent generations, without requiring Lamarck’s inheritance. He proved that evolution under those effects is more rapid than in a situation of no change.

In 1958 the Austrian physicist Erwin Schroedinger said something similar: behavior can indirectly alter genetic code, by enabling organisms to survive and reproduce where non-intelligent organisms would simply die.

The British geneticist Conrad Waddington (“Genetic Assimilation Of An Acquired Character”, 1953) discovered “genetic assimilation”, the process of differential selection by which an individual’s response to an environmental stimulus can eventually become a fixed behavior in the species even in the absence of stimulus. Waddington also pointed out that the behavior of a living being changes the environment, and therefore helps to create the selection pressure that will influence its own evolution. Both phenomena point to the importance of the behavior of the organism for its own evolution in a sort of Lamarckian fashion.

Likewise, the German zoologist Ernst Mayr argued that any change in behavior by a population (for example, the acquisition of a new habit due to a move to a new ecological niche) has an effect on the selection pressures that will operate on that population.

In 2000 the US biologist Michael Skinner discovered a non-genetic form of inheritance that resurrected Lamarckian inheritance, although on a smaller scale ("Epigenetic Transgenerational Actions of Endocrine Disruptors and Male Fertility", 2005). He showed that environmental chemicals can cause the inheritance of disease in rats through three generations. Later similar "epigenetic transgenerational inheritance" of traits and diseases was discovered in plants and other animals. Skinner argued that changes in the environment can alter our genes directly and proposed a unified theory of evolution mixing Darwin and Lamarck ("Environmental Epigenetics and a Unified Theory of the Molecular Aspects of Evolution", 2015).


The Origin of Speciation

The modern synthesis offers a powerful paradigm for the evolution of life, but looks still inadequate to explain the origin of species. The problem is that it is very difficult to create a new animal. New traits must be assembled in such a way that they allow the organism to survive at least a few generations. The new traits must stabilize. The mutating individuals must avoid being rapidly re-assimilated into the original species through interbreeding. And, last but not least, both sexes must arise at the same time.

Darwin did not solve the mystery of the origin of species, despite the fact that he titled his book that way. Only after the advent of genetics, and mainly thanks to the work of the German zoologist Ernst Mayr, were biologists able to advance hypotheses. If a population splits in two because of whatever accident, both random mutations and environmental differences (natural selection) will cause the two groups to evolve differently until they become two separate species.  If the two groups ever meet again, they are more likely to compete than to interbreed, as any species that have similar behavior in the same territory.

Today, there is consensus that species are born (at least) from geographic isolation of a population, but then it is not clear what biological mechanism originates hybrid infertility (this population cannot inbreed with other populations anymore) and fertile diploids (this population has both male and female that can breed).

It is not clear whether the same sudden discontinuity at the level of the phenotype (the organism) occurs as well at the level of the genotype (its genome). We know that the genotype is not the same for every member of a species, that small changes occur all the time. It may well be that changes can accumulate for a long period of time without any visible consequence on the phenotype while they are reaching a crisis point. At that point of genetic “drift”, the smallest change in the genotype may have catastrophic consequences for the phenotype.

In the opinion of Harold Morowitz, this is the way organisms acquire new levels of organization, the way they evolve towards more and more complexity. All of a sudden a “gateway” opens up that leads to a whole new range of possibilities. For example, a glue that can hold cells together may be responsible for the sudden appearance of multicellular organisms which in turn quickly acquired a completely new behavior.

The US linguist Philip Lieberman believes in “functional branch-points”. He recalls two principles. The first principle is that natural selection acts on individuals who each vary: species that successfully change and adapt are able to maintain a stock of varied traits coded in the genes of the individuals who make up their population. The second principle is the "mosaic" principle, which holds that parts of the body of an organism are governed by independent genes. There are no central genes that control the overall assembly of the body.  Given these principles, a series of small, gradual changes in structure can lead to an abrupt change in the behavior of the organism; and an abrupt change in behavior may cause an abrupt change in morphology which causes the formation of a new species. New species are formed at "functional branch-points".

By surveying “adaptive radiation” (the spread of species of common ancestry into different niches) and “evolutionary convergence” (the occupation of the same niche by outcomes of different adaptive radiation), the US biologist Edward-Osborne Wilson argued that opportunity is likely to cause an explosion of species formation.

The problem is that the genetic mechanism that fosters variation is not well understood. Several researchers have observed that bacterial cells tend to choose for themselves advantageous mutations over harmful mutations. Darwinism and modern genetics, instead, prescribe that mutations must be absolutely random. One possible explanation that is not in conflict with Darwinism is that, under conditions of stress, cells generate many more mutations than they would normally do, and of these mutations the most advantageous survive and are observed. If confirmed, this would imply that cells know when the survival of their species is in jeopardy and enter a state of frenzy in which they produce as many mutations as possible, hoping that at least one will be able to adapt and resolve the stress. Natural selection is certainly a weak process for evolving species, but it would be far more effective if it turns out that it is coupled with another process which is capable of generating a lot of diversity every time evolution is desirable because of environmental pressure.


Design Without Progress

A not so subtle argument has to do with the concept itself of “evolution”. Evolution intuitively implies a progress from less to more, from lower to higher. Whether Darwin intended it that way or not, the idea that species evolve towards better and better beings does not follow logically from his premises. In particular, any change in the genes is more likely to do harm than to do good to the organism: how can this possibly lead to better organisms?

The US paleontologist Stephen Jay Gould does not believe that there is any inherent "progress" towards bigger complexity in evolution. Life evolves largely by accident. He opposes a biased interpretation of the fossil record. For example, he pointed out that bacteria still represent the dominant form of life on this planet. One should focus on variety and diversity, not "complexity". He objected to choosing one feature as representing a trend. If one considers the whole diversity of life, there is no trend towards progress or higher complexity. Simple forms still predominate in most environments.

We are unlikely accidents, not the fruit of progress.  Any replay of the tape of life would yield a different, unpredictable evolutionary history, albeit still a meaningful one. Evolution is not in the hands of determinism and not in the hands of randomness, but in the hands of contingency.  Chances that humans would be recreated if history were played back are kind of slim.  Gould thought that consciousness evolved only once in all the experiments that life performed on Earth (whereas eyes evolved many times in many species, and so did wings, in both birds and insects).  Consciousness is therefore unlikely to occur, and human consciousness must be considered a sheer accident. If the tape of life were played back again, it is unlikely that a conscious being would emerge.

Ernst Mayr put it bluntly when he argued that evolution does not seem to reward smart organisms over stupid ones.

On the other hand life may be more probable than it appears to be, since it happened on Earth as soon as it could happen.

As Francis Crick put it, natural selection has the function of making unlikely events very common. 

The mind itself came into the picture quite late in the evolutionary process. If mind is unique to humans, then a tiny change in the evolutionary chain could have resulted in no humans, and therefore no mind. Mind does not look like a momentous episode, but as a mere accident. 

Evolution is still a blind process. At any point in evolutionary history the outcome is uncertain.  Evolution does not proceed towards complexity but randomly produces variety.  Progress is purely accidental.  If we interpret Darwin literally, there is only variation, not progress.


Evolutionary Crises

Francis Galton, Darwin’s cousin, did not believe that species could be created “gradually”, as Darwin’s theory implied. Galton believed that new species can arise only in bursts, and so he modified Darwin’s theory in a key way. He reasoned that variation allows for a lot of change, but only within a species. A species is a stable state, and has a lot of resilience. When something destabilizes that state, then there occurs a sudden change, and a new species is created, i.e. a new stable state is rapidly reached.

The weakness of Darwin’s theory to explain the complexity of life led the German geneticist Richard Goldschmidt in the 1930s to similarly conclude that evolution must proceed by great leaps rather than by small steps.

Expanding on Galton’s theory, Gould introduced the idea of "punctuated equilibrium" ("Punctuated equilibria", 1972): evolution occurs through rapid bursts of speciation after long periods of stasis, as opposed to the traditional view of gradual, continuous unfolding of species.  Mostly nothing happens; however, when something happens, it happens quickly. Incidentally, we know for sure that this is the way progress occurred in human civilization: long periods of stasis were followed by sudden bursts of progress (we are living in one of those).

About 600 million years ago the first living beings that exhibited bilateral symmetry appeared on Earth. These “bilaterians” were symmetrical beings, characterized by the mirror-image balance of most limbs and organs (the notable exception being the heart, which is still asymmetric to this day). Today bilaterians rule the planet. Bilaterians include most species, from insects to mammals: two legs, two wings, two eyes, two lungs, two brain hemispheres, two kidneys, two nostrils, etc. Organs and limbs that are not duplicated (such as the mouth or the anus or the penis) are located exactly along the axis of symmetry.

It is not clear what the evolutionary advantage of bilaterians was. Although many possible candidates can be advanced, none seems to justify the sudden domination by bilaterians. The early ones were microscopic, and already rather complex. Basically, the rest of evolution was only a magnification of something that had already been created 600 million years ago.

A few million years later there was a sudden explosion of species (the “Cambrian explosion”). Again, several hypotheses have been advanced to explain why suddenly species multiplied rapidly (that animals began to alter the environment, that animals developed emotional responses that made them more likely to survive, that they started eating each other, etc), but none seems to justify the fossil record.


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