The uniformity of earth’s life, more astonishing than its diversity, is accountable by the high probability that we derived, originally, from some single cell, fertilized in a bolt of lightning as the earth cooled.
Lewis Thomas, The Lives of a Cell
Nothing in biology makes sense except in the light of evolution.
Theodosius Dobzhansky
How can life possibly emerge from inanimate matter? This is still shrouded in mystery. For the religious, this is the most direct proof of God’s existence. For example, Psalms 19:1 in the Old Testament states that, “The heavens declare the glory of God; the skies proclaim the work of his hands.” While this and other verses in the Bible do not specifically indicate which properties or features of the world represent evidence of God’s intelligent nature, they presuppose that the world exhibits such features, and that they are readily discernable to a reasonably conscientious person.
In other words, the order and complexity we observe in the world, including life, is so complex it had to be designed. This is known as the argument from design, or teleological argument, which has a long tradition in religion and philosophy.[1]
But do we need to invoke an intelligent designer? No one can doubt that there are fundamental differences between living organisms and non-living entities. However, in the last four decades or so scientists have identified several self-organizing mechanisms that could have made life possible in the primordial broth prevalent in the early Earth. In fact, they have created artificial cells in the lab that can grow and divide like natural bacteria. Once a self-replicating cell emerges, evolution takes over.
Here, I examine the evidence that these two natural processes, self-organization, and evolution, are responsible for complex life on Earth, and perhaps elsewhere in the universe.
Self-organization and the emergence of life
Something is self-organizing if, left to itself, it tends to become more organized. This may strike you as counterintuitive: we normally expect that, left to themselves, things get messy. Let me explain. Things can start in a highly random state and, without being shaped from the outside, become more organized. We can find evidence of this everywhere we look in nature: the pacemaker cells of the heart; neurons in the visual cortex; crickets that chirp in unison; and swarms of flashing fireflies. No matter how disordered or uncoordinated the different elements in the system are at the start, eventually all become synchronized.[2]
You’re probably familiar with the 1952 Miller-Urey experiment, which demonstrated that amino acids, the chemical constituents of the proteins used in all living organisms, can be synthesized from inorganic compounds under conditions intended to replicate those of the early Earth. Since then, other experiments have shown that amino acids can be produced in the lab under the right conditions. Scientists have proposed various external sources of energy that may have triggered these reactions, including lightning and radiation. For example, these pre-biological evolutionary steps may have taken place in submarine hydrothermal vents, resulting in various chemical interactions and divisions that produced amino acids.
In the 1960s, biophysicist Alec Bangham of the Animal Physiology Institute in Cambridge, UK, made a remarkable discovery about lipids: they can put themselves together. When he extracted lipids from egg yolks and threw them into water, he found that the lipids would naturally organize themselves into double-layered bubbles roughly the size of a cell. Bangham’s bubbles became known as liposomes. Subsequent studies of liposomes demonstrated that if lipids existed at the dawn of life, they would naturally, and quickly, formed simple cell membranes.[3]
More recently, a series of impressive discoveries shows how cell-like structures could have self-assembled from fatty chemicals likely to have been present on the primitive Earth. In an article published in Nature in 2001, researchers Jack Szostak, David Bartel and Luigi Luisi declared that the way to make a synthetic cell was to get a protocell and a genetic molecule to grow and divide in parallel, with the molecules being encapsulated in the cell. If the molecules gave the cell a survival advantage over other cells, the outcome would be “a sustainable, autonomously replicating system, capable of Darwinian evolution ... It would be truly alive,” they wrote.[4]
The trio managed to make substantial progress in this program; their experiments came close to creating a spontaneously dividing cell from chemicals assumed to have existed on the primitive Earth. The research shed light on how even the most complex building blocks of the cell, such as nucleotides, could have formed. Subsequent research by Szostak and others discovered that bases like adenine will easily form from simple chemicals like hydrogen cyanide. They also discovered possible mechanisms for synthesizing nucleotides from prebiotic chemicals.[5]
In 2009, researchers at the Cold Spring Harbor Laboratory reported that they had developed two RNA molecules that can promote each other’s synthesis. RNA, a close cousin of DNA, almost certainly preceded it as the genetic molecule of living cells. Besides carrying information, RNA can also act as an enzyme to promote chemical reactions. RNA is more versatile, being able not only to store information, like DNA, but also to use that information to catalyze reactions, a job now performed by proteins.
The system was not “alive” in the conventional sense, but it performed central functions of life-like replication and adapting to new conditions. This solved the “chicken-and-egg” problem about which ability came first into the world. The answer is that RNA could be both. Although these molecules were not self-sufficient enough to be alive, they nevertheless showed that manmade molecules can evolve over successive generations.[6]
In 2010, researchers led by Craig Venter at the J. Craig Venter Institute (JCVI) in San Diego, California, announced that they had created synthetic “minimal” cells. They had replaced the genes in the cells of a simple bacterium, Mycoplasma mycoides, with a genome that they had synthesized with the aid of a computer. The only DNA in the cells was the designed synthetic DNA sequence, including a “watermark” sequence they added to uniquely identify the code. A colony of cells injected with the digitized genome sequence (which they named JCVI–syn1.0) grew and multiplied, just like any other “living” colony. The scientists continued to remove chunks of DNA from syn1.0’s genome, and in 2016, they unveiled an even sparer version, known as syn3.0, that could metabolize and reproduce with just 473 genes. However, Venter and his colleagues noticed that the cells were producing daughter cells of bizarre shapes and sizes.[7] The biologist Elizabeth Strychalski and her colleagues from the US National Institute of Standards and Technology reintroduced only seven genes into these synthetic bacterial cells and found that, amazingly, this was enough to restore normal, uniform cell division and growth.[8]
There could be many potential practical applications in the creation of synthetic cells, such as producing valuable chemicals, sensing environmental conditions, delivering life-saving drugs, and performing other tasks in industry and medicine. Minimal cells could also provide insight into the origin of life by illuminating which capabilities were essential for primordial cells. The creation of synthetic life-like cells in the lab shows that, in essence, life is information that does not need a vital or supernatural force to be passed from one living being to another.
The evolution of complexity
Once we figure out how the first self-replicating molecule may have formed, the next question is, how did it get to be so complex? Even the simplest of cells contains hundreds of proteins and enzymes that interact in complex ways. Creationists often cite the complexity of the cell as evidence of God’s influence, because it seems impossible that cells could have become so complex without outside (or divine) intervention.[9] But scientists have shown that complexity can arise “spontaneously” given strong enough selective pressure. They now have a better understanding of how selection pressures can turn single cells focused solely on their own survival into a complex, multicellular organism where cells coordinate and work together.
Probably the best non-technical account of how this process, driven by natural selection, could lead to complex organisms is found in the book The Blind Watchmaker by the evolutionary biologist Richard Dawkins. The eponymous “watchmaker” refers to one of the most famous creationist arguments, made by the 18th-century theologian William Paley: Just as a watch is too complicated and too functional to have sprung into existence by accident, so too must all living things, with their far greater complexity, be purposefully designed. In the book, Dawkins provides a detailed account of the basic principles underlying evolution and illustrates how simple organisms slowly change over time to create a world of enormous complexity and diversity. Moreover, the complex process of natural selection is unconscious and automatic, hence the “watchmaker in nature” is a blind one – working without foresight or purpose.[10]
In the three decades or so since Dawkins’ book was first published scientists have made quite a bit of progress in testing some of these mechanisms in practice. For example, in one experiment, researchers showed how multicellular yeast can arise in less than two months in the lab by applying strong selective pressure for multicellularity. “Although known transitions to complex multicellularity, with clearly differentiated cell types, occurred over millions of years, we have shown that the first crucial steps in the transition from unicellularity to multicellularity can evolve remarkably quickly under appropriate selective conditions,” write the authors.[11]
Researchers have been able to observe evolution in real time. Since 1988, Richard Lensky, professor at Michigan State, and his colleagues, have followed the descendants of a single E. coli bacterium, a microbe that normally populates our intestines. Bacteria have short life spans and, in this experiment, went through more than six generations a day, which means that they observed over 50,000 bacterial lifetimes. Every day, for 25 years, members of Lenski’s lab transferred the E. coli into a new flask with sugar and other nutrients.
In 2003, after about 31,500 generations, the scientists observed that one bacteria population had “discovered” how to use citrate – a chemical compound derived from citric acid – as a food source. Citrate was given to all the bacteria to help them absorb minerals but cannot normally be digested in the presence of oxygen. The researchers found that a series of genetic mutations in the population enabled citrate to enter the cell even when oxygen was present. Moreover, an additional set of mutations multiplied the gene inside the DNA to make the bacteria more efficient in their absorption of citrate. The ability to digest citrate allowed the population to increase in size and diversity. Eventually, this population “wiped out” others that did not develop this capability.[12] This is exactly how natural selection should operate in practice (see Box 2).
Box 2: Evolution by Natural Selection Evolution is the product of two opposing forces: processes that introduce variation in traits, and processes that make some variants rarer or more common. A trait is a characteristic such as eye color, height, or a behavior, that is expressed when an organism’s genes interact with its environment. Genes vary within populations, so organisms show differences in their traits. The main cause of variation is mutation, which changes the sequence of a gene. Altered genes, or alleles, are then inherited by offspring. Two main processes cause variants to become more common or rare in a population: natural selection and genetic drift. Natural selection causes traits that aid survival and reproduction to become more common, and traits that hinder survival and reproduction to become less common. Natural selection occurs because only a few individuals in each generation will survive, since resources are limited, and organisms produce many more offspring than their environment can support. Over many generations, mutations produce successive, small, random changes in traits, which are then filtered by natural selection and the beneficial changes retained. This adjusts traits so they become suited to an organism's environment: these adjustments are called adaptations. Genetic drift refers to random fluctuations in the frequencies of alleles from generation to generation, due to chance events. It may cause gene variants to disappear completely, and thereby reduce genetic variation. In contrast to natural selection, the changes due to genetic drift are not driven by adaptive pressures, and may be beneficial, neutral, or detrimental to reproductive success. The effects of genetic drift are more pronounced in small populations. There is also the founder effect, which shows how the isolation of small populations from larger ones can accelerate evolutionary change. This happens because a small population’s average characteristics are likely to differ from those of the larger group from which it is drawn. This effect may explain the splitting of humanity into different racial groups. See, e.g., Guttman, B. (2005). Evolution: A beginners’ guide, Oneworld Publications.
Outside of the laboratory we have observed this real-time during the global coronavirus pandemic. The rapid spread of new variants, such as Delta and Omicron, offers clues to how SARS-CoV-2 adapts quickly to evade immunity. These variants carry mutations that blunt the potency of antibodies raised against past versions of SARS-CoV-2. And the evolutionary forces propelling this “antigenic change” are likely to grow stronger as most of the planet gains immunity to the virus through infection, vaccination, or both. Most virus specialists now believe that the new pathogen will never be eradicated. Rather, it will become endemic – the fifth coronavirus to permanently establish itself in humans, alongside four “seasonal” coronaviruses that cause relatively mild colds and have been circulating in humans for decades or more.[13]
This, and many other examples, show that “unassisted” evolution can produce key genetic innovations. In this sense, DNA is a kind of living fossil that opens a window to our past; every change or new trait, from the ability to process certain foods, to our enlarged brains, is due to one or more stepwise changes in DNA. The study of similarities and differences in the DNA sequences of living organisms has allowed researchers to reconstruct the family tree linking those organisms. “The DNA record,” writes geneticist Sean B. Carroll “allows us to see beyond flesh, bones, and blood, directly into the fundamental text of evolution.”[14] This rapidly expanding DNA record vividly demonstrates how natural selection works and how it generates complexity.
The study of genes from long-extinct animals, for example, has shed light on the way evolution works at the cellular level. For the first time, scientists have demonstrated the step-by-step progression of how evolution created a new piece of molecular machinery by reusing and modifying existing parts. In one study, for example, scientists were able to determine how a progression of small changes produced the intricate mechanisms found in stress hormone receptors in lampreys and hagfish, two surviving jawless primitive species. This study also illustrates how evolution can innovate and improve functions over time, thus producing the intricate mechanisms found in living cells without the assist of an external or intelligent agent.[15]
Transitional forms in the fossil record
One common objection from creationists is that there is no evidence supporting the splitting of the species, either animal or plant. The Bible is clear that Adam was formed from the dust of the Earth (Gen. 2:7) and that he was the first man (1 Cor. 15:45). Thus, we should not find any transitional forms between apes and humans. Any fossil is fully ape or fully human, no in-between. As one creationist website declares, “Absolutely no transitional forms either in the fossil record or in modern animal and plant life have been found. All appear fully formed and complete. The fossil record amply supplies us with representation of almost all species of animals and plants but none of the supposed links of plant to animal, fish to amphibian, amphibian to reptile, or reptile to birds and mammals are represented nor any transitional forms at all.”[16]
Not quite. In 2006 scientists discovered in the Canadian Arctic fossils of a 375 million-years-old fish (dubbed Tiktaalik roseae) that, they argued, was the long-sought “missing link” in the evolution of some fishes from water to a life walking on four limbs on land. On closer examination the scientists found telling anatomical traits of a transitional creature, a fish that is still a fish but exhibiting changes that anticipate the emergence of land animals – a predecessor of amphibians, reptiles and dinosaurs, mammals and eventually humans. The head and braincase, they found, were changing, a mobile neck was emerging, and a bone associated with under-water feeding and gill respiration was diminishing in size – a beginning of the bone’s adaptation for an eventual role in hearing for land animals. According to a researcher in the field, the anatomy of this early transformation in life from water to land had never been observed with such clarity.[17]
Another prominent example is Archaeopteryx, one of the most famous transitional fossils that provides evidence for the evolution of birds from theropod dinosaurs. There is evidence that birds evolved from a type of dinosaur during the Mesozoic era (250 million to 66 million years ago). One candidate is Archaeopteryx, which despite its broad wings and inferred ability to fly or glide has more in common with other small Mesozoic dinosaurs than it does with modern birds. It shares several features with the deinonychosaurs, including jaws with sharp teeth, three fingers with claws, feathers (which suggest homeothermy), and various skeletal features. These features make Archaeopteryx a clear candidate for a transitional fossil between dinosaurs and birds, making it important in the study both of dinosaurs and of the origin of birds.[18]
Paleoanthropologists have also unearthed fossils that represent new links to the evolution of humans. For years, scientists have searched for links between Australopithecus, a genus of early hominins that existed in Africa about 3.5 million years ago, and even earlier possible ancestors. In 2006, scientists found 4.2 million-years-old fossils that were anatomically intermediate between the earlier species Ardipithecus ramidus and the later species Australopithecus afarensis. In 2008, two remarkably well-preserved skeletons of a new hominid species were found in a cave in South Africa. The fossils, which combine apelike and human features, display the modular way in which evolution operates: They have mostly known features but in combinations that have never been seen before. Some scientists believe that the fossils belong to a new species that is the most plausible known ancestor of archaic and modern humans.[19]
To conclude: Embracing evolution and complexity
This is one of the longest, and possibly more complex ideas in the blog as it involves two key concepts: self-organization and evolution. I hope it has opened your mind to the creative forces and processes that may have contributed to the origin and evolution of life on Earth, and that even today shape how populations change as they interact with the environment. Taken together, the chemical, genetic and fossil evidence, of which I discussed only a fraction, presents a compelling, powerful rebuttal to skeptics and religious creationists. It shows the power of self-organization and evolution to give rise to complex systems that appear to be designed. No divine help is needed.
Critically, this applies not only to the emergence of life, but of other complex systems. Indeed, understanding the interplay of self-organization and evolution can help you understand other complex systems. For example, an economy is a self-organized emergent process of people just trying to make a living and get their genes into the next generation, and out of that “simple” process emerges the diverse array of products and services available to us today. The Internet is another example of self-organized emergent behavior that has evolved into an “autonomous” complex system. These systems are the result of human action not human design.
Understanding self-organization and evolution provides you with powerful mental models that can help you make sense not only of the biological realm, but also other complex systems including social, cultural, and economic interactions. As such, they should be part of everybody’s mental model toolbox.
[1]Ayala, F. J. (2006). "The Blasphemy of Intelligent Design". History and Philosophy of the Life Sciences 28(3):409–21. [2]One common argument of creationists is that, according to the second law of thermodynamics, disorder (entropy) increases inexorably with time. Thus, self-organization is impossible since it violates this law. (e.g., Bradley, W. L. (2004). “Information, entropy, and the origin of life,” In Dembski W. A. & Ruse, M. (Eds.) Debating Design: From Darwin to DNA, Cambridge University Press, 331-351). However, this is true of closed systems but not of open systems such as the Earth’s ecosystem, which is “energized” by sunlight. Also, watch this interesting YouTube video, The Surprising Secrets of Synchronization, for examples of synchronization in real life: https://www.youtube.com/watch?v=t-_VPRCtiUg. [3]Bangham, A. D. (1983) Liposome Letters, Academic Press. Also, Zimmer, C. (1995). First Cell. Discover Mag. (31 Oct 1995). [4] Szostak, J. W., Bartel D. P. & Luisi P. L. (2001) Synthesizing life, Nature, 409, 387-390 (18 Jan 2001). [5] See, e.g., Ricardo, A. & Szostak, J. W. (2009) Life on Earth, Scientific American, Special Issue: Understanding Origins. [6] Joyce, G.F. & Szostak, J. W. (2018) Protocells and RNA self-replication. Cold Spring Harbor Laboratory Press, Sep 8, 2018. [7] “Artificial life made in lab can grow and divide like natural bacteria,” by Layal Liverpool, New Scientist, Mar 29, 2021. [8] “Scientists coax cells with the world’s smallest genomes to reproduce normally,” by Mitch Leslie, Science, Mar 29, 2021. [9]Rana, F. (2011). Creating Life in the Lab: How new discoveries in synthetic biology make a case for the creator. Baker Books. [10]Dawkins, R. (1986). The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design. W. W. Norton & Company. [11]Ratcliff, W. C. et al. (2012). Experimental evolution of multicellularity. PNAS, published online Jan 17, 2012. [12]Blount, Z. D. et al. (2012). Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature, published online Sep 19,2012. See also: “8 examples of evolution in action,” by LordZB, Science, Nov 19, 2011, Carroll S. B. (2020). A series of fortunate events: chance and the making of the planet, life and you. Princeton University Press. [13]Callaway, E. (2012). Beyond Omicron: what’s next for COVID’s viral evolution. Nature, 7 Dec, 2021. [14] Carroll, B. S. (2007) The making of the fittest: DNA and the ultimate forensic record of evolution, W. W. Norton & Co., p.26. [15] Bridgham, J. T et al. (2006) Evolution of hormone-receptor complexity by molecular exploitation, Science, 312, 97-101. [16] https://www.jesus-is-savior.com/Evolution%20Hoax/Evidences/1.htm. Retrieved Sep 10, 2022. [17] Downs, J. P et. al. (2008). The cranial endoskeleton of Tiktaalik roseae, Nature, 455, 925-929. [18] Yalden, D. W. (1984). What size was Archaeopteryx? Zoological Journal of the Linnean Society. 82 (1–2): 177–188. See also “Archaeopteryx: An Early Bird”. University of California Museum of Paleontology. University of California, Berkeley. [19] Gibbons, A. (2011). Skeletons Present an Exquisite Paleo-Puzzle. Science, 333 (6048): 1370–1372.
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