|Spiral galaxy in Coma Cluster [Courtesy NASA]
What do scientists understand about the origin of life?
David H. Bailey
Updated 5 April 2019 (c) 2019
Both creationist and intelligent design writers assert that science has yet to understand the origin of life, and further claim that this is a fatal flaw in evolutionary theory [Behe1996; Dembski1998]. More importantly, creationist-minded members of the public have, in numerous cases, attempted to capitalize on this perceived weakness to persuade school boards and teachers that the prevailing theory of evolution is seriously flawed, so that "alternative theories" (creationism and/or intelligent design) should be given equal time. For example, in the 2005 Dover case, the Dover Area School Board passed a resolution saying that "The Theory [of evolution] is not a fact. Gaps in the Theory exist for which there is no evidence. A theory is defined as a well-tested explanation that unifies a broad range of observations." It continued, "Intelligent Design is an explanation of the origin of life that differs from Darwin's view." [Lebo2008, pg. 62].
So what are the facts here? To what extent does modern science understand the origin of life, and what difference does it make?
It is true that as of the present time, scientists do not yet fully understand biogenesis (as the origin of life is often termed). In particular, the origin of the first self-reproducing biomolecules, on which evolutionary processes could operate to produce more complicated systems, remains unknown, and there are numerous unanswered questions on the development of life leading up to multicellular organisms (see below). What's more, unlike bony structures that leave fossil records, the early stages of biological evolution on the planet very likely have been completely erased, so that we may never know for sure the full details of what transpired. If anything, the very rapid appearance of life on Earth after it first formed suggests that the origin of life was quite likely. But we have no way to know for sure.
It should be kept in mind that research in biogenesis is fundamentally no different, philosophically or methodologically, than research in any other field of science -- the fact that this event occurred approximately four billion years ago makes no difference whatsoever. Scientists routinely study phenomena at the atomic and subatomic level that is far smaller than what can be viewed by eye, or even via optical microscopes, and they also study phenomena in distant galaxies that are far beyond current technology to visit in person and, more to the point, occurred millions or even billions of years ago (since these objects are often millions or billions of light-years away). Hundreds of papers are published in the biogenesis arena every year, presenting empirical evidence and assessing theories in light of this evidence, just the same as in many other fields. Yes, there are unanswered questions in biogenesis, but there are also unanswered questions even in areas of science that one would think are extremely well established, such as gravitational physics [Grossman2012a], cosmology [Barnes2013; Susskind2005] and reproductive biology [Ridley1995] (see also Controversies). Thus claims by creationists and intelligent design writers that unknowns in the origin of life arena "prove" that scientists do not have all the answers are only met with puzzled stares by real research scientists. Of course scientists do not have all the answers -- exploring unknown, unanswered questions is what science is all about and what researchers explore in approximately two million peer-reviewed papers published each year [Ware2012]. For additional discussion, see What is science?.
The Miller-Urey experiment
The first major result in the field of biogenesis was a 1953 experiment by Stanley Miller and Harold Urey. In this experiment, the researchers tested an earlier hypothesis that conditions on the early Earth may have favored the synthesis of organic compounds from inorganic compounds. They placed water plus some gases in a sealed flask, then passed electric sparks through the mixture to simulate the effects of sunlight and lightning. Over the next week or so, the mixture in the flask slowly turned a reddish-brown color. Upon analyzing the resulting "goo," they discovered that it contained several amino acids, which are the building blocks of proteins [Davies1999, pg. 86-94]. The Miller-Urey experiment firmly established that basic biochemical building blocks such as amino acids can spontaneously form given the right conditions. Nonetheless, researchers have more recently pointed out that in current models of early Earth's atmosphere and oceans, carbon dioxide and nitrogen would have reacted to form nitrites, which quickly destroy amino acids. Thus the Miller-Urey experiment might not be truly representative of what really happened on the early Earth, although some variation of the experiment might still be valid [Fox2007].
The RNA world hypothesis
Going beyond the synthesis of basic amino acids, one leading hypotheses is that ribonucleic acid (RNA) played a key role. For example, researchers recently found that certain RNA molecules can greatly increase the rate of specific chemical reactions, including, remarkably, the replication of parts of other RNA molecules. Thus perhaps a molecule like RNA could "self-catalyze" itself in this manner, perhaps with the assistance of some related molecules, and then larger conglomerates of such compounds, packaged within simple membranes (such as simple hydrophobic compounds), could have formed very primitive cells [NAS2008, pg. 22]. Nonetheless, even the "RNA world" hypothesis, as the above scenario is popularly known, faces challenges. As biochemist Robert Shapiro notes, "Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA." [Shapiro2007]. Shapiro likened research in the field to a golfer, who having completed an 18-hole course then presumed that the ball could also play in his absence. Arguments between the warring factions have been heated at times. At a 2008 meeting, Shapiro and John Sutherland, a biochemist at the University of Cambridge, waged a shouting match over what level of evidence should be required for the RNA world model [Service2019].
But research on the RNA world hypothesis continues, with some remarkable recent discoveries. In May 2009, a team led by John Sutherland (mentioned above) solved a problem that has perplexed researchers for at least 20 years, namely how the basic nucleotides (building blocks) of RNA could spontaneously assemble. As recently as 1999, the appearance of these nucleotides on the primitive Earth was widely thought to be a "near miracle" by researchers in the field [Joyce1999]. In the 2009 study, Sutherland and his team used the same starting chemicals that have been employed in numerous earlier experiments, but they tried many different orders and combinations. They finally discovered one order and combination that formed the RNA nucleotides cytosine and uracil, which are collectively known as the pyrimidines [Wade2009]. Then in March 2015, Sutherland's team announced that two simple compounds, which almost certainly were abundant on the early Earth, can launch a cascade of chemical reactions that can produce all three major classes of biomolecules: nucleic acids, amino acids and lipids. Jack Szostak, another researcher in the field described the result as "a very important paper" [Service2015]. Among other things, Sutherland's group has been able to generate 12 of the 20 amino acids that are used in living organisms [Wade2015a].
More recently, in May 2016, a team led by Thomas Carell, a chemist at Ludwig Maximilian University of Munich in Germany, reported that his team had found a plausible way to form adenine and guanine, the building blocks known as purines (the two building blocks that Sutherland's team had not been able to produce) [Service2016]. One difficulty is that the set of reactions that form the purines is different from the set that Sutherland found to form the pyrimidines. In the latest development, in November 2018 Carell's team announced that he had found a single simple set of reactions that could have formed all four RNA bases on the early Earth. Carell started with only six molecular building blocks -- oxygen, nitrogen, methane, ammonia, water and hydrogen cyanide -- which researchers are quite confident were present on the early Earth [Service2018].
When did life start?
One key question is when this biogenesis event occurred. The most recent consensus picture is as follows: the solar system was created 4.568 billion years ago in the aftermath of a stellar explosion; this was followed 4.53 billion years by the formation of the Earth; the Moon formed 4.51 billion years ago from a collision of some other celestial body with the Earth; by 4.46 billion years ago, Earth had cooled enough to have both land and water. Then the first RNA formed about 4.35 billion years ago. By 4.1 billion years ago, zircon crystals from that era show a ratio of carbon 12 and carbon 13 isotopes that is typical of life. The Earth continued to be bombarded by meteorites fairly heavily until about 3.8 billion years ago. The earliest fossils attributed to microorganisms have been dated to 3.43 billion years ago. This is shown in diagram form in Robert Service's excellent 2019 Science article, which provides an overview of the latest research in the area [Service2019].
Other 21st century developments
In light of these results, there is a sense in the biogenesis field that progress is accelerating. Here is a brief summary of other recent developments, listed in chronological order, starting with 2010, most recent listed last.
- In February 2010 scientists at the Scripps Research Institute in San Diego announced that they have synthesized RNA enzymes, known as ribozymes, that can replicate themselves without the help of any proteins or other cellular components. What's more, these simple molecules can act as catalysts and continue the process indefinitely. The researchers began with ribozymes that occur naturally, and put these in a growth medium, where subsets "competed" with others. Eventually more successful (and more complex) ribozymes came to dominate the culture. As researcher Gerald Joyce noted, "The key thing is it replicates itself, and passes information from parent to progeny down the line. ... Some functions are more fit than others, and those that are more fit 'breed' more, and are perpetuated more efficiently, and so it goes Darwinian." [Kazan2010].
- Also in February 2010, researchers at the University of Colorado showed that a very simple RNA molecule can catalyze chemical reactions, without any other proteins present. Their form of RNA involved only five nucleotides. As researcher Michael Yarus noted, "This work shows that RNA enzymes could have been far smaller, and therefore far easier to make under primitive conditions, than anyone has expected." [SD2010e].
- In September 2010, researchers announced a finding that they believe may explain why complex life originated only once. They note that prokaryotes (organisms without a nucleus or membrane-bound organelles) existed on the Earth for two billion years without achieving any significant increase in complexity. After the rise of eukaryotes (cells with complex structures enclosed within membranes), complexity of life increased sharply. By analyzing the power requirements of early life, they argue that the key to this transition was the incorporation of mitochondria into the cell, which greatly increased the capacity for genome complexity [Lane2010; LePage2010]. But other researchers are not so sure. For example, researchers from University College Dublin and the European Molecular Biology Laboratory in Heidelberg, Germany have published evidence indicating that bacteria of a class often found in sewage treatment plants and bogs may be descended from a "missing link" organism connecting prokaryotic to eukaryotic cells along an evolutionary path [Devos2010; SD2010f].
- In December 2010, a team of researchers at the University of Oxford uncovered evidence that humans and Trichoplax adhaerens, the world's simplest known multicellular animal, share virtually the same enzyme for sensing and regulating oxygen levels in cells. In fact, when the key enzyme from Trichoplax was put it in a human cell, it worked just as well as the human enzyme. Interestingly, this enzyme is absent in all single-celled organisms. These results suggests that this mechanism evolved at the same time as the earliest multicelluar animals, and in fact may have been critical for the pivotal development of complex multicellular life [SD2010g]. Along this line, in October 2012 a separate team of researchers have found clues that "choanoflagellates" (a certain strain of multi-lobed bacteria) may have been key in the leap from one-cell to multi-cell organisms [SD2012c].
- In April 2011, researchers in Italy found that if they mixed formamide, a simple chemical present in space, with material from a meteorite, and then heated the mixture, that they produced nucleic acids (building blocks of DNA and RNA), the amino acid glycine, and a precursor to sugar. The team also found that the meteorite mineral stabilized RNA, which is otherwise broken down with water [Marshall2011].
- In August 2011, a team of Australian and British geologists published their discovery of fossilized, single-cell organisms, 3.4 billion years old, near the Strelley Pool rock formation in Western Australia. This confirms the prevailing view that life evolved on Earth surprisingly soon after the end (3.85 billion years ago) of a period of heavy bombardment of meteorites, which would have sterilized the Earth's surface of any living organisms. These structures look entirely like living cells -- some are in clusters that appear to have been in the process of cell division [Wade2011b]. In November 2013, one of this team and some other researchers found well-preserved remnants of a complex ecosystem in a rock layer 3.5 billion years old [SD2013g].
- In October 2011, scientists discovered that what they have termed the last universal common ancestor (LUCA) of all biological species currently on Earth was significantly more complex than earlier thought. Until recently, most biologists believed that LUCA was little more than a crude assemblage of bimolecular components. But a team headed by Manfredo Seufferheld of the University of Illinois found that different versions of a certain enzyme in cells are closely related in all three branches of life: bacteria, archaea and eukaryotes. Thus most likely this enzyme was present in the LUCA, before the three main branches of the tree of life diversified [SD2011h]. It is hoped that additional research along this line will pin down the precise genetic structure of LUCA.
- In April 2012, researchers found viruses in a hot, acidic lake in Lassen Volcanic National Park in California containing both a RNA-derived gene and a gene for DNA replication, typical of a DNA virus. This lends support to the hypothesis that viruses performed the transfer of genetic information from RNA to DNA during the earliest epoch of life on Earth [Holmes2012].
- One aspect of the "RNA world" hypothesis that heretofore has stymied researchers is the difficulty in demonstrating that RNA molecules or components could form long, information-rich chains, in water solutions. In February 2013, a team of researchers at the Georgia Institute of Technology and the Institute for Research in Biomedicine in Barcelona, Spain announced that by giving a component of RNA known as TAP a "tail," these units become "rosettes" that spontaneously form chains in water, like a large stack of plates, up to 18,000 units long. "The nice thing [about this study] is this is a demonstration of self-assembly in water," noted Ramanarayanan Krishnamurthy, a chemist at the Scripps Research Institute in California. The next step will be to see whether such assemblies can encode information, as one possible chemical route to the origin of life [Service2013].
- In August 2013, two separate developments caught the interest of many who have speculated that perhaps life on Earth really started on Mars. Steven Brenner, an origin-of-life researcher at the Westheimer Institute in Florida, announced his finding that boron and molybdenum stabilize the formation of RNA in the presence of water, and thus may well have been key to the original formation of RNA. The early Earth did not have much of either element, but both appear to have been more abundant on Mars billions of years ago. In a separate finding, a few days later, a team led by Christopher Adcock of the University of Nevada, Las Vegas, announced their finding that phosphates (which are an essential component of life) were also more abundant on Mars -- in particular, the Martian phosphate compounds are far more soluble in water than were the phosphates on the early Earth. For details on both studies, see [Kaufman2013].
- In December 2013, the Georgia Tech team announced that they had found a surprisingly simple recipe to produce a collection of long, ribbonlike molecules resembling those of RNA. What's more, these molecules appear to react somewhat spontaneously, without a great deal of chemical coaxing. Thus these molecules could have been a precursor to RNA. As Stephen Freeland, a researcher not involved in the study explained, "nothing like this has been seen before." The next step is to verify whether these reactions work in a chemical mix more akin to the hypothesized "primordial soup." For details, see [Singer2014a].
- In April 2014, researchers at the University of Cambridge announced that they had found that the formation of metabolic processes, key to all life and a major gap in understanding the origin of life, could have occurred spontaneously in the Earth's early oceans, catalyzed by metal ions rather than enzymes, as they are in cells today. This suggests that life may have arisen metabolically first, then generated RNA later [Geddes2014].
- In December 2014, researchers at the Academy of Sciences in Prague fired a high-powered laser (simulating a meteorite impact) at samples of formamide, a liquid that would have been plentiful on the early Earth. They found that all four RNA bases (adenine, guanine, cytosine and uracil), three of which are also in DNA, had been formed in the reaction [Barras2014].
- In October 2015 geochemists at the University of California, Los Angeles announced evidence that life very likely existed 4.1 billion years ago on Earth, which is at least 300 million years earlier than the previous research consensus. The research consisted of studying 10,000 zircon crystals from the Jack Hills area of Western Australia. Zircons, which are related to the synthetic cubic zirconium that is used for imitation diamond, are extremely durable and virtually impermeable, so that material trapped inside them constitutes a very reliable picture of the environment when they formed. One of these zircons contained graphite (carbon) in two locations. These carbon dots had a ratio of carbon-12 to carbon-13 that is a characteristic signature of photosynthetic life. Researchers are very confident that this carbon is at least 4.1 billion years old, because the zircon that contains them is that old, based on careful measurements of its uranium-to-lead ratio [SD2015c].
- In February 2016, Nik Hud, researchers at the Georgia Institute of Technology found evidence that even RNA might have had chemical precursors, in a "pre-Darwinian" world. In particular, ribosomes and RNA-like molecules might have formed spontaneously from chemical machinery alone [Singer2016].
- In July 2016, researchers at Heinrich Heine University in Dusseldorf, Germany searched DNA databases for gene families shared by at least two species of bacteria and two archaea (even more primitive biological organisms). After analyzing millions of genes and gene families, they found that only 355 gene families are truly shared across all modern organisms, and thus are the most probable genes shared by the "last universal common ancestor" (LUCA) of life. Further, these researchers found that the probable LUCA organism was an anerobe, namely it grew in an evironment devoid of oxygen. These results suggest that LUCA originated near undersea volcanoes [Service2016a].
- In August 2016, researchers at the Scripps Research Institute created a ribozyme (a special RNA enzyme) that can both amplify genetic information and generate functional molecules. In particular, it can efficiently replicate short segments of RNA and can transcribe longer RNA segments to make functional RNA molecules with complex strictures. These features are close to what scientists envision was an RNA replicator that could have supported life on the very early Earth, before the emergence of current biology, where protein enzymes handle gene replication and transcription [SD2016b].
- In March 2017, British geologists announced that they had found fossil specimens from a geological formation near Hudson Bay, Canada, with dates measured as between from 3.77 billion years to 4.22 billion years old, earlier than any previous claim for biological organisms on Earth. These specimens are similar in appearance to tube-like structures found in modern-day undersea hydrothermal vents. If these findings are upheld, particularly at the 4.22 billion-year-old level, this will be very quickly after the earliest oceans formed [Zimmer2017a].
- In May 2018, a team of researchers led by Philipp Holliger at the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK, produced RNA enzymes that can copy RNA molecules even longer than themselves. The problem with many of these RNA experiments is that while RNA can only act as an enzyme if it is in a folded shape, RNA enzymes can only copy RNA molecules that not folded. Holliger's solution was to build RNA out of "trinucleotides," slighter larger nucleotide molecules, and to conduct the experiments in an icy solution. Nonetheless, biologists consider his work to be a major step towards completely "natural" synthesis and enzymatic processing of RNA [LePage2018].
- In April 2019, a team of researches at Scripps Research Institute found evidence that both RNA and DNA could have arisen from the same precursor molecules. In particular, they showed that the compound thiouridine, which could have been a precursor to RNA, could also be converted into a DNA building block, namely deoxyadenosine (the "A" of the DNA four-letter code) [SD2019a].
What is the impact on the larger theory of evolution?
It must be kept in mind that the process of evolution after biogenesis is very well attested in fossils, radiometric measurements, DNA, and numerous other lines of evidence, completely independent of how the first biological structures formed. In other words, those unknowns that remain in biogenesis theory have no bearing on the central hypothesis of evolution, namely that all species are related in a family tree, having proliferated and adapted over many millions of years. Thus there is no substance to the creationist-intelligent design claim that unknowns in the origins area are a fatal flaw of evolutionary theory.
This line of reasoning by creationists and intelligent design writers, namely that the absence of a full explanation of biogenesis invalidates the whole of evolutionary theory, is a classic instance of the "forest fallacy" -- picking a flaw or two in the bark of a single tree, and then trying to claim that the forest doesn't exist. Indeed, to the extent that creationist and intelligent design writers continue to emphasize the biogenesis issue as the premier flaw of evolution, they risk being discredited, even in the public eye, as new and ever-more-remarkable developments are publicly announced.
Along this line, the origin of life with respect to the larger theory of evolution is in perfect analogy to the origin of the universe at the big bang with respect to the Standard Model of modern physics (the over-arching theory that describes interactions of forces and matter from the smallest scales of time and space to the largest). It is undeniably true that scientists do not yet fully understand the big bang, and it is also true that scientists recognize that the current Standard Model is not the final word. But this is hardly reason to dismiss or minimize the enormous corpus of research in modern physics, and the astonishing levels of precision to which these theories have been tested. For additional details, see Big bang, Physics and What is science?.
It is undeniably true that scientists do not yet have a fully-developed chain of evidence for the origin of life -- no knowledgeable scientist has ever claimed otherwise. Numerous scenarios have been explored, but there are still some gaps and unanswered questions. Nonetheless, thousands of scientific papers, documenting countless experimental studies, have been published on these topics, and several previous show-stopping obstacles, such as the formation of certain building blocks of RNA, have been overcome. Indeed, some of the above results, such as the recent results by Sutherland and Carell on the synthesis of RNA nucleotides, represent astonishing progress in the field. Almost certainly even more remarkable results will be published in the next few years. It would be utter folly to presume that no additional progress will be made.
Given these developments, most observers believe that it is extremely unwise to reject out of hand the possibility that research eventually will discover a complete natural process that could satisfactorily explain the origin or early development of life on Earth. Among other things, that would be a premier example of a "God of the gaps" theological error. Along this line, it may well be the case that all traces of the first self-reproducing systems and the earliest unicellular life may have been destroyed in the chaotic chemistry of the early Earth, so that we may never know for certain the precise path that actually was taken. But even if scientific research eventually demonstrates some plausible natural path, this would already defeat the claims of creationists and others that life could only have originated outside the realm of natural forces and processes. And, frankly, such a discovery could be announced at any time.
What's more, as pointed out above, the line of reasoning by creationists and intelligent design writers, namely that the absence of a full explanation of biogenesis invalidates the whole of evolutionary theory, implying that creationism and intelligent design must be considered on an equal par with evolution, is a classic instance of the "forest fallacy," and has no validity whatsoever.
One fundamental difficulty with both the creationist and intelligent design approaches to the origin of life can be seen by considering the following "thought experiment." Suppose a major international society announced that it had received a communication from a super-intelligent Entity, and the authenticity of this communication could not be denied because it included, say, solutions to mathematical problems that are utterly beyond the present level of human knowledge and computer technology. Suppose also that this communication disclosed that this Entity had initiated or created life on Earth. The next day inquisitive humans would then ask questions such as "What time frame was required for this creation?," "What physical laws and processes were utilized by this Entity?," "Can we replicate these processes in a laboratory?," "Why was Earth appropriate for life?," "Was life similarly initiated or created elsewhere?," "Who created this Entity?," "Who created the universe?," "Why?"
In other words, even if we found indisputable evidence that some supreme Entity had created life, virtually all of the fundamental questions of existence and evolution that have intrigued scientists and theologians alike for centuries would remain unanswered. In this light, the creationist-intelligent design approach of merely asserting "God did it," and resisting deeper investigation, is tantamount to a "thinking stopper," reveling in ignorance instead of thirsting for knowledge. Surely there is a more productive approach to harmonize science and religion.