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Do scientists understand the origin of life?

David H. Bailey
1 Jan 2017 (c) 2017

Introduction

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. 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. Hundreds of papers are published in this general area 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] and reproductive biology [Ridley1995]. Thus claims by creationists 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. For additional discussion, see What is science?.

Biogenesis from 1950 to 2000

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.

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]. These difficulties have led scientists to hypothesize even simpler building blocks, such as self-catalyzing networks of biomolecular agents. Shapiro sketches five basic required characteristics of such a system: (a) a boundary is needed to separate life from non-life; (b) an energy source is needed to drive the organization process; (c) a coupling mechanism must link the release of energy to the organization process that produces and sustains life; (d) a chemical network must be formed, to permit adaptation and evolution; and (e) the network must grow and reproduce. Such hypothesized systems are now termed "metabolism first" schemes [Shapiro2007]. Much remains to be done to establish the validity of this scenario, but if it is upheld, in the words of biologist Stuart Kauffman, then "life is vastly more probable than we supposed. Not only are we at home in the universe, but we are far more likely to share it with unknown companions." [Kauffman1995, pg. 69].

21st century developments

Even with these developments, a sober view of the biogenesis field is that researchers have not yet found a complete or near-complete scenario for the origin of life. However, a series of very interesting new results have been published in the field just in the past few years, and there is a sense in the field that progress is accelerating. Here is a brief summary of these results:
  1. As mentioned above, many scientists have had doubts that the environment assumed in the Miller-Urey experiment was truly representative of the early earth's environment, since nitrites, for instance, would likely have neutralized any resulting biochemical compounds. In 2007, biochemist Jeffrey Bada, noting that significant amounts of iron and carbonate minerals were likely present in the early atmosphere, conjectured that these compounds may have neutralized the deleterious effects of the nitrites. To test this hypothesis, Jeffrey Bada performed a new Miller-Urey-type experiment by adding iron and carbonate minerals. As in the original experiment, Bada found numerous amino acids in the resulting mixture. Thus the basic findings of the Miller-Urey experiment might still have validity in spite of the nitrite problem [Fox2007].

  2. In May 2009, a team led by John Sutherland, a chemist at the University of Manchester in England, solved a problem that has perplexed researchers for at least 20 years (see above), namely how the basic nucleotides (building blocks) of RNA could spontaneously assemble. As recently as a few years ago, the appearance of these nucleotides on the primitive earth was thought to be a "near miracle." 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 nucleotide ribocytidine phosphate. What's more, when the mixture was exposed to ultraviolet light, a second nucleotide of RNA was formed. Two other nucleotides remain, but the synthesis of the first two was thought to be more difficult [Wade2009].

    In the latest research by Sutherland's group, his team announced in March 2015 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 ben able to generate 12 of the 20 amino acids that are used in living organisms [Wade2015a].

  3. As mentioned above, Sutherland's group has been successful in synthesizing two of the four nucleotides of RNA. In May 2016, a team led by Thomas Carell, a chemist at Ludwig Maximilian University of Munich in Germany, succeeded in synthesizing purine, one of the remaining nucleotides. What's more, the process they discovered was remarkably simple, involving chemicals known to exist on the early earth. One problem was that Carell needed to find a way to stop all but one critical amine from reacting on a aminopyrimidines molecule. But they found that the presence of a mild acid did the job, and the one amine that remained was exactly the one that forms purine [Service2016].

  4. 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].

  5. 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].

  6. In June 2010, a team of researchers at the Georgia Institute of Technology and the University of Roma La Sapienza succeeded in synthesizing guanine, one of the four bases of RNA. The other three, adenine, cytosine and uracil, have previously been synthesized. The researchers were able to form guanine by subjecting a solution of formamide (H2NCOH), a simple compound that often has been suggested as a starting material for biotic compounds, to ultraviolet radiation during heating. Thomas Orlando, one of the researchers, explained, "Our model prebiotic reaction is attractive because most aspects of the process were likely to occur on the early Earth and it reduces chemical constraints." [SD2010a].

  7. 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].

  8. 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].

  9. 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].

  10. 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].

  11. 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].

  12. 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].

  13. 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].

  14. In 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].

  15. 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].

  16. 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].
Further details on the search for the first self-replicating biomolecules are given in an excellent 2011 New Scientist article by Michael Marshall [Marshall2011a].

Other research in primordial life on the early earth

In addition to the fundamental problem of biogenesis, there have been several other related results in the larger arena of evolution on the very early earth after biogenesis. Here again is a just brief sampling of developments within the past two or three years (as of 2012):
  1. It is possible that the original living molecules were seeded from outer space, either from a planet in our solar system, or from beyond the solar system. In 1996, NASA scientist David McKay and some colleagues made quite a stir by publishing a paper claiming evidence that a meteorite found in Antarctica, known as ALH 84001, which had been identified as originating from Mars, had signs of past life, such as microscopic objects shaped like bacteria. This announcement was greeted with considerable skepticism (which was entirely appropriate, given the gravity of the claim). In November 2009, McKay published a new study with results that he claims rules out one possible alternate explanation, namely that the earlier published biological indicators were caused by carbonate decomposition under high temperatures and pressures [Fisher2009]. Also, in 2010 a team led by Darrell Strobel of Johns Hopkins University found that acetylene is anomalously absent from the surface of Titan (Saturn's largest moon), and hydrogen is anomalously scarce there, lending strength to a 2005 conjecture by Chris McKay of NASA's Ames Research Center that microbial life might exist on Titan [Shiga2010]. It should be noted, however, that even if extraterrestrial origin is ultimately confirmed as the source of the early life on earth, that only pushes the question of the origin of life to some other planet -- it does not answer the question of how life started in the first place. For additional details, see Fermi.

  2. In May 2010, a team led by human genome entrepreneur Craig Venter succeeded in synthesizing the entire genome of a bacteria, which was then used to take over a cell. Based on a computer-designed sequence, the team ordered DNA in sections of 1000 base pairs from a commercial DNA synthesis firm, then assembled them into a single piece with 1,080,000 bases. In a second step, they directed the synthetic DNA to take over control of a bacterial cell, generating proteins according to the new DNA instead of its own. Venter characterizes the converted cell as "the first self-replicating species we've had on the planet whose parent is a computer" [Wade2010a]. Scientists are quick to emphasize that Venter's team has not created life from scratch, since bacteria and yeast were used to combine and duplicate over million base pairs in the synthetic genome. But the demonstration is undeniably a landmark achievement along the path to completely synthetic life, and underscores the progress modern science has achieved in understanding life. As physicist Richard Feynman once quipped (as one of several quotes that have been encoded in the new genome), "What I cannot build I cannot understand." [Callaway2010].

  3. 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].

  4. 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.

  5. 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 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].

  6. 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].

  7. In a startling new development, 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].

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. 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?.

Summary

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 2009 and 2015 results by John Sutherland's group on the synthesis of RNA nucleotides and other biomolecules, 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, including the present author, believe that it is extremely unwise to base one's religious or philosophical creed on the presumed impossibility of scientific research eventually discovering a complete natural process that could satisfactorily explain the origin or early development of life on earth. 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.

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 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.

References

[See Bibliography].