Tag: origin of life

Have Researchers Developed a Computer Algorithm that Explains the Origin of Life?

By Fazale Rana – November 4, 2020

As a chemistry major at West Virginia State College during the early 1980s, I was required to take a library course on the chemical literature before I could graduate. During the class, we learned how to use the many library reference materials devoted to cataloging and retrieving the vast amount of chemistry research published in the scientific literature. Included in this list was the multivolume Beilstein’s Handbook of Organic Chemistry.

Beilstein’s Handbook of Organic Chemistry

Beilstein’s Handbook consists of hundreds of volumes with entries for well over 10 million compounds. The books that originally made up Beilstein’s Handbook took up rows of shelves in the library with new volumes added to the collection every few years. Today, the Beilstein’s volumes are no longer published as printed editions. Instead the entries are now housed online in the Beilstein’s Handbook database, with the old print volumes serving as little more than artifacts of a bygone era in the annals of chemistry.

Learning to master Beilstein’s Handbook is no easy task. In fact, there are textbooks devoted to teaching chemists how to use this massive database effectively. It is well worth the effort. If you know what you are doing, Beilstein’s Handbook holds the key to finding quickly anything you need to know about any organic compound, provided it has been published somewhere.

Beilstein Synthesis and the Origin-of-Life Problem

The utility of Beilstein’s Handbook is endless and its applications far-reaching. In fact, Beilstein’s has even served as the inspiration for origin-of-life chemists seeking to make sense of prebiotic chemistry and chemical evolution. These investigators think that if they can master an approach to prebiotic chemistry called a Beilstein synthesis, then they may well gain key insight into how chemical evolution generated the first life on Earth. In short, a Beilstein synthesis involves a chemical reaction taking place in a single flask with a large number of chemical compounds serving as the reactants. This process is so named as a nod to the 10 million entries in the Beilstein’s database.

Origin-of-life scientists are interested in Beilstein synthesis because they think that these types of reactions more closely reflect the chemical and physical complexity of early Earth’s environment. Yet, very few origin-of-life researchers have even attempted this type of reaction. Understanding what transpired during a Beilstein synthesis has long been an intractable problem. Until very recently, the analytical capabilities didn’t exist to efficiently and effectively characterize the myriad products that would form during a Beilstein reaction, let alone identify and characterize the different chemical routes in play. For this reason, origin-of-life researchers have focused on singular prebiotic processes involving a limited number of compounds, reacting under highly controlled laboratory conditions. In these types of reactions, it is far easier to make sense of experimental outcomes—but the ease of interpretation comes with a cost.

Over the last 70 years, the focus on singular sets of reactions and highly controlled conditions has produced some successes for origin-of-life researchers—albeit qualified ones. Focusing on isolated reactions and specific sets of conditions has made it possible for researchers to identify a number of physicochemical processes that could have contributed to the early stages of chemical evolution—at least, in principle. Unfortunately, serious concerns remain about the geochemical relevance of these types of experiments. These reactions perform well in the laboratory, under the auspices of chemists, but significant questions abound about the productivity of the same laboratory processes in the milieu of early Earth. (For a detailed discussion of this problem, I recommend my blog article “Prebiotic Chemistry and the Hand of God.”)

Additionally, these highly controlled reactions—carried out under pristine conditions—fail to take into account the chemical and physical complexity of early Earth. Undoubtedly, this complexity will impact the physicochemical processes on early Earth, shaping the outcome of plausible prebiotic reaction routes. No one really knows if this complexity will facilitate chemical evolution or frustrate it, but now we have some idea, thanks to the work of a research team from the Polish Academy of Sciences. These investigators moved the origin-of-life research community closer to achieving a prebiotic Beilstein synthesis by developing and deploying a computer algorithm (called Alchemy) to perform computer-assisted organic chemistry designed to mimic the earliest stages of chemical evolution. In effect, they performed an in silico Beilstein reaction with some rather intriguing results.1

Alchemy and the Prebiotic Chemistry

The researchers used Alchemy to identify the reaction pathways and products that could have formed under plausible early Earth conditions. They initiated the computer-assisted reactions by starting with hydrogen sulfide, water, ammonia, nitrogen, methane, and hydrogen cyanide as the original set of reactants, under the assumption that these small molecules would have been present on early Earth. After the reactions reached completion, the researchers removed any products that possessed an “invalid” chemical structure, then incorporated the remaining reaction products into the original set of starting compounds, and ran the computer-assisted reactions again. They repeated this process 7 times.

For each generation of reactions, they “computed” reaction pathways and products using a set of 614 rules. These rules were developed by encoding into the algorithm all of the known prebiotic reactions published in the scientific literature. They also encoded plausible conditions of early Earth. As they developed the list of rules, the researchers also paid close attention to chemical functional groups that would be incompatible with one another. As it turns out, it was possible to group these 614 rules into 72 chemical reaction classes. The algorithm began each generation of reactions by identifying suitable reactants for each class of reactions and then “reacting” them to discover the types of products that would form.

Alchemy Results

Through the course of 7 generations of reactions, Alchemy produced almost 37,000 chemical compounds from the initial set of 6 gaseous molecules. Of these compounds, only 82 were biotic. And, of this collection, 41 were peptides (formed when amino acids react together to form an adduct).

As it turns out the biotic compounds had some unusual properties that distinguished them from the vast collection of abiotic molecules. These compounds:

  • Are more thermodynamically stable
  • Display less hydrophobicity (water-insolubility)
  • Harbor fewer distinct functional groups
  • Possess fewer reactive functional groups
  • Have a balanced number of functional groups that were hydrogen-bond donors and acceptors

The researchers also discovered that there were a number of distinct pathways that could produce biotic compounds. That is to say, they observed synthetic redundancy for the biotic compounds. They discovered that they could eliminate nearly half of the 72 reaction classes from the algorithm and still generate all 82 biotic compounds. In contrast, the abiotic compounds failed to display synthetic redundancy. Only 8 of the reaction classes could be eliminated and still generate the same suite of abiotic molecules.

Additionally, the team discovered that some of the compounds generated by the in silico reactions—such as formic acid, cyanoacetylene, and isocyanic acid—served as synthetic hubs, giving rise to a large number of additional products. It is quite possible that the existence of these reaction hubs contributes to the synthetic redundancy of the biotic compounds.

Through the course of 7 generations of chemical synthesis, the researchers found that the Alchemy algorithm produced all of the prebiotic reactions reported in the scientific literature, to date. This finding isn’t surprising because the research team used these reactions to help design the rules used to guide Alchemy.

The algorithm also yielded prebiotic reactions that, heretofore had not been discovered by origin-of-life researchers. The research team demonstrated the validity of these pathways, discovered in silico, by successfully executing these same reactions in the laboratory.

Emergent Properties of Prebiotic Reactions

One of the most exciting discoveries made by the team from the Polish National Academy of Sciences was the emergent properties that arose after 7 generations of in silico prebiotic reactions:

  • Unexpectedly, some of the reaction products catalyzed additional chemical reactions, which expanded the range of available prebiotic reactions.
  • Reaction cycles and reaction cascades emerged, with the reaction cycles displaying the property of self-regeneration. In fact, after 7 generations, the chemical space of the prebiotic reactions became densely populated with reaction cycles.
  • Surfactants, such as fatty acids, emerged. They also discovered peptides with surfactant properties. These types of compounds can, in principle, form vesicles that can encapsulate materials yielding proto-cellular structures.

In many respects, this work reflects science at its best. It ushers in a new era in prebiotic chemistry, demonstrating the power of computer-assisted organic chemistry to shed light on chemical evolution. Coupled with the increased capacity to analyze complex chemical mixtures (thanks to advances in analytical chemistry), Alchemy and other similar software may make it possible to provide meaningful interpretations of real-life Beilstein reactions.

This work also shows that, in principle, complex chemical mixtures can give rise to some interesting emergent features that have bearing on chemical evolution and the rise of the chemical complexity and organization required for the origin of life. Nevertheless, we are still a far distance from arriving at any real understanding as to how life could have emerged through evolutionary processes.

Are the Alchemy Results Geochemically Relevant?

It is critical to keep in mind that this work involves computer modeling of chemical processes that could have taken place under the putative conditions of early Earth. And, though the algorithm developed by the investigators from the Polish National Academy of Sciences is quite sophisticated, it still represents a simplified set of scenarios that, at times, fails to fully and realistically account for our planet’s early conditions.

For example, some of the starting materials selected for the in silico reactions, such as ammonia and methane, likely weren’t present on the early Earth at appreciable levels. In fact, most planetary scientists believe that Earth’s early atmosphere was composed of water, nitrogen, and carbon dioxide. When this type of gas mixture is used in spark-discharge experiments—such as the ones carried out by legendary origin-of-life researcher Stanley Miller—no organic compounds form. In other words, this gas mixture is unreactive.

The researchers also ignored the concentration of the reactants. Laboratory studies indicate that many prebiotic reactions require relatively high concentrations of the reactants. Given the expansiveness of early Earth’s environment (particularly, its oceans), it is hard to imagine that the concentrations needed for many prebiotic reactions could ever have been achieved. In other words, it is quite likely that the concentration of prebiotic reactants on Earth was too dilute to be meaningful for chemical evolution.

The research group also ignored kinetic effects. Not all chemical reactions proceed at the same rate. So, while a chemical reaction may be possible, in principle, in reality it may transpire too slowly to be meaningful. By not taking into account rates of chemical reactions, the researchers undermined the geochemical relevance of their computer-assisted reactions.

The availability and types of energy sources on early Earth were ignored as well. Many prebiotic reactions require energy sources to trigger them. In many instances these energy sources have to be highly specific to initiate chemical reactions. Energy sources need to be powerful enough to kick-start the reactions, but not so powerful as to cause the breakdown of the reactants and ensuing products.

The researchers also failed to take into account the stereochemistry of the reactants and products. For this reason, they have failed to shed any insight into the homochirality problem, which beleaguers origin-of-life research.

So, the results of Alchemy have questionable geochemical relevance, and thus, questionable bearing on the origin-of-life issue. Still, the work demonstrates the value of Beilstein reactions—even, if performed in silico—and does indicate that emergent properties can originate out of chemical complexity, in principle.

It is also worth noting that this work sheds potential light on the earliest stages of chemical evolution. Even if building block materials are in place, there still needs to be an explanation for the emergence of information-rich biopolymers and stable membrane-bound vesicles that would form protocells. The work of the Polish National Academy of Sciences investigators provides clues as to how this might happen, but significant hurdles remain.

The Homopolymer Problem

One of the interesting findings of the in silico experiments was the recognition that prebiotic reactions generated around 40 peptides. The peptides became larger and more numerous for each generation. These compounds are formed from amino acids, which combine into “chain-like” molecules and could be viewed as the stepping stones to proteins. Some of the peptides produced in the prebiotic pathways display “nonbiological” bonding. This type of bond formation arises from reactions between the hydroxyl and carboxylic acid side groups of serine and aspartic acid (produced in the prebiotic reactions), respectively, and the carboxylic acid moiety and amino groups bound to the alpha carbon. These nonstandard linkages would render these peptides irrelevant for the production of larger proteins because of the homopolymer problem.

The late Robert Shapiro first identified this problem a number of years ago. For biopolymers to be able to adopt higher-order three-dimensional structures or to carry out critical functions, such as self-replication, the backbone must consist of identical repeating units. For intermolecular interactions to stabilize the higher-order structure of biopolymers or for these biopolymers to serve as templates for self-replication, the backbone’s structure must repeat without any interruption. This means that the subunit molecules that form the self-replicator must consist of the same chemical class.

Chemists call chain-like molecules with structurally repetitive backbones homopolymers. (Homo = “same”; poly = “many”; mer = “units”). DNA, RNA, proteins, and the proposed pre-RNA world self-replicators, such as peptide-nucleic acids, are all homopolymers and satisfy the chemical requirements necessary to function as self-replicators.

Undirected chemical processes can produce homopolymers under carefully controlled, pristine laboratory conditions. However, as Shapiro pointed out, these processes cannot generate these types of molecules under early Earth’s conditions. The chemical compounds found in the complex chemical mixture that origin-of-life researchers think existed on early Earth would interfere with homopolymer formation. Instead, polymers with highly heterogeneous backbone structures would be produced. The likely chemical components of any prebiotic soup would not only interrupt the structural regularity of the biopolymer’s backbone, but they would also prematurely terminate its formation or introduce branch sites.

The homopolymer problem is an intractable problem for chemical evolution—at least for replicator-first scenarios. Even though the in silico experiments demonstrated that amino acids can form and even combine into useful peptides, they also demonstrated that undesirable switching, branching, and termination reactions take place. Ironically, the in silico experiments have also provided added validation for the homopolymer problem.

The Membrane Problem

Another interesting feature of this work is the generation of surfactant molecules, such as fatty acids and amphiphilic peptides. Presumably, these materials could form vesicles with the capacity to encapsulate materials, leading to the first protocells. Yet, this process seems unlikely under the conditions of early Earth. Laboratory studies demonstrate that vesicles assembled from fatty acids are metastable and highly sensitive to fluctuation of environmental conditions. In fact, fatty acid vesicles assemble only under exacting solution conditions and require precise lipid compositions.2

Again, these insights raise questions about the geochemical relevance of this result. So, even though surfactants can form under prebiotic conditions, their assembly into bilayer-forming vesicles is not a given, by any means.

Prebiotic Chemistry and the Anthropic Principle

Even though the sophisticated work from the Polish National Academy of Sciences was designed to validate the notion of chemical evolution, the study’s results produced some interesting theistic implications. There are good reasons to think that origin-of-life researchers will never determine how evolutionary pathways generated the first life-forms because of seemingly intractable problems facing chemical evolution. In the face of these dismal prospects, it becomes hard to argue that mechanism alone can explain the origin of life and the design of core biochemical systems. The conviction that a Creator isn’t necessary stands on shaky ground.

Still, even if one grants the possibility that life had an evolutionary origin, it is impossible to escape the necessary role a Mind must have played in the appearance of first life on Earth—at least based on some intriguing results that emerge from the computer-assisted Beilstein reaction. As a case in point, it is provocative that the 82 biotic compounds which formed—a small fraction of the nearly 37,000 compounds generated by the in silico reactions—all share a suite of physicochemical properties that make these compounds unusually stable and relatively unreactive. These qualities cause these materials to persist in the prebiotic setting. It is also intriguing that these 82 compounds display synthetic redundancy, with the capability of being generated by several distinct chemical routes. It is also fortuitous that these compounds possess the just-right set of properties—many of which overlap with the set of properties that distinguish them from the vast number of abiotic compounds—that make them ideally suited to survive on early Earth and useful as building block materials for life.

In other words, there appear to be constraints on prebiotic chemistry that inevitably lead to the production of key biotic molecules with the just-right properties that make them unusually stable and ideally suited for life. This remarkable coincidence is a bit “suspicious” and highly fortuitous, suggesting a fitness for purpose to the nature of prebiotic chemistry. To put it another way: There is an apparent teleology to prebiotic chemistry. It appears that the laws of physics and chemistry may well have been rigged at the outset to ensure that life’s building blocks naturally emerged under the conditions of early Earth. Could it be that this coincidence reflects the fact that a Mind is behind it all?

It is remarkable to me as a biochemist and a Christian that the more insight we gain into the origin of life, the more the evidence points to the necessary role of a Creator, whether the Creator chose to directly intervene to create the first life-forms or whether he rigged the universe in such a way that life would inevitable emerge because of the design and constraints imposed by the laws of nature.

It really is a new era in origin-of-life research.

Endnotes

  1. Agnieszka Wołos et al., “Synthetic Connectivity, Emergence, and Self-Regeneration in the Network of Prebiotic Chemistry,” Science 369 (September 25, 2020): eaaw1955, doi: 10.1126/science.aaw1955.
  2. Jacquelyn A. Thomas and F. R. Rana, “Influence of Environmental Conditions, Lipid Composition, and Phase Behavior on the Origin of Cell Membranes,” Origins of Life and Evolution of Biospheres 37 (2007): 267-85, doi:10.1007/s11084-007-9065-6.

Resources

Reprinted with permission by the author

Original article at:
https://reasons.org/explore/blogs/the-cells-design

Meteorite Protein Discovery: Does It Validate Chemical Evolution?

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By Fazale Rana – June 10, 2020

“I’ll toss my coins in the fountain,

Look for clovers in grassy lawns

Search for shooting stars in the night

Cross my fingers and dream on.”

—Tracy Chapman

Like most little kids, I was regaled with tales about genies and wizards who used their magical powers to grant people the desires of their heart. And for a time, I was obsessed with finding some way to make my own wishes become a reality, too. I blew on dandelions, hunted for four-leafed clover, tried to catch fairy insects and looked for shooting stars in the night sky. Unfortunately, nothing worked.

But, that didn’t mean that I gave up on my hopes and dreams. In time, I realized that sometimes my imagination outpaced reality.

I still have hopes and dreams today. Hopefully, they are more realistic than in than the ones I held to in my youth. I even have hopes and dreams about what I might accomplish as a scientist. All scientists do. It’s part of what drives us. Scientists like to solve problems and extend the frontiers of knowledge. And, they hope that they will make discoveries that do that very thing, even if their hopes sometimes outpace reality.

Recently, a team of biochemists turned to a meteorite—a small piece of a shooting star—with the hope that their dream of finding meaningful insights into the evolutionary origin-of-life question would be realized. Using state-of-the art analytical methods, the Harvard University researchers uncovered the first-ever evidence for proteins in meteorites.1 Their work is exemplary work—science at its best. These biochemists view this discovery as offering an important clue to the chemical evolutionary origin of life. Yet, a careful analysis of their claims leads to the nagging doubt that origin-of-life researchers really aren’t any closer to understanding the origin of life and realizing their dream.

Meteorites and the Origin of Life

Origin-of-life researchers have long turned to meteorites for insight into the chemical evolutionary processes they believe spawned life on Earth. It makes sense. Meteorites represent a sampling of the materials that formed during the time our solar system came together and, therefore, provide a window into the physical and chemical processes that shaped the earliest stages of our solar system’s history and would have played a potential role in the origin of life.

One group of meteorites that origin-of-life researchers find to be most valuable toward this end are carbonaceous chondrites. Some classes of carbonaceous chondrites contain relatively high levels of organic compounds that formed from materials that existed in our early solar system. Many of these meteorites have undergone chemical and physical alterations since the time of their formation. Because of this metamorphosis, these meteorites offer clues about the types of prebiotic chemical processes that could have reasonably transpired on early Earth. However, they don’t give a clear picture of what the chemical and physical environment of the early solar system was like.

Fortunately, researchers have discovered a unique type of carbonaceous chondrite: the CV3 class. These meteorites have escaped metamorphosis, undergoing virtually no physical or chemical alterations since they formed. For this reason, these meteorites prove to be exceptionally valuable because they provide a pristine, unadulterated view of the nascent solar system.

The Discovery of Proteins in Meteorites

Origin-of-life investigators have catalogued a large inventory of organic compounds from carbonaceous chondrites, including some of the building blocks of life, such as amino acids, the constituents of proteins. Even though amino acids have been recovered from meteorites, there have been no reports of amino acid polymers (protein-like materials) in meteorites—at least until the Harvard team began their work.

Figure: Reaction of Amino Acids to Form Proteins. Credit: Shutterstock

The team’s pursuit of proteins in meteorites started in 2014 when they carried out a theoretical study that indicated to them that amino acids could polymerize to form protein-like materials in the gas nebulae that condense to form solar systems.2 In an attempt to provide experimental support for this claim, the research team analyzed two CV3 class carbonaceous chondrites: the Allende and Acfer 086 meteorites.

Instead of extracting these meteorites for 24 hours with water at 100°C (which is the usual approach taken by origin-of-life investigators), the research team adopted a different strategy. They reasoned that the protein-like materials that would form from amino acids in gaseous nebulae would be hydrophobic. (Hydrophobic materials are water-repellent materials that are insoluble in aqueous systems.) These types of materials wouldn’t be extracted by hot water. Alternatively, these hydrophobic protein-like substances would be susceptible to breaking down into their constituent amino acids (through a process called hydrolysis) under the standard extraction method. Either way, the protein-like materials would escape detection.

So, the researchers employed a Folch extraction at room temperature. This technique is designed to extract materials with a range of solubility properties while avoiding hydrolytic reactions. Using this approach, the Harvard researchers were able to detect evidence for amino acid polymers consisting of glycine and hydroxyglycine in extracts taken from the two meteorites.3

In their latest work, the research team performed a detailed structural characterization of the amino acid polymers from the Acfer 086 meteorite, thanks to access to a state-of-the-art mass spectrometer that had the capabilities of analyzing low levels of materials in the meteorite extracts.

The Harvard scientists determined that a distribution of amino acid polymer species existed in the meteorite sample.The most prominent one was a duplex formed from two protein-like chains that were 16 amino acids in length, comprised of glycine and hydroxyglycine residues. They also detected lithium ions associated with some of the hydroxyglycine subunits. Bound to both ends of the duplex was an unusual iron oxide moiety formed from two atoms of iron and three oxygen atoms. Lithium atoms were also associated with the iron oxide moiety.

Researchers are confident that this protein-like material—which they dub hemolithin—is not due to terrestrial contamination for two reasons. First, hydroxyglycine is a non-protein amino acid. Secondly, the protein duplex is enriched in deuterium—a signature that indicates it stems from an extraterrestrial source. In fact, the deuterium enrichment is so excessive, the researchers think it may have formed in the gas nebula before it condensed to form our solar system.

Origin-of-Life Implications

If these results stand, they represent an important scientific milestone—the first-ever protein-like material recovered from an extraterrestrial source. A dream come true for the Harvard scientists. Beyond this acclaim, origin-of-life researchers view this work as having important implications for the origin-of-life question.

For starters, this work affirms that chemical complexification can take place in prebiotic settings, providing support of chemical evolution. The Harvard scientists also speculate that the iron oxide complex at the ends of the amino acid polymer chains could serve as an energy source for prebiotic chemistry. This complex can absorb photons of light and, in turn, use that absorbed energy to drive chemical processes, such as cleaving water molecules.

More importantly, this work indicates that amino acids can form and polymerize in gaseous nebulae prior to the time that these structures collapse and condense into solar systems. In other words, this work suggests that prebiotic chemistry may have been well under way before Earth formed. If so, it means that prebiotic materials could have been endogenous to (produced within) the solar system, forming an inventory of building block materials that could have jump-started the chemical evolutionary process. Alternatively, the formation of prebiotic materials prior to solar system formation opens up the possibility that these critical compounds for the origin of life didn’t have to form on early Earth. Instead, prebiotic compounds could have been delivered to the early Earth by asteroids and comets—again, contributing to the early Earth’s cache of prebiotic substances.

Does the Protein-in-Meterorite Discovery Evince Chemical Evolution?

In many respects, the discovery of protein species in carbonaceous chondrites is not surprising. If amino acids are present in meteorites (or gaseous nebula), it stands to reason that, under certain conditions, these materials will react to form amino acid polymers. But, even so, a protein-like material made up of glycine and hydroxyglycine residues has questionable biochemical utility and this singular compound is a far cry from the minimal biochemical complexity needed for life. Chemical evolutionary processes must traverse a long road to move from the simplest amino acid building blocks (and the polymers formed from these compounds) to a minimal cell.

More importantly, it is questionable if the amino acid polymers in carbonaceous chondrites (or in gaseous nebula) made much of a contribution to the inventory of prebiotic materials on early Earth. Detection and characterization of the amino acid polymer in the Acfer 086 meteorite was only possible thanks to cutting-edge analytical instrumentation (the mass spectrometer) with the capability to detect and characterize low levels of materials. This requirement means that proteins found in the Acfer 086 meteorite samples must exist at relatively low levels. Once delivered to the early Earth, these materials would have been further diluted to even lower levels as they were introduced into the environment. In other words, these compounds most likely would have melded into the chemical background of early Earth, making little, if any, contribution to chemical evolution. And once the amino acid polymers dissolved into the early Earth’s oceans, a significant proportion may well have undergone hydrolysis (decomposition) into constituent amino acids.

Earth’s geological record affirms my assessment of the research team’s claims. Geochemical evidence from the oldest rock formations on Earth, dating to around 3.8 billion years ago, makes it clear that neither endogenous organic materials nor prebiotic materials delivered to early Earth via comets and asteroids (including amino acids and protein-like materials) made any contribution to the prebiotic inventory of early Earth. If these materials did add to the prebiotic store, the carbonaceous deposits in the oldest rocks on Earth would display a carbon-13 and deuterium enrichment. But they don’t. Instead, these deposits display a carbon-13 and deuterium depletion, indicating that these carbonaceous materials result from biological activity, not extraterrestrial mechanisms.

So, even though the Harvard investigators accomplished an important milestone in origin-of-life research, the scientific community’s dream of finding a chemical evolutionary pathway to the origin of life remains unfulfilled.

Resources

Endnotes
  1. Malcolm W. McGeoch, Sergei Dikler, and Julie E. M. McGeoch, “Hemolithin: A Meteoritic Protein Containing Iron and Lithium,” (February 22, 2020), preprint, https://arxiv.org/abs/2002.11688.
  2. Julie E. M. McGeoch and Malcolm W. McGeoch, “Polymer Amide as an Early Topology,” PLoS ONE 9, no. 7 (July 21, 2014): e103036, doi:10.1371/journal.pone.0103036.
  3. Julie E. M. McGeoch and Malcolm W. McGeoch, “Polymer Amide in the Allende and Murchison Meteorites,” Meteoritics and Planetary Science 50 (November 5, 2015): 1971–83, doi:10.1111/maps.12558; Julie E. M. McGeoch and Malcolm W. McGeoch, “A 4641Da Polymer of Amino Acids in Acfer 086 and Allende Meteorites,” (July 28, 2017), preprint, https://arxiv.org/pdf/1707.09080.pdf.

Reprinted with permission by the author

Original article at:
https://reasons.org/explore/blogs/the-cells-design

Prebiotic Chemistry and the Hand of God

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BY FAZALE RANA – JANUARY 16, 2019

“Many of the experiments designed to explain one or other step in the origin of life are either of tenuous relevance to any believable prebiotic setting or involve an experimental rig in which the hand of the researcher becomes for all intents and purposes the hand of God.”

—Simon Conway Morris, Life’s Solution

If you could time travel, would you? Would you travel to the past or the future?

If asked this question, I bet many origin-of-life researchers would want to travel to the time in Earth’s history when life originated. Given the many scientifically impenetrable mysteries surrounding life’s genesis, I am certain many of the scientists working on these problems would love to see firsthand how life got its start.

It is true, origin-of-life researchers have some access to the origin-of-life process through the fossil and geochemical records of the oldest rock formations on Earth—yet this evidence only affords them a glimpse through the glass, dimly.

Because of these limitations, origin-of-life researchers have to carry out most of their work in laboratory settings, where they try to replicate the myriad steps they think contributed to the origin-of-life process. Pioneered by the late Stanley Miller in the early 1950s, this approach—dubbed prebiotic chemistry—has become a scientific subdiscipline in its own right.

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Figure 1: Chemist Stanley Miller, circa 1980. Image credit: Wikipedia

Prebiotic Chemistry

In effect, the goals of prebiotic chemistry are threefold.

  • Proof of principle. The objective of these types of experiments is to determine—in principle—if a chemical or physical process that could potentially contribute to one or more steps in the origin-of-life pathway even exists.
  • Mechanism studies. Once processes have been identified that could contribute to the emergence of life, researchers study them in detail to get at the mechanisms undergirding these physicochemical transformations.
  • Geochemical relevance. Perhaps the most important goal of prebiotic studies is to establish the geochemical relevance of the physicochemical processes believed to have played a role in life’s start. In other words, how well do the chemical and physical processes identified and studied in the laboratory translate to early Earth’s conditions?

Without question, over the last 6 to 7 decades, origin-of-life researchers have been wildly successful with respect to the first two objectives. It is safe to say that origin-of-life investigators have demonstrated that—in principle—the chemical and physical processes needed to generate life through chemical evolutionary pathways exist.

But when it comes to the third objective, origin-of-life researchers have experienced frustration—and, arguably, failure.

Researcher Intervention and Prebiotic Chemistry

In an ideal world, humans would not intervene at all in any prebiotic study. But this ideal isn’t possible. Researchers involve themselves in the experimental design out of necessity, but also to ensure that the results of the study are reproducible and interpretable. If researchers don’t set up the experimental apparatus, adjust the starting conditions, add the appropriate reactants, and analyze the product, then by definition the experiment would never happen. Utilizing carefully controlled conditions and chemically pure reagents is necessary for reproducibility and to make sense of the results. In fact, this level of control is essential for proof-of-principle and mechanistic prebiotic studies—and perfectly acceptable.

However, when it comes to prebiotic chemistry’s third goal, geochemical relevance, the highly controlled conditions of the laboratory become a liability. Here researcher intervention becomes potentially unwarranted. It goes without saying that the conditions of early Earth were uncontrolled and chemically and physically complex. Chemically pristine and physically controlled conditions didn’t exist. And, of course, origin-of-life researchers weren’t present to oversee the processes and guide them to their desired end. Yet, it is rare for prebiotic simulation studies to fully take the actual conditions of early Earth into account in the experimental design. It is rarer for origin-of-life investigators to acknowledge this limitation.

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Figure 2: Laboratory technician. Image credit: Shutterstock

This complication means that many prebiotic studies designed to simulate processes on early Earth seldom accomplish anything of the sort due to excessive researcher intervention. Yet, it isn’t always clear when examining an experimental design if researcher involvement is legitimate or unwarranted.

As I point out in my book Creating Life in the Lab (Baker, 2011), one main reason for the lack of progress relates to the researcher’s role in the experimental design—a role not often recognized when experimental results are reported. Origin-of-life investigator Clemens Richert from the University of Stuttgart in Germany now acknowledges this very concern in a recent comment piece published by Nature Communications.1

As Richert points out, the role of researcher intervention and a clear assessment of geochemical relevance is rarely acknowledged or properly explored in prebiotic simulation studies. To remedy this problem, Richert calls for origin-of-life investigators to do three things when they report the results of prebiotic studies.

  • State explicitly the number of instances in which researchers engaged in manual intervention.
  • Describe precisely the prebiotic scenario a particular prebiotic simulation study seeks to model.
  • Reduce the number of steps involving manual intervention in whatever way possible.

Still, as Richert points out, it is not possible to provide a quantitative measure (a score) of geochemical relevance. And, hence, there will always be legitimate disagreement about the geochemical relevance of any prebiotic experiment.

Yet, Richert’s commentary represents an important first step toward encouraging more realistic prebiotic simulation studies and a more cautious approach to interpreting the results of these studies. Hopefully, it will also lead to a more circumspect assessment on the importance of these types of studies for accounting for the various steps in the origin-of-life process.

Researcher Intervention and the Hand of God

One concern not addressed by Richert in his commentary piece is the fastidiousness of many of the physicochemical transformations origin-of-life researchers deem central to chemical evolution. As I discuss in Creating Life in the Lab, mechanistic studies indicate that these processes are often dependent upon exacting conditions in the laboratory. To put it another way, these processes only take place—even under the most ideal laboratory conditions—because of human intervention. As a corollary, these processes would be unproductive on early Earth. They often require chemically pristine conditions, unrealistically high concentrations of reactants, carefully controlled order of additions, carefully regulated temperature, pH, salinity levels, etc.

As Richert states, “It’s not easy to see what replaced the flasks, pipettes, and stir bars of a chemistry lab during prebiotic evolution, let alone the hands of the chemist who performed the manipulations. (And yes, most of us are not comfortable with the idea of divine intervention.)”2

Sadly, since I made the point about researcher intervention nearly a decade ago, it has often been ignored, dismissed, and even ridiculed by many in the scientific community—simply because I have the temerity to think that a Creator brought life into existence.

Even though Richert and his many colleagues in the origin-of-life research community do whatever they can to eschew a Creator’s role in the origin-of-life, could it be that abiogenesis (life from nonlife) required the hand of God—divine intervention?

I would argue that this conclusion follows from nearly seven decades of work in prebiotic chemistry and the consistent demonstration of the central role that origin-of-life researchers play in the success of prebiotic simulation studies. It is becoming increasingly evident for whoever will “see” that the hand of the researcher serves as the analog for the hand of God.

Resources

Endnotes
  1. Clemens Richert, “Prebiotic Chemistry and Human Intervention,” Nature Communications 9 (December 12, 2018): 5177, doi:10.1038/s41467-018-07219-5.
  2. Richert, “Prebiotic Chemistry.”

Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2019/01/16/prebiotic-chemistry-and-the-hand-of-god

Ribosomes: Manufactured by Design, Part 2

ribosomesmanufacturedbydesign

BY FAZALE RANA – NOVEMBER 8, 2017

“I hope there are no creationists in the audience, but it would be a miracle if a strand of RNA ever appeared on the primitive Earth.”1

Hugh Ross and I witnessed the late origin-of-life researcher, Leslie Orgel, make this shocking proclamation at the end of a lecture he presented at the 13th International Conference on the Origin of Life (ISSOL 2002).

Orgel was one of the originators of the RNA world hypothesis. And because of his prominence in the origin-of-life research community, the conference organizers granted Orgel the honor of opening ISSOL 2002 with a plenary lecture on the status of the RNA world hypothesis. During his presentation, Orgel described problem after problem with the leading origin-of-life explanation, reaching the tongue-in-cheek conclusion that it would require a miracle for this evolutionary scenario to yield RNA, let alone the first life-forms. (For a detailed discussion of the problems with the RNA world hypothesis, see my book Creating Life in the Lab.)

Despite these problems, many origin-of-life researchers—including Leslie Orgel (while he was alive)—remain convinced that the RNA world scenario must be the explanation for the emergence of life via chemical evolution. Why? For one key reason: the intermediary role RNA plays in protein synthesis.

The RNA World Hypothesis

The RNA world hypothesis posits that biochemistry was initially organized exclusively around RNA and only later did evolutionary processes transform the RNA world into the familiar DNA-protein world of contemporary organisms. If this model is correct, then the DNA-protein world represents the historically contingent outworking of evolutionary history. To put it another way, contemporary biochemistry has been cobbled together by unguided evolutionary forces and the role RNA plays in protein synthesis is an accidental outcome.

The discovery of ribozymes in the 1980s provided initial support for the RNA world scenario. These RNA molecules possess functional capabilities, behaving just like enzymes. In other words, RNA not only harbors information like DNA, it also carries out cellular functions like proteins. Origin-of-life researchers take RNA’s dual capacities as evidence that life could have been organized around RNA biochemistry. These same researchers presume that evolutionary processes later apportioned RNA’s twofold capabilities between DNA (information storage) and proteins (function). Origin-of-life researchers often point to RNA’s intermediary role in protein synthesis as evidence for the RNA world hypothesis. Again, RNA’s reduced role in contemporary biochemical systems stands as a vestige of evolutionary history, with RNA viewed as a sort of molecular fossil.

Ribosomes serve as a prime illustration of RNA’s role as a go-between in protein synthesis. As subcellular particles, ribosomes catalyze (assist) the chemical reactions that form the bonds between the amino acid subunits of the proteins. Two subunits of different sizes (comprised of proteins and RNA molecules) combine to form a functional ribosome. In organisms like bacteria, the large subunit (LSU) contains 2 ribosomal RNA (rRNA) molecules and about 30 different protein molecules. The small subunit (SSU) consists of a single rRNA molecule and about 20 proteins. In more complex organisms, the LSU is formed by 3 rRNA molecules that combine with around 50 distinct proteins, and the SSU consists of a single rRNA molecule and over 30 different proteins.

The rRNA molecules function as scaffolding, organizing the myriad ribosomal proteins. They also catalyze the chain-forming reactions between amino acids. In other words, the ribosome is a ribozyme. At the ISSOL 2002 meeting, I heard Orgel adamantly insist that the RNA world hypothesis must be valid because rRNA catalyzes protein bond formation.

Orgel’s perspective gains support considering the inefficiency of ribozymes as catalysts. Protein enzymes are much more efficient than ribozymes. In other words, it seemingly would be better and more efficient to design ribosomes so that proteins catalyzed bond formation between amino acids, not rRNA. This reason convinces origin-of-life researchers that the role rRNAs play in protein synthesis is a haphazard consequence of life’s historically contingent evolutionary history.

But recent work by scientists from Harvard and Uppsala Universities paints a different picture of the compositional makeup of ribosomes, and in doing so, undermines what many origin-of-life researchers believe to be the most compelling evidence for the RNA world hypothesis. These researchers demonstrate that the compositional makeup of ribosomes does not appear to be the accidental outworking of an unguided, contingent process. Instead, an exquisite molecular logic accounts for the composition and structural properties of the protein and rRNA components of ribosomes.2

Is There a Rationale for Ribosome Structure?

As part of their research efforts, the Harvard and Uppsala University investigators were specifically trying to answer several questions related to the composition of ribosomes, including:

  1. Why are ribosomes made up of so many proteins?
  2. Why are ribosomal proteins nearly the same size?
  3. Why are ribosomal proteins smaller than typical proteins?
  4. Why are ribosomes made up of so few rRNA molecules?
  5. Why are rRNA molecules so large?
  6. Why do ribosomes employ rRNA as the catalyst to form bonds between amino acids, instead of proteins which are much more efficient as enzymes?

Ribosomes Make Ribosomes

Before a cell can replicate, ribosomes must manufacture the proteins needed to form more ribosomes—in fact, ribosomes need to manufacture enough proteins to form a full complement of these subcellular complexes. This ensures that both daughter cells have the sufficient number of protein-manufacturing machines to thrive once the cell division process is completed. Because of this constraint, cell replication cannot proceed until a duplicate population of ribosomes is produced.

Ribosome Composition is Optimal for Efficient Production of Ribosomes

As discussed in an earlier blog post, the Harvard and Uppsala University investigators discovered that if ribosomal proteins were large, or if these biomolecules were variable in size, ribosome production would be slow and inefficient. Building ribosomes with smaller, uniform-size proteins represents the faster way to duplicate the ribosome population, permitting the cell replication to proceed in a timely manner. They also determined that the optimal number of ribosomal proteins is between 50 to 80—the number of ribosomal proteins found in nature. In short, the composition of these sub cellular complexes appears to be undergirded by an elegant molecular rationale.

As part of their mathematical modeling study, these researchers also provided an explanation for why ribosomes are made up of large RNA molecules. Because the number of steps involved in rRNA production is fewer than the steps required for protein manufacture, rRNA molecules can be made more rapidly than proteins. This being the case, ribosome production is more efficient when these organelles are built using fewer and larger rRNA molecules as opposed to smaller, more numerous ones.

The research team learned that ribosomes containing more rRNA can be built faster than ribosomes made up of more proteins. This fact helps explain why rRNA operates as the catalytic portion of ribosomes (linking amino acids together to construct proteins), though less efficient as a catalyst than proteins.

These insights also explain the compositional differences among ribosomes found in bacteria, eukaryotic cells, and mitochondria. Bacteria, which typically replicate faster than eukaryotic cells, possess ribosomes that contain proportionally more rRNA and fewer proteins than ribosomes found in eukaryotic cells. Mitochondria—organelles found in eukaryotic cells—possess ribosomes with a much greater ratio of proteins to rRNA than eukaryotic cells. This observation makes sense because ribosomes in mitochondria don’t produce themselves.

It Would Be a Miracle if a Strand of RNA Appeared on the Primitive Earth

An exquisite molecular rationale undergirds the number and size of rRNA molecules in ribosomes and accounts for why the ribosome is a ribozyme. The work of the Harvard and Uppsala University scientists undermines the view that ribosomes were cobbled together as a result of the evolutionary transition from the RNA world to the DNA/protein world. If the presence and role of RNA molecules in ribosomes were simply vestiges of life’s origin out of an RNA world, then there should not be an elegant molecular logic that accounts for ribosome compositions in bacteria and eukaryotic organisms. In other words, it doesn’t appear as if ribosomes are the unintended outcome of an unguided evolutionary process.

This conclusion gains support from earlier work by life scientist Ian S. Dunn. As I wrote about in a previous blog post, Dunn has uncovered a molecular rationale for the intermediary role messenger RNA (mRNA) plays in protein synthesis. Again, it indicates that the intermediary role of RNA molecules in protein synthesis is a necessary design of a DNA/protein world, not a molecular vestige of life’s evolutionary origin that proceeds through an RNA world.

Given these new insights and the intractable problems with the RNA world scenario, I must agree with Leslie Orgel. It would be a miracle if a strand of RNA appeared on the primitive Earth—unless a Creator intervened.

Resources to Dig Deeper

Endnotes

  1. Fazale Rana, Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator(Grand Rapids, MI: Baker Books, 2011), 161.
  2. Shlomi Reuveni, Måns Ehrenberg, and Johan Paulsson, “Ribosomes Are Optimized for Autocatalytic Production,” Nature 547 (July 20, 2017): 293–7, doi:10.1038/nature22998.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/11/08/ribosomes-manufactured-by-design-part-2

Ribosomes: Manufactured by Design, Part 1

ribosomesmanufacturedbydesign1

BY FAZALE RANA – NOVEMBER 1, 2017

Before joining Reasons to Believe in 1999, I spent seven years working in R&D at a Fortune 500 company, which meant that I spent most of my time in a chemistry laboratory alongside my colleagues trying to develop new technologies with the hope that one day our ideas would become a reality, making their way onto store shelves.

From time to time, my work would be interrupted by an urgent call from one of our manufacturing plants. Inevitably, there was some crisis requiring my expertise as a chemist to troubleshoot. Often, I could solve the plant’s problem over the phone, or by analyzing a few samples sent to my lab. But, occasionally, the crisis necessitated a trip to the plant. These trips weren’t much fun. They were high pressure, stressful situations, because the longer the plant was offline, the more money it cost the company.

But, once the crisis abated, we could breathe easier. And that usually afforded us an opportunity to tour the plant.

It was a thrill to see working assembly lines manufacturing our products. These manufacturing operations were engineering marvels to behold, efficiently producing high-quality products at unimaginable speeds.

The Cell as a Factory

Inside each cell, an ensemble of manufacturing operations exists, more remarkable than any assembly line designed by human engineers. Perhaps one of the most astounding is the biochemical process that produces proteins—the workhorse molecules of life. These large complex molecules work collaboratively to carry out every cellular operation and contribute to the formation of all the structures within the cell.

Subcellular particles called ribosomes produce proteins through an assembly-line-like operation, replete with sophisticated quality control checkpoints. (As discussed in The Cell’s Design, the similarity between the assembly-line production of proteins and human manufacturing operations bolsters the Watchmaker argument for God’s existence.)

Ribosomes

About 23 nanometers in diameter, ribosomes play a central role in protein synthesis by catalyzing (assisting) the chemical reactions that form the bonds between the amino acidsubunits of proteins. A human cell may contain up to half a million ribosomes. A typical bacterium possesses about 20,000 of these subcellular structures, comprising one-fourth the total bacterial mass.

Two subunits of different sizes (comprised of proteins and RNA molecules) combine to form a functional ribosome. In organisms like bacteria, the large subunit (LSU) contains 2 ribosomal RNA (rRNA) molecules and about 30 different protein molecules. The small subunit (SSU) consists of a single rRNA molecule and about 20 proteins. In more complex organisms, the LSU is formed by 3 rRNA molecules that combine with around 50 distinct proteins and the SSU consists of a single rRNA molecule and over 30 different proteins. The rRNAs act as scaffolding that organizes the myriad ribosomal proteins. They also catalyze the chain-forming reactions between amino acids.

Ribosomes Make Ribosomes

Before a cell can replicate, ribosomes must manufacture the proteins needed to form more ribosomes—in fact, the cell’s machinery needs to manufacture enough ribosomes to form a full complement of these subcellular complexes. This ensures that both daughter cells have the sufficient number of protein-manufacturing machines to thrive once the cell division process is completed. Because of this constraint, cell replication cannot proceed until a duplicate population of ribosomes is produced.

Is There a Rationale for Ribosome Structure?

Clearly, ribosomes are complex subcellular particles. But, is there any rhyme or reason for their structure? Or are ribosomes the product of a historically contingent evolutionary history?

New work by researchers from Harvard University and Uppsala University in Sweden provides key insight into the compositional make up of ribosomes, and, in doing so, help answer these questions.1

As part of their research efforts, the Harvard and Uppsala University investigators were specifically trying to answer several questions related to the composition of ribosomes, including:

  1. Why are ribosomes made up of so many proteins?
  2. Why are ribosomal proteins nearly the same size?
  3. Why are ribosomal proteins smaller than typical proteins?
  4. Why are ribosomes made up of so few rRNA molecules?
  5. Why are rRNA molecules are so large?
  6. Why do ribosomes employ rRNA as the catalyst to form bonds between amino acids, instead of proteins which are much more efficient as enzymes?

Ribosome Composition Is Optimal for Efficient Production of Ribosomes

Using mathematical modeling, the Harvard and Uppsala University investigators discovered that if ribosomal proteins were larger, or if these biomolecules were variable in size, ribosome production would be slow and inefficient. Building ribosomes with smaller, uniform-size proteins represents the faster way to duplicate the ribosome population, permitting the cell replication to proceed in a timely manner.

These researchers also learned that if the ribosomal proteins were any shorter, inefficient ribosome production also results. This inefficiency stems from biochemical events needed to initiate protein production. If proteins are too short, then the initiation events take longer than the elongation processes that build the protein chains.

The bottom line: The mathematical modeling work by the Harvard and Uppsala University research team indicates that the sizes of ribosomal proteins are optimal to ensure the most rapid and efficient production of ribosomes. The mathematical modeling also determined that the optimal number of ribosomal proteins is between 50 to 80—the number of ribosomal proteins found in nature.

Ribosome Composition Is Optimal to Produce a Varied Population of Ribosomes

The insights of this work have bearing on the recent discovery that within cells a heterogeneous population of ribosomes exists, not a homogeneous one as biochemists have long thought.2 Instead of every ribosome in the cell being identical, capable of producing each and every protein the cell needs, a diverse ensemble of distinct ribosomes exists in the cell. Each type of ribosome manufactures characteristically distinct types of proteins. Typically, ribosomes produce proteins that work in conjunction to carry out related cellular functions. The heterogeneous makeup of ribosomes contributes to the overall efficiency of protein production, and also provides an important means to regulate protein synthesis. It wouldn’t make sense to use an assembly line to make both consumer products, such as antiperspirant sticks, and automobiles. In the same manner, it doesn’t make sense to use the same ribosomes to make the myriad proteins, performing different functions for the cell.

Because ribosomes consist of a large number of small proteins, the cell can efficiently produce heterogeneous populations of ribosomes by assembling a ribosomal core and then including and excluding specific ribosomal proteins to generate a diverse population of ribosomes.3 In other words, the protein composition of ribosomes is optimized to efficiently replicate a diverse population of these subcellular particles.

The Case for Creation

The ingenuity of biochemical systems was one of the features of the cell’s chemistry that most impressed me as a graduate student (and moved me toward the recognition that there was a Creator). And the latest work by researchers on ribosome composition from Harvard and Uppsala Universities provides another illustration of the clever way that biochemical systems are constructed. The composition of these subcellular structures doesn’t appear to be haphazard—a frozen accident of a historically contingent evolutionary process—but instead is undergirded by an elegant molecular rationale, consistent with the work of a mind.

The case for intelligent design gains reinforcement from the optimal composition of ribosomal proteins. Quite often, designs produced by human beings have been optimized, making this property a telltale signature for intelligent design. In fact, optimality is most often associated with superior designs.

As I pointed out in The Cell’s Design, ribosomes are chicken-and-egg systems. Because ribosomes are composed of proteins, proteins are needed to make proteins. As with ingenuity and optimality, this property also evinces for the work of intelligent agency. Building a system that displays this unusual type of interdependency requires, and hence, reflects the work of a mind.

On the other hand, the chicken-and-egg nature of ribosome biosynthesis serves as a potent challenge to evolutionary explanations for the origin of life.

The Challenge to Evolution

Because ribosomes are needed to make the proteins needed to make ribosomes, it becomes difficult to envision how this type of chicken-and-egg system could emerge via evolutionary processes. Protein synthesis would have to function optimally at the onset. If it did not, it would lead to a cycle of auto-destruction for the cell.

Ribosomes couldn’t begin as crudely operating protein-manufacturing machines that gradually increased in efficiency—evolving step-by-step—toward the optimal systems, characteristic of contemporary biochemistry. If error-prone, ribosomes will produce defective proteins—including ribosomal proteins. In turn, defective ribosomal proteins will form ribosomes even more prone to error, setting up the auto-destruct cycle. And in any evolutionary scheme, the first ribosomes would have been error-prone.

The compositional requirement that ribosomal proteins be of the just-right size and uniform in length only exacerbates this chicken-and-egg problem. Even if ribosomes form functional, intact proteins, if these proteins aren’t the correct number, size, or uniformity then ribosomes couldn’t be replicated fast enough to support cellular reproduction.

In short, the latest insights in the protein composition of ribosomes provides compelling reasons to think that life must stem from a Creator’s handiwork.

So does the compositional makeup of ribosomal RNA molecules, which will be the topic of my next blog post.

Resources

Endnotes

  1. Shlomi Reuveni et al., “Ribosomes Are Optimized for Autocatalytic Production,” Nature 547 (July 20, 2017): 293–97, doi:10.1038/nature22998.
  2. Zhen Shi et al., “Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-Wide,” Molecular Cell 67 (July 6, 2017): 71–83, doi:10.1016/j.molcel.2017.05.021.
  3. Jeffrey A. Hussmann et al., “Ribosomal Architecture: Constraints Imposed by the Need for Self-Production,” Current Biology 27 (August 21, 2017): R798–R800, doi:10.1016/j.cub.2017.06.080.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/11/01/ribosomes-manufactured-by-design-part-1

Evolutionary Paradigm Lacks Explanation for Origin of Mitochondria and Eukaryotic Cells

evolutionayparadigmlacks

BY FAZALE RANA – OCTOBER 3, 2017

You carried the cross
Of my shame
Oh my shame
You know I believe it
But I still haven’t found
What I’m looking for

—Adam Clayton, Dave Evans, Larry Mullen, Paul David Hewson, Victor Reina

One of my favorite U2 songs is “I Still Haven’t Found What I’m Looking For.” For me, it’s a reminder that because of Christ, my life has meaning, purpose, and a sense of destiny. Still, I will never discover ultimate fulfillment in this world no matter how hard I search, but in the world to come—the new heaven and new earth.

Though their pursuit is scientific and not religious, many scientists have also failed to find what they have been looking for. Physicists are on a quest to find the Theory of Everything—a Grand Unified Theory (GUT) that can account for everything in physics. However, a GUT eludes them.

On the other hand, life scientists appear to have found it. They claim to have discovered biology’s GUT: the theory of evolution. Many biologists assert that evolutionary mechanisms can fully account for the origin, history, and design of life. And they are happy to sing about their discovery any chance they get.

Yet, despite this claim, the evolutionary paradigm seems to come up short time and time again when it comes to explaining key events in life’s history. And this failure serves as the basis for my skepticism regarding the evolutionary paradigm.

Currently, evolutionary biologists lack explanations for the key transitions in life’s history, including thes

  • origin of life,
  • origin of eukaryotic cells,
  • origin of sexual reproduction,
  • origin of body plans,
  • origin of consciousness,
  • and the origin of human exceptionalism.

To be certain, evolutionary biologists have proposed models to explain each of these transitions, but the models consistently fail to deliver, as a recent review article published by two prominent evolutionary biologists from the Hungarian Academy of Sciences illustrates.1 In this article, these researchers point out the insufficiency of the endosymbiont hypothesis—the leading evolutionary model for the origin of eukaryotic cells—to account for the origin of mitochondria and, hence, eukaryogenesis.

The Endosymbiont Hypothesis

Lynn Margulis (1938–2011) advanced the endosymbiont hypothesis for the origin of eukaryotic cells in the 1960s, building on the ideas of Russian botanist, Konstantin Mereschkowski. Taught in introductory high school and college biology courses, Margulis’s work has become a cornerstone idea of the evolutionary paradigm. This classroom exposure explains why students often ask me about the endosymbiont hypothesis when I speak on university campuses. Many first-year biology students and professional life scientists alike find the evidence for this idea compelling and, consequently, view it as providing broad support for an evolutionary explanation for the history and design of life.

According to the hypothesis, complex cells originated when symbiotic relationships formed among single-celled microbes after free-living bacterial and/or archaeal cells were engulfed by a “host” microbe. (Ingested cells that take up permanent residence within other cells are referred to as endosymbionts.)

Presumably, organelles such as mitochondria were once endosymbionts. Once engulfed, the endosymbionts took up permanent residency within the host, with the endosymbiont growing and dividing inside the host. Over time, the endosymbionts and the host became mutually interdependent, with the endosymbionts providing a metabolic benefit for the host cell. The endosymbionts gradually evolved into organelles through a process referred to as genome reduction. This reduction resulted when genes from the endosymbionts’ genomes were transferred into the genome of the host organism. Eventually, the host cell evolved the machinery to produce the proteins needed by the former endosymbiont and processes to transport those proteins into the organelle’s interior.

Evidence for the Endosymbiont Hypothesis

The similarity between organelles and bacteria serve as the main line of evidence for the endosymbiont hypothesis. For example, mitochondria—which are believed to be descended from a group of alpha-proteobacteria—are about the same size and shape as a typical bacterium and have a double membrane structure like gram-negative cells. These organelles also divide in a way that is reminiscent of bacterial cells.

Biochemical evidence also exists for the endosymbiont hypothesis. Evolutionary biologists view the presence of the diminutive mitochondrial genome as a vestige of this organelle’s evolutionary history. They see the biochemical similarities between mitochondrial and bacterial genomes as further evidence for the evolutionary origin of these organelles.

The presence of the unique lipid, cardiolipin, in the mitochondrial inner membrane also serves as evidence for the endosymbiont hypothesis. This important lipid component of bacterial inner membranes is not found in the membranes of eukaryotic cells—except for the inner membranes of mitochondria. In fact, biochemists consider it a signature lipid for mitochondria and a vestige of this organelle’s evolutionary history.2

Does the Endosymbiont Hypothesis Successfully Account for the Origin of Mitochondria?

Despite the seemingly compelling evidence for the endosymbiont hypothesis, evolutionary biologists lack a genuine explanation for the origin of mitochondria, and, in a broader context, the origin of eukaryotic cells. In their recently published critical review, Zachar and Szathmary point out that evolutionary biologists have proposed over twenty different evolutionary scenarios for the mitochondrial origins that umbrella underneath the endosymbiont hypothesis. Of these, they identify eight that are reasonable, casting the others aside. Still, these eight hypotheses fail to fully account for the origin of mitochondria. The Hungarian biologists delineate twelve questions that any successful endosymbiogenesis model must answer. In turn, they demonstrate that none of these models answers all the questions. In doing so, the two researchers call for a new theory.

In the article’s abstract, the authors state, “The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. . . . Contending theories widely disagree on ancestral partners, initial conditions and unfolding events. There are many open questions but there is no comparative examination of hypotheses. We have specified twelve questions about the observable facts and hidden processes leading to the establishment of the endosymbiont that a valid hypothesis must address. There is no single theory capable of answering all questions.”3

Space doesn’t permit me to discuss each of the questions posed by the pair of biologists. Still, I would like to call attention to a few problems confronting the endosymbiont hypothesis, highlighted in their critical review.

Lack of Transitional Intermediates. Biologists have yet to discover any single-celled organisms that represent transitional intermediates between prokaryotes and eukaryotic cells. (There are some eukaryotes that lack mitochondria, but they appear to have lost these organelles.) All complex cells display the eukaryotic hallmark features. In other words, it looks as if eukaryotic cells emerged in a short period of time, without any transitional forms. In fact, some biologists dub the transition the eukaryotic big bang.

Chimeric Nature of Eukaryotic Cells. Eukaryotic cells possess an unusual combination of features. Their information-processing systems resemble those of archaea, but their membranes and energy metabolism are bacteria-like. There is no plausible evolutionary scenario to explain this blend of features. It would require the archaeon host to replace its membranes while retaining all its information-processing genes. Evolutionary biologists know of no instance in which this type of transition took place, nor do they know how it could have occurred.

Absence of Membrane Bioenergetics in the Host. All prokaryotic organisms rely on their plasma membrane to produce energy. If eukaryotic cells emerged via endosymbiogenesis, then the plasma membranes of eukaryotic cells should possess vestiges of that past function. Yet, the plasma membranes of eukaryotic cells show no traces of this essential biochemical feature.

Mechanism of Inclusion. The most plausible way for the endosymbiont to be taken up by the host cell is through a process called phagocytosis. But why wouldn’t the engulfed cell be digested by the host? How did the endosymbiont escape destruction? And, if it somehow survived, why doesn’t the mitochondria possess a triple membrane system, with the outermost membrane derived from the phagosome?

Early Selective Advantage. Once inside the host, why didn’t the endosymbiont simply reproduce, overrunning the host cell? What benefit would it be for the host cell to initially harbor the endosymbiont? Currently, evolutionary biologists don’t have answers to troubling questions such as these.

The challenges delineated by the Hungarian biologists aren’t the only ones faced by evolutionary models for endosymbiogenesis. As I discuss in a previous article, mitochondrial protein biogenesis poses another difficult problem for the endosymbiont hypothesis.

The authors of the critical review sum it up this way: “The integration of mitochondria was a major transition, and a hard one. It poses puzzles so complicated that new theories are still generated 100 years since endosymbiogenesis was first proposed by Konstantin Mereschkowsky and 50 years since Lynn Margulis cemented the endosymbiotic origin of mitochondria into evolutionary biology. . . . One would expect that by this time, there is a consensus about the transition, but far from that even the most fundamental points are still debated.”4

Though evolutionary biologists claim to have life’s history all figured out, in reality they are like most of us—they still haven’t found what they are looking for.

Resources

Endnotes

  1. Istvan Zachar and Eors Szathmary, “Breath-Giving Cooperation: Critical Review of Origin of Mitochondria Hypotheses,” Biology Direct 12 (August 14, 2017): 19, doi:10.1186/s13062-017-0190-5.
  2. In previous posts (here, here, and here), I explain the rationale for mitochondrial DNA and the presence of cardiolipin in the inner mitochondrial membrane from a creation model/intelligent design vantage point and, in doing so, demonstrate that the two biochemical features aren’t uniquely explained by the endosymbiont hypothesis.
  3. Zachar and Szathmary, “Breath-Giving Cooperation.”
  4. Zachar and Szathmary, “Breath-Giving Cooperation.”
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/10/03/evolutionary-paradigm-lacks-explanation-for-origin-of-mitochondria-and-eukaryotic-cells

What Does the Discovery of Earth’s Oldest Fossils Mean for Evolutionary Models?

whatdoesdiscoveryofearths

BY FAZALE RANA – MARCH 29, 2017

Communication can be a complex undertaking. Often, people don’t say what they really mean. And if they do, their meaning is often veiled in what they say. That’s why it’s important to learn how to read between the lines. Understanding the real meaning when something isn’t explicitly stated usually requires experience and some insider’s knowledge.

Thanks to my expertise in biochemistry and origin-of-life research and 20 years of experience as a Christian apologist, I can usually read between the lines when scientists respond to discoveries that challenge the evolutionary paradigm, such as the recently reported discovery of Earth’s oldest fossils. Because of their fear that intelligent design proponents and creationists will make use of these types of discoveries to advance the case for a Creator, scientists can be adept at masking their concern when they discuss the implications of these discoveries. But if you know how to read between the lines, their consternation is as plain as day.

Earth’s Oldest Fossils

An international team made up of scientists from the United Kingdom, United States, Canada, and Australia recently reported on the discovery of microfossils from a geological formation in the northern part of Quebec, Canada.1 Formed from ancient hydrothermal vents, this iron-rich geological system dates somewhere between 3.77 and 4.3 billion years in age.

The putative microfossils consist of microscopic hematite filaments and tubes, like those found in modern hydrothermal vents. Today, iron-oxidizing microbes produce hematite filaments and tubes when sheaths of extracellular materials become coated by iron oxyhydroxide. Added evidence for the biogenicity of these microfossils comes from carbonate and apatite associated with the hematite structures. These compounds can also be produced as by-products of the metabolic activity of microorganisms. The research team also discovered graphite inclusions enriched in carbon-12, a geochemical signature of life. Finally, the Raman spectrum of the carbonaceous deposits display features that also point to the biological origin of this material.

Matthew Dodd, one of the research team members, argues that “we can think of alternative explanations for each of these singular observations, but why all of these features occur together can really only be explained by one thing, which is a biological interpretation.”2

The discovery of these microfossils comes on the heels of the discovery of stromatolites in newly exposed rock outcroppings in Greenland, dating at 3.7 billion years.3 Both recent discoveries corroborate earlier work that yielded several different geochemical markers for biological activity. In short, an impressive weight of evidence points to the early appearance of complex and diverse microbial life on Earth.

Skepticism about Bioauthenticity

Despite this impressive collection of evidence, several scientists have expressed skepticism about the bioauthenticity of the fossils. Journalist Sarah Kaplan explains why: “Findings like these are subject to intense scrutiny because they have potentially far-reaching implications for the study of early organisms on Earth and other planets.”4

As I have discussed previously when the discovery of 3.7-billion-year-old stromatolite fossils were unearthed in Greenland, one of the implications of the early appearance of metabolically complex and diverse microbial life on Earth is that it calls into question evolutionary explanations for the origin of life. These discoveries indicate that life appeared suddenly on Earth, in a geological instant. Yet traditionally, origin-of-life researchers maintained that life’s origin via chemical evolution would have required hundreds of millions of years, perhaps even a billion years.

This concern can be read between the lines in the objections raised by scientists responding to this discovery.

Some argue that the research team hasn’t amassed enough evidence to convince them of the biogenicity of the fossils, pointing out that extraordinary claims require extraordinary evidence. But the claim that life appeared early in Earth’s history is only extraordinary within the evolutionary paradigm. To view these microfossils as extraordinary highlights the trouble these fossil finds cause for an evolutionary approach to the origin-of-life question.

Others argue that iron-oxidizing microbes are too complex to have appeared this early in Earth’s history. Some assert that the rock layers containing the fossils are much younger than 3.77 billion years, raising concerns about the dating methods used to determine the age of the rocks harboring the microfossils. Again, both complaints reveal concerns about the impact that this fossil find has on the evolutionary explanation for life’s beginning. The hope is that by forcing the fossils to appear much later in Earth’s history, scientists can explain the metabolic complexity of the organisms that produced the hematite deposits by giving evolutionary processes more time. Yet there is no reason to dispute the dates for the rock formations in northern Canada, and the case for the biogenicity of the fossils is strong.

Some dismiss the bioauthenticity of the microfossils because it would require life to originate under hostile conditions, caused by the late heavy bombardment. These hostile conditions would have frustrated the origin-of-life process, potentially sterilizing Earth, making it difficult to imagine how life could have emerged, let alone diversified, at 3.77 billion years ago—at least from an evolutionary vantage point. If these fossils aren’t authentic, then scientists don’t have to confront the counterintuitive fact that life appeared under hostile conditions.

It seems to me that these scientists are dangerously close to evaluating the validity of the 3.77-billion-year-old microfossils based on how well they fit into the evolutionary paradigm, instead of evaluating evolutionary explanations for the origin of life based on the fossil evidence—a complete reversal of the way that the scientific method is supposed to work.

Nevertheless, a quick read between the lines reveals just how awkwardly this fossil find fits within the evolutionary paradigm.

Implications for Creation Models

Though the discovery of 3.77-billion-year-old microfossils confounds evolutionary origin-of-life models, it affirms RTB’s origin-of-life model. As described in Origins of Life, two key predictions of this model include (1) life appearing on Earth soon after the planet’s formation and (2) first life possessing intrinsic complexity. And these predictions are satisfied by this latest advance.

The writing is on the wall: the case for a Creator’s role in the origin of life is becoming more and more evident.

Resources

Endnotes

  1. Matthew S. Dodd et al., “Evidence for Early Life in Earth’s Oldest Hydrothermal Vent Precipitates,”Nature 543 (March 2017): 60–64, doi:10.1038/nature21377.
  2. Sarah Kaplan, “Newfound 3.77-Billion-Year-Old Fossils Could Be Earliest Evidence of Life on Earth,” Washington Post, March 1, 2017, https://www.washingtonpost.com/news/speaking-of-science/wp/2017/03/01/newfound-3-77-billion-year-old-fossils-could-be-earliest-evidence-of-life-on-earth.
  3. Allen P. Nutman et al., “Rapid Emergence of Life Shown by Discovery of 3,700-Million-Year-Old Microbial Structures,” Nature 537 (September 2016): 535–38, doi:10.1038/nature19355.
  4. Kaplan, “Newfound 3.77-Billion-Year-Old Fossils.”
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/03/29/what-does-the-discovery-of-earth-s-oldest-fossils-mean-for-evolutionary-models

Ancient Muds Bog Down Evolutionary Explanation for Life’s Origin

ancientmuds

BY FAZALE RANA – NOVEMBER 30, 2016

When I was a kid, I played a lot of sandlot football. And nothing was more fun than playing football after a hard rain on a muddy field. It was a blast to slosh around in the mud. But if the field was too muddy, it was hard to run, making it difficult to advance the ball down the field.

Scientists like playing in the mud, too. And recently, a scientist from the University of Washington had a good time working with ancient mud from early Earth (dating to 3.8 billion years in age). As a result of her efforts, Eva Stüeken now argues that the nitrogen in some of the oldest muddy sediments on Earth was produced by microorganisms.

Her interpretation of the nitrogen in ancient muds adds to the mounting evidence for an early and rapid origin of life, making it more difficult for the scientific community to advance an evolutionary explanation for life’s start.1

In earlier studies, geochemists measured about 430 parts per million (ppm) nitrogen in biotiteminerals recovered from 3.8-billion-year-old sediments of the Isua Formation of Greenland. Typically, the highest levels of nitrogen co-occur with graphite granules. (Some geochemists regard the graphite granules as a biomarker.) Because nitrogen is an integral component of biomolecules such as DNA and proteins, the occurrence of this element in the biotite can be taken as a biosignature.

Unfortunately, it is not that straightforward. Some geochemists claim that the nitrogen in the ancient mud comes from abiotic sources. For example, lightning and volcanism can fix atmospheric nitrogen, conceivably accounting for its presence in the biotite grains.

To test this idea, University of Washington earth scientist Eva Stüeken modeled the amount of abiotic nitrogen that would be expected in ancient muds if it came exclusively from abiotic processes. She determined that abiotic pathways were insufficient to explain nitrogen levels, meaning that some of the nitrogen must be biogenic.

Early Life on Earth

The presence of nitrogen in ancient muds adds to the mounting geochemical and fossil evidence that points to the presence of life on early Earth. (See the Resources section below to learn about other evidences for early life on Earth.) It looks like life appeared on Earth as soon as our planet could sustain it. In fact, a case can be made that life could not have originated and persisted on Earth prior to 3.8 billion years ago. This constraint means that life must have originated within a geological instant.

Both the geochemical and fossil evidence indicate that Earth’s first life was microbial in nature. Though morphologically simple, the geochemical data indicates this life was biochemically diverse and complex. There are good reasons to think that the first life-forms could engage in a wide range of metabolic activities including: photosynthesis, methanogenesis, methanotrophism, and sulfur disproportionation. While far from conclusive, the biogenic nitrogen in the ancient muds suggests that Earth’s first life also had the capacity to fix nitrogen.

Evidence for Evolution or Creation?

As discussed in Origins of Life, the sudden, early appearance of metabolically sophisticated life on Earth is difficult to accommodate within an evolutionary framework. Traditionally, origin-of-life researchers have maintained that the origin-of-life process would have required hundreds of millions of years—maybe even a billion years. To put it another way, when viewed from an evolutionary standpoint, no one would have expected that life’s origin would have happened so rapidly.

This latest insight about the ancient muds creates an additional problem for evolutionary models. It argues against the existence of a prebiotic soup on early Earth. This idea is a cornerstone for most origin-of-life models. Accordingly, life emerged on early Earth out of a prebiotic soup—a complex chemical mixture—as the molecules in the soup became more complex and, eventually, self-organized into the first cellular entities.

If a prebiotic soup existed on Earth, it should leave behind a geochemical signature in the oldest rocks on Earth. Geochemists have uncovered chemical residues in the oldest rock formations on Earth—including the nitrogen in the ancient muds—but inevitably, these residues turn out to be biogenic in origin, not abiotic. In other words, there is no geochemical evidence for a prebiotic soup. This idea is all covered with the mud.

On the other hand, the sudden appearance of biochemically complex life on early Earth bears the signature of the Creator’s handiwork. They are also key predictions for the RTB model for life’s origin.

Resources

Origins of Life: Biblical and Evolutionary Models Face Off by Fazale Rana and Hugh Ross (book)
Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator by Fazale Rana (book)
“Science News Flash: 3.7-Billion-Year-Old Fossils Perplex Origin-of-Life Researchers” by Fazale Rana (article)
“Early Life was More Complex than We Thought” by Fazale Rana (article)
“When Did Life First Appear on Earth?” by Fazale Rana (article)
“Origin-of-Life Predictions Face Off: Evolution vs. Biblical Creation” by Fazale Rana (article)
“Fossils Indicate Early Life Was Metabolically Complex and Diverse” by Fazale Rana (podcast)
“Life May Have Begun 300 Million Years Earlier Than We Thought” by Fazale Rana (podcast)

Endnotes

  1. Eva Stüeken, “Nitrogen in Ancient Mud: A Biosignature?” Astrobiology 16 (September 2016): 730–35, doi:10.1089/ast.2016.1478.

Science News Flash: 3.7-Billion-Year-Old Fossils Perplex Origin-of-Life Researchers

sciencenewsflash3.7billionyearoldfossils

BY FAZALE RANA – SEPTEMBER 7, 2016

Good things can come from bad circumstances.

This idea is beautifully illustrated by the research efforts of a team of Australian scientists. Climate change has triggered the excessive melting of ice and snow in western Greenland. This loss of snow and ice concerns many people, but, on the other hand, it has been a boon for the scientific community. It has exposed a new outcropping of rocks, giving geologists first-time access to a rare window of the earth’s distant past. As it turns out, these rocks harbor what appears to be the oldest fossils on Earth—stromatolites that date to around 3.7 billion years in age.1

billion-year-old-fossils-perplex-origin-of-life-researchers-1Image: Stromatolites in western Australia

This latest insight has important implications for understanding the origin of life. In fact, on the day researchers from Australia reported this discovery in scientific literature, it made headlines in news outlets around the world.2

Evidence for Early Life on Earth

As Hugh Ross and I discuss in Origins of Life, geochemists have unearthed a number of chemical markers in the Isua Supracrustal Belt (ISB) of western Greenland that strongly hint at microbial life on Earth between 3.7 and 3.8 billion years ago. But origin-of-life researchers debate the bio-authenticity of these geochemical signatures, because a number of potential abiotic processes can produce similar geochemical profiles.

Most scientists doubted that fossils would ever be unearthed in the Isua rock formations because these outcrops have undergone extensive metamorphosis, experiencing high temperatures and pressures—conditions that would destroy fossils. But these newly exposed formations contain regions that have experienced only limited metamorphosis, making it possible for fossils to survive.

Careful microscopic and chemical characterization of the Isua stromatolites affirms their biogenecity. These analyses also indicate that they formed in shallow water marine environments.

These recently discovered stromatolites (and the previously detected geochemical life signatures in the Isua formations) indicate that a complex and diverse ecology of microorganisms existed on Earth as far back as 3.7 billion years ago.

Prior to the discovery of 3.7 billion-year-old stromatolites, origin-of-life researchers widely agreed that microbial life existed on Earth around 3.4–3.5 billion years ago, based on the recovery of stromatolites, microbial mats, microfossils, and geochemical signatures in rock formations found in western Australia. Many origin-of-life researchers have expressed amazement that complex microbial ecologies were present on Earth as early as 3.4 billion years ago. For example, paleontologist J. William Schopf marveled:

“No one had foreseen that the beginning of life occurred so astonishingly early.”3

The researchers who recovered and analyzed the Isua stromatolites expressed similar surprise:

“The complexity and setting of the Isua stromatolites points to sophistication in life systems at 3,700 million years ago, similar to that displayed by 3,480–3,400 million-year-old Pilbara stromatolites.”4

From a naturalistic perspective, the only way for these researchers to make sense of this discovery is to conclude that life must have originated prior to 4 billion years ago. They state: “This implies that by ~3,700 million years ago life already had a considerable prehistory, and supports model organism chronology that life arose during the Hadean (>4,000 million years ago).”5

Implications for Evolutionary Models

However, the researchers’ explanation for the appearance of a complex, diverse microbial ecosystem at 3.7 billion years ago is problematic, when the natural history of early Earth is considered.

Traditionally, planetary scientists have viewed the early Earth as hot and molten, from the time of its formation (4.5 billion years ago) until ~3.8 billion years ago. This era of Earth’s history is called the Hadean. Accordingly, oceans were not present on early Earth until around 3.8 billion years ago. They believe a number of factors contributed to the hellish environment of our early planet, chief of which were the large impactors striking the earth’s surface. Some of these impact events would have been so energetic that they would have volatilized any liquid water on the planet’s surface and rendered the surface and subsurface as a molten state. In light of this scenario, it would be impossible for life to originate much earlier than 3.8 billion years ago. To put it another way, if the traditional understanding of early Earth history is correct, then it looks as if complex microbial ecologies appeared on Earth suddenly—within a geological instant. It is impossible to fathom how the explosive appearance of early life could happen via evolutionary mechanisms.

More recently, a number of planetary scientists have proposed that early Earth only remained molten for the first 200–300 million years of its history. After which time, oceans became permanent (or maybe semi-permanent) features on the planet’s surface. The basis for this view has been the discovery of zircon crystals that date between 4.2–4.4 billion years ago. Geochemical signatures within these crystals are consistent with their formation in an aqueous setting, implying that oceans were present on Earth prior to 3.8 billion years ago.

But this revised scenario doesn’t help the evolutionary approach to life’s origin. Around 3.8 billion years ago, a gravitational perturbation in the early solar system sent asteroids towards Earth. Some estimates have the earth experiencing over 17,000 impact events during this time. This event, called the late heavy bombardment (LHB), was originally regarded as a sterilization event. If so, then any life present on Earth prior to the LHB would have been obliterated. That being the case, again, it appears as if complex microbial ecologies appeared on Earth suddenly, within a geological instant.

Recently, some planetary scientists have challenged the notion that the LHB was a sterilization event. They argue that life on the planet’s surface would have been destroyed, but life in some environments, such as hydrothermal vents, could have survived. In other words, there would have been refugiums on Earth that served as “safe houses” for life, ushering it through the LHB.

Yet the latest discovery by the Australian scientists doesn’t fit this scenario. The Isua stromatolites formed at the earth’s surface in a shallow water environment. In fact, the research team generated data that effectively ruled out stromatolite formation near hydrothermal vents. But if the refugium model has validity, the Isua fossils should have formed in a high-temperature milieu.

Finally, pushing life’s origin back to more than 4 billion years ago doesn’t solve the problem of a sudden origin-of-life—it merely displaces it to another window of time in Earth’s history. Origin-of-life researchers have geochemical evidence suggesting that life was present on Earth between 4.2–4.4 billion years ago. Given that the earth was molten for the first 200–300 million years of its existence (minimally), that doesn’t leave much time for life to originate.

No matter the scenario, a naturalistic, evolutionary approach to the origin-of-life can’t seem to accommodate the sudden appearance of life on Earth. On the other hand, if a Creator brought life into being, this is precisely the mode and tempo expected for life’s appearance on Earth.

Implications for Creation Models

While the discovery of 3.7 billion-year-old stromatolites confounds evolutionary explanations for life’s origins, it affirms RTB’s origin-of-life model. This model is derived from the biblical creation accounts and make two key and germane predictions: (1) life should appear on Earth soon after the planet’s formation; and (2) first life should possess intrinsic complexity. And both of these predictions are satisfied by this latest advance.

Resources
Origins of Life: Biblical and Evolutionary Models Face Off by Fazale Rana and Hugh Ross (book)
Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator by Fazale Rana (book)
“Life May Have Begun 300 Million Years Earlier Than We Thought” by Fazale Rana (podcast)
“Early Life Was More Complex Than We Thought” by Fazale Rana (article)
“When Did Life First Appear on Earth?” by Fazale Rana (article)
“Insight into the Late Heavy Bombardment and RTB’s Creation Model” by Fazale Rana (article)
“Origin-of-Life Predictions Face Off: Evolution vs. Biblical Creation” by Fazale Rana (article)

Endnotes

  1. Allen P. Nutman et al., “Rapid Emergence of Life Shown by Discovery of 3,700-Million-Year-Old Microbial Structures,” Nature, published electronically August 31, 2016, doi:10.1038/nature19355.
  2. For a detailed discussion of this discovery and its implications for the creation/evolution controversy, listen to “Fossils Indicate Early Life Was Metabolically Complex and Diverse,” Apologia (Ex Libris), podcast audio, August 31, 2016, https://www.reasons.org/podcasts/apologia-premium/fossils-indicate-early-life-was-metabolically-complex-and-diverse.
  3. J. William Schopf, Cradle of Life: The Discovery of Earth’s Earliest Fossils (Princeton, NJ: Princeton University Press, 1999), 3.
  4. Allen P. Nutman, “Rapid Emergence of Life.”
  5. Ibid.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/09/07/science-news-flash-3.7-billion-year-old-fossils-perplex-origin-of-life-researchers

Have Origin-of-Life Researchers Found the RNA World “Money Train”?

haveoriginsofliferesearchersfoundtherna

BY FAZALE RANA – AUGUST 31, 2016

As I write this blog post, amateur treasure hunters in Poland are trying to determine if a local legend is true. According to the lore, during the end of World War II, as the Germans escaped the advancing Soviet army, a train loaded with $200 million in gold, silver, and valuable art disappeared in a complex series of secret tunnels beneath a castle in the Owl Mountains. The treasure hunters claim they have evidence for the location of the buried train and now local authorities are excavating three sites of potential interest. But skepticism abounds. It’s not clear if the legend has any basis in reality. The treasure hunters and local officials may be looking for a treasure that may never have existed.

Over the last several decades, origin-of-life researchers have been on a quest for their own version of a “money train”: a self-replicating ribozyme. If they can find such a molecule—which may not have ever existed—they will go a long way toward validating one of the most prominent origin-of-life models: the RNA world hypothesis. Recent work by scientists from the Scripps Institute adds to the hope that a self-replicating ribozyme may one day be discovered.1 But careful assessment of their work indicates that their hope may not be based in reality.

The RNA World Hypothesis

Many origin-of-life investigators think that RNA predated both DNA and proteins as the premier replicator and information-harboring molecule. Accordingly, RNA operated as a self-replicator that catalyzed its own synthesis. The RNA world hypothesis supposes that, over time, numerous RNA molecules representing a wide-range of catalytic activity emerged. At this point in life’s history, biochemistry centered exclusively on RNA. With time, proteins (and eventually DNA) joined RNA in the cell’s arsenal. During the transition to the contemporary DNA-protein world, RNA’s original function became partitioned between proteins and DNA, and RNA assumed its current intermediary role. RNA ancestral molecules presumably disappeared without leaving a trace of their primordial existence.

In the mid-1980s, the discovery of RNA molecules with enzymatic activity (called ribozymes) propelled the RNA world hypothesis to prominence.

Since then, several scientific teams working in the laboratory have produced a number of ribozymes with a range of biological activity using a technique called in vitro evolution. For many origin-of-life researchers, this work adds more credibility to the RNA world scenario. In principle, it demonstrates that life centered on RNA biochemistry is conceivable.

The Quest for a Self-Replicating RNA

The real “money train” for the RNA world is a self-replicating ribozyme, but researchers have made limited progress toward discovering this type of ribozyme. For example, they have produced a variety of ribozymes that (1) assist in the synthesis of ribonucleotides; (2) join two RNA chains together (in a process called ligation); and (3) add ribonucleotide subunits to the end of an RNA molecule, extending the chain. All of these activities are necessary for replication of RNA molecules, yet, to date, biochemists have been unable to make RNA with genuine self-replicating capability.

The latest work by scientists from The Scripps Research Institute (TSRI) adds to these accomplishments, moving origin-of-life researchers closer to a self-replicating RNA. But the train still hasn’t arrived at the station.

The researchers from TSRI extended the work of earlier studies, using in vitro evolution to modify a ribozyme dubbed the class I RNA polymerase ribozyme. This molecule—initially generated by researchers in the 1990s—can join together some RNA molecules once they bind to a template to produce larger RNA molecules. Later, researchers modified the original ribozyme so that it could use a template to form RNA chains over 100 nucleotides in length. Unfortunately, the modified version of the class I RNA polymerase ribozyme is quite finicky. While it can only transcribe RNA with certain nucleotide sequences and cannot transcribe RNA molecules with complex three-dimensional structures.

TSRI scientists randomly mutated the RNA sequence of the modified version of the class I RNA polymerase to generate a population of 100 trillion molecules. From this population, they selected those ribozymes that could transcribe two different RNA molecules with a complex three-dimensional structure. Once they identified the ribozymes with the desired properties, they repeated the process, mutating the newly identified ribozymes to produce a new population of molecules. After 24 rounds, they had successfully evolved a ribozyme (they called the 24-3 ribozyme) that can copy RNA molecules with complex three-dimensional structures and, in turn, make copies of RNA molecules it had already copied. That is, the 24-3 polymerase can amplify specific RNA molecules 10,000 fold.

While this is an important advance for the RNA world hypothesis, the 24-3 polymerase can’t copy itself, a necessary requirement for self-replication.

Evolution or Intelligent Design?

This work has important implications for the creation-evolution debate. Origin-of-life researchers and evolutionary biologists count these types of studies as support for the RNA world hypothesis. More broadly, they point to these types of studies as evidence that evolutionary processes can generate information-rich molecules from random sequences and transform existing biomolecules into ones with new or improved function.

As a Christian apologist, I have to acknowledge that these scientists have a point. In principle, evolutionary mechanisms can generate bioinformation.2 But, I would argue that studies in in vitro evolution have failed to provide any evidence that evolutionary processes can generate information under the conditions of early Earth.

As I discuss in Creating Life in the Lab, the process of in vitro evolution relies on a carefully developed experimental design and researcher intervention. The protocol begins with a large pool of RNA molecules with random nucleotide sequences, and hence, random structures. From this pool, researchers select (through the experiment’s design) RNA molecules with a predetermined set of chemical properties. These selected RNA molecules are recovered and their number amplified by the enzyme reverse transcriptase and the polymerase chain reaction (PCR). PCR also employs an enzyme, a DNA polymerase. The new RNA sequence is then randomly altered to generate a new pool of RNA molecules using another enzyme called T7 RNA polymerase, and the process is repeated again and again until RNA molecules with the desired chemical properties emerge. Production of the RNA self-replicators also required researchers to modify the structure of ribozymes generated by in vitro evolution using rational design principles to improve upon the ribozymes’ function.

The “evolution” of RNA molecules in the laboratory is a carefully orchestrated process devised and managed by intelligent agents. Its success hinges on thoughtful experimental design. Researchers are manipulating the evolutionary process, guiding it to the desired outcome. It must be noted that essential to the success of in vitro evolution studies are the enzymes (protein molecules with a complex, fine-tuned structure), reverse transcriptase, T7 RNA polymerase, and DNA polymerase—molecules that would never have existed in an RNA world. It stretches the bounds of credulity to think that this process, or one like it, could have occurred naturally on early Earth.

As thrilling as this most recent achievement is, origin-of-life researchers have fallen short of demonstrating that information-rich RNA molecules can evolve under the uncontrolled conditions of early Earth.

It is ironic: The very experiments designed to bolster an evolutionary explanation for the origin of life provide powerful support for the role intelligent agency must play in the genesis of life.

Resources
Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator by Fazale Rana (book)
“Too Good to be True: Evolution and the Origin of Bioinformation” by Fazale Rana (article)
“Intelligent Design: The Right Conclusion, but the Wrong Reasons” by Fazale Rana (article)
“Does New Approach Solve Origin-of-Life Problem?” by Fazale Rana (article)

Endnotes

  1. David P. Horning and Gerald F. Joyce, “Amplification of RNA by an RNA Polymerase Ribozyme,” Proceedings of the National Academy of Sciences, USA, published electronically August 15, 2016, doi:10.1073/pnas.1610103113.
  2. Some people might find it surprising that I would acknowledge this point, because many Christian apologists assert that evolutionary mechanisms cannot generate information. In my view, that claim is patently false, as work in in vitro evolution has demonstrated, time and time again.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/08/31/have-origin-of-life-researchers-found-the-rna-world-money-train