Yuncheng Yu
Introduction
How did life originate on Earth? That question has always fascinated and challenged humanity. Attempts to answer it scientifically are currently at the center of astrobiology research. A commonly accepted answer, proposed almost a century ago, describes the origin of life from ingredients in a “primordial soup” that existed in Earth’s prebiotic oceans billions of years ago.1 Theories suggest that this “soup” was warm with a low concentration solution of relatively simple molecules. Previous experiments showed that those molecules could have been synthesized by lightning under the conditions on Earth at the time.2 According to the hypothesis, some of those molecules came together to create life’s building blocks, such as DNA and proteins. But how those blocks formed still remains largely unexplained in the “soup” theory, and researchers are looking for clarity. We have developed a laboratory toolbox, inspired by an important discovery four decades ago, to investigate the conditions that could have formed life’s building blocks in the prebiotic Earth. |
WE DEVELOPED A LABORATORY TOOLBOX, INSPIRED BY AN IMPORTANT DISCOVERY |
In the 1977 Galapagos Hydrothermal Expedition, an unexpected discovery revealed the existence of deep- sea hydrothermal vents that can support life through undersea chemical synthesis.3 Those hydrothermal vents are hot springs, produced by underwater volcanoes, occurring when cold deep seawater permeates the Earth’s crust and contacts hot magma (Figure 1A). Found in regions where tectonic plates diverge in the deep ocean, those vents may replicate scenarios that existed on prebiotic Earth. Thus, hydrothermal vents have attracted significant interest in recent years and are at the center of new theories intended to explain how life originated on Earth.4 Interestingly, in March 2017, scientists reported the discovery of fossilized bacteria inside a 4 billion-year-old rock that had formed around hydrothermal vents. That finding could be the oldest evidence of life on Earth.5
The recent evidence in support of hydrothermal vents as enablers of early life contrasts with shortcomings in the “primordial soup” theory. One of the main problems in the previous theory is that the synthesis of the complex building blocks of life requires high concentrations of the necessary simpler molecules, such as amino acids and sugars. In the immensity of the primitive oceans, those simpler molecules probably existed at concentrations too low for that synthesis to occur. Meanwhile, pore networks (Figure 1B) in mineral formations near hydrothermal vents created small compartments or microenvironments. Those hydrothermal microenvironments could have enabled the synthesis of life’s building blocks by concentrating simpler molecules on the prebiotic Earth.
FIGURE 1. Replication of hydrothermal microenvironments in the lab. (A) Hydrothermal vent at the bottom
of the ocean with a constant heat source of hot magma and constant cooling from deep seawater. (B) Pore networks in nearby rock formations create hydrothermal microenvironments in which convective flow occurs. (C) The convective flow is similar to what occurs in lava lamps, although it happens at a smaller scale in the
microenvironments, represented here by our porelike chamber filled with pink solution for visualization
and a US quarter coin for scale. (D) Schematic of our experimental setup for replicating a hydrothermal
microenvironment, heated at the bottom and cooled at the top.
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Using the same mechanism as a lava lamp, hydrothermal microenvironments in the pore networks exhibit thermal gradients that generate what is called a convective flow (Figure 1A–C). In the lava lamp, thermal gradients are introduced by the temperature difference between the bottom, where the hot lamp is located, and the top exposed to air. Similarly, but at a smaller scale (volumes on the order of a thousandth of a teaspoon), thermal gradients in
the pore microenvironments are established from the temperature difference between the hot magma and the cold deep seawater (Figure 1A–B). Inside the pores, the convective flow can carry around a variety of microscopic materials, from small to large molecules and even microparticles, a phenomenon that could have supplied the conditions necessary to synthesize life’s building blocks. To better understand how those hydrothermal microenvironments could have supported the formation of complex molecules such as DNA and proteins, we applied engineering principles to develop a laboratory toolbox, which we used to replicate and investigate the conditions found inside individual pores in rock formations.6 This laboratory toolbox consists of simple and highly versatile porelike chambers that can be subjected to controlled thermal gradients (Figure 1D) complemented with microscopy techniques and computer simulations of the experimental system. Using our toolbox, we studied how the flow patterns caused by thermal gradients could affect the distribution and concentration of chambers, dilute materials, such as |
microparticles and simple molecules, can be concentrated at specific locations in their inner walls. This localized increase in concentration of simple molecules implies the
possibility of relevant molecules coming together to create life’s building blocks in prebiotic oceans. Thus, our work offers evidence in favor of hydrothermal microenvironments as potential incubators where life on Earth could have emerged.
possibility of relevant molecules coming together to create life’s building blocks in prebiotic oceans. Thus, our work offers evidence in favor of hydrothermal microenvironments as potential incubators where life on Earth could have emerged.
Methods and Design
To mimic hydrothermal microenvironments in the laboratory, we considered two aspects: (1) the geometry of small pores in rock formations near hydrothermal vents and (2) the thermal gradients due to the cold ocean water and the proximity of hot magma (Figure 1A–B). Therefore, we created lab-scale hydrothermal microenvironments by fabricating cylindrical chambers from transparent plastic blocks (Figure 1C) in an effort to emulate small pores. After we filled the chamber with liquid, the bottom of the chamber was sealed with aluminum tape and the top was sealed with a thin glass sheet. Then, we placed the porelike chamber on top of a heated surface to establish thermal gradients between
the hot bottom of the chamber and its top surface cooled by air (Figure 1D). Pores of different shapes were fabricated by adjusting the ratio between height and diameter. In addition, the heated surface was programmed to maintain a constant temperature. These measures gave us control over a variety of experimental conditions that could be investigated to better understand the phenomena occurring inside hydrothermal microenvironments.
These experiments focused on flow behavior and how flow could locally change the concentration of materials inside the porelike chambers. We used fluorescent nanoparticles to see what was happening inside the pores. A blue light source excited the microparticles so that they emitted green light and could be viewed under a microscope. The fluorescent microparticles acted as tracers and were recorded using a high-speed video camera. When carried by the flow, the microparticles revealed the flow patterns inside the chambers and how they were distributed and eventually deposited on the chamber’s inner walls. We also used dye molecules to verify that these observations apply to materials at the molecular level as well. In this way, we see how the flow behavior could locally produce high concentrations of molecules at specific locations within the porelike chambers. If such behavior is proven correct, it has the potential to address the problem of low concentrations of simpler molecules in the “primordial soup”, and could provide evidence to support hydrothermal microenvironments as enablers of early life.
Also, we used specialized computer software to simulate and analyze complex flow patterns, transport of materials, and the speed of chemical reactions occurring inside the porelike chambers. The combination of experiments and computer simulations constituted a complete toolbox to investigate the importance of hydrothermal microenvironments for the conditions that could have formed life’s building blocks on the prebiotic Earth.
To mimic hydrothermal microenvironments in the laboratory, we considered two aspects: (1) the geometry of small pores in rock formations near hydrothermal vents and (2) the thermal gradients due to the cold ocean water and the proximity of hot magma (Figure 1A–B). Therefore, we created lab-scale hydrothermal microenvironments by fabricating cylindrical chambers from transparent plastic blocks (Figure 1C) in an effort to emulate small pores. After we filled the chamber with liquid, the bottom of the chamber was sealed with aluminum tape and the top was sealed with a thin glass sheet. Then, we placed the porelike chamber on top of a heated surface to establish thermal gradients between
the hot bottom of the chamber and its top surface cooled by air (Figure 1D). Pores of different shapes were fabricated by adjusting the ratio between height and diameter. In addition, the heated surface was programmed to maintain a constant temperature. These measures gave us control over a variety of experimental conditions that could be investigated to better understand the phenomena occurring inside hydrothermal microenvironments.
These experiments focused on flow behavior and how flow could locally change the concentration of materials inside the porelike chambers. We used fluorescent nanoparticles to see what was happening inside the pores. A blue light source excited the microparticles so that they emitted green light and could be viewed under a microscope. The fluorescent microparticles acted as tracers and were recorded using a high-speed video camera. When carried by the flow, the microparticles revealed the flow patterns inside the chambers and how they were distributed and eventually deposited on the chamber’s inner walls. We also used dye molecules to verify that these observations apply to materials at the molecular level as well. In this way, we see how the flow behavior could locally produce high concentrations of molecules at specific locations within the porelike chambers. If such behavior is proven correct, it has the potential to address the problem of low concentrations of simpler molecules in the “primordial soup”, and could provide evidence to support hydrothermal microenvironments as enablers of early life.
Also, we used specialized computer software to simulate and analyze complex flow patterns, transport of materials, and the speed of chemical reactions occurring inside the porelike chambers. The combination of experiments and computer simulations constituted a complete toolbox to investigate the importance of hydrothermal microenvironments for the conditions that could have formed life’s building blocks on the prebiotic Earth.
FIGURE 2. Chaotic flow facilitates fast and localized concentration of materials on the inner walls of porelike chambers. (A) Chaotic and periodic flow patterns from experiments and computer simulations of convective
flow. (B) Dye molecules and fluorescent microparticles deposited inside pores by convective flow. (C) Computational model of microparticles’ distribution on the surface of porelike chambers (D) Two factors,
thermal gradient and geometric structure, determine how different types of convective flow could deposit
materials on the inner walls of the pores. Both fast and localized concentration of materials occur in the
chaotic regime.
Results
We replicated the conditions expected in hydrothermal microenvironments occurring in porous mineral formations near deep-sea hydrothermal vents. Across our experiments and simulations, we initially studied the convective flow patterns inside porelike chambers. If we look at an individual chamber (Figure 1D), water at the bottom of the pore (closer to the hot surface) is hotter than water at the top (closer to the cool air). Because cool water is denser than warm water, cool water from the top would sink, whereas warm water at the bottom would move to the top of the pore. However, the cold water, now at the bottom, would heat from the hot surface while the warm water, now at the top, would
cool from the exposure to air. That is the mechanism that continuously maintains a convective flow in both hydrothermal microenvironments and the lava lamp. In the porelike chambers, the fluid motion exhibited different flow patterns, with various levels of organization, as we changed the thermal gradients and the pore’s geometry.
As we traced the motion of microparticles inside hydrothermal microenvironments, we identified two extreme cases for the flow patterns: periodic and chaotic. (Figure 2A). Periodic flow trajectories are highly ordered and repetitive, so microparticles cycle in infinite and almost identical loops. In the opposite scenario, chaotic flow is highly disordered, so microparticles essentially never follow the same trajectory twice. The continuum of flow patterns, between periodic and chaotic, offers many possibilities for how the flow carries materials and, perhaps, how they are deposited on the inner walls of the pores in hydrothermal microenvironments.
The most significant observation was the accumulation of microparticles and molecules on the walls of the chambers during the convective flow experiments (Figure 2B). We studied two main aspects of this phenomenon. First, we tried to determine whether materials present in our lab-replicated microenvironments could be deposited on specific locations in the inner walls of the chamber. Second, we looked at how fast the deposition could happen according to the flow conditions inside the pore. To do so, we took advantage of the variety of flow patterns supplied by the thermal gradients and the geometries of the porelike chambers. The investigation of the two deposition aspects, where and how fast, is intended to find the best scenarios that could produce the high concentrations required to synthesize life’s building blocks in hydrothermal microenvironments.
We determined that convective flows more efficiently deposit materials on the chamber walls in comparison with the chamber without flow. But how that deposition happens and its localization depend on the flow trajectories inside the chambers. For periodic flow trajectories, materials are deposited at higher concentrations in specific locations near the top and bottom of the pores (Figure 2C). As flow transitions from periodic to chaotic, the preferential deposition gradually decreases and materials are more uniformly distributed on the chamber walls (Figure 2C). The results indicate a plausible mechanism, based on convective flow, for localized concentration of materials in conditions found in hydrothermal microenvironments.
We replicated the conditions expected in hydrothermal microenvironments occurring in porous mineral formations near deep-sea hydrothermal vents. Across our experiments and simulations, we initially studied the convective flow patterns inside porelike chambers. If we look at an individual chamber (Figure 1D), water at the bottom of the pore (closer to the hot surface) is hotter than water at the top (closer to the cool air). Because cool water is denser than warm water, cool water from the top would sink, whereas warm water at the bottom would move to the top of the pore. However, the cold water, now at the bottom, would heat from the hot surface while the warm water, now at the top, would
cool from the exposure to air. That is the mechanism that continuously maintains a convective flow in both hydrothermal microenvironments and the lava lamp. In the porelike chambers, the fluid motion exhibited different flow patterns, with various levels of organization, as we changed the thermal gradients and the pore’s geometry.
As we traced the motion of microparticles inside hydrothermal microenvironments, we identified two extreme cases for the flow patterns: periodic and chaotic. (Figure 2A). Periodic flow trajectories are highly ordered and repetitive, so microparticles cycle in infinite and almost identical loops. In the opposite scenario, chaotic flow is highly disordered, so microparticles essentially never follow the same trajectory twice. The continuum of flow patterns, between periodic and chaotic, offers many possibilities for how the flow carries materials and, perhaps, how they are deposited on the inner walls of the pores in hydrothermal microenvironments.
The most significant observation was the accumulation of microparticles and molecules on the walls of the chambers during the convective flow experiments (Figure 2B). We studied two main aspects of this phenomenon. First, we tried to determine whether materials present in our lab-replicated microenvironments could be deposited on specific locations in the inner walls of the chamber. Second, we looked at how fast the deposition could happen according to the flow conditions inside the pore. To do so, we took advantage of the variety of flow patterns supplied by the thermal gradients and the geometries of the porelike chambers. The investigation of the two deposition aspects, where and how fast, is intended to find the best scenarios that could produce the high concentrations required to synthesize life’s building blocks in hydrothermal microenvironments.
We determined that convective flows more efficiently deposit materials on the chamber walls in comparison with the chamber without flow. But how that deposition happens and its localization depend on the flow trajectories inside the chambers. For periodic flow trajectories, materials are deposited at higher concentrations in specific locations near the top and bottom of the pores (Figure 2C). As flow transitions from periodic to chaotic, the preferential deposition gradually decreases and materials are more uniformly distributed on the chamber walls (Figure 2C). The results indicate a plausible mechanism, based on convective flow, for localized concentration of materials in conditions found in hydrothermal microenvironments.
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Chaotic flow’s positive influence on the rate of deposition on the pore walls was significant, providing up to 1,000 times faster deposition speeds than under no-flow conditions. Thus, we identified the best settings under which both fast deposition and localized concentration of materials on the pore walls could happen. Figure 2D summarizes those results, indicating a broad range of optimum conditions (shown in red) given by various combinations of pore geometries and thermal gradients across the pores. In general, the set of optimum conditions seen in Figure 2D emerge when chaotic flow is present.
Chaotic flow, generated by thermal gradients, can quickly deposit materials at high concentrations in specific regions within porelike chambers. Using this finding, others in our research group later showed that, as a result of high local concentrations, chemical reactions in those chambers can proceed faster.6 Taken together, these results could explain how relatively simple molecules, present at low concentrations in prebiotic oceans, were enriched inside hydrothermal microenvironments. Higher concentrations then allowed simpler molecules to create the more complex building blocks of life on Earth. |
Conclusion
The “primordial soup”, a widely accepted theory for the origin of life on Earth, fails to explain how relatively simple molecules came together at concentrations high enough to form life’s more complex building blocks. However, with the discovery of deep-sea hydrothermal vents, scientists have come upon a promising scenario that could offer a more complete picture of life’s early stages.
Small pores in rock formations near hydrothermal vents, exposed to the thermal interaction between the cold deep seawater and hot magma, created hydrothermal microenvironments where life’s building blocks could have been synthesized. After engineering a toolbox to replicate conditions that occur inside the microenvironments, we have shown that chaotic convective flow offers a mechanism to quickly concentrate simple molecules in specific locations in the inner walls of the pores. Therefore, our research suggests that, on the prebiotic Earth, simpler molecules could achieve high concentrations inside those hydrothermal microenvironments. Those increasing concentrations allowed simple molecules to come together to create the building blocks of life. Our findings offer a much-needed explanation lacking in the primordial soup theory.
The “primordial soup”, a widely accepted theory for the origin of life on Earth, fails to explain how relatively simple molecules came together at concentrations high enough to form life’s more complex building blocks. However, with the discovery of deep-sea hydrothermal vents, scientists have come upon a promising scenario that could offer a more complete picture of life’s early stages.
Small pores in rock formations near hydrothermal vents, exposed to the thermal interaction between the cold deep seawater and hot magma, created hydrothermal microenvironments where life’s building blocks could have been synthesized. After engineering a toolbox to replicate conditions that occur inside the microenvironments, we have shown that chaotic convective flow offers a mechanism to quickly concentrate simple molecules in specific locations in the inner walls of the pores. Therefore, our research suggests that, on the prebiotic Earth, simpler molecules could achieve high concentrations inside those hydrothermal microenvironments. Those increasing concentrations allowed simple molecules to come together to create the building blocks of life. Our findings offer a much-needed explanation lacking in the primordial soup theory.
Acknowledgments
I thank Dr. Victor Ugaz for advising and providing me the opportunity to conduct my research and interests in his lab, and Dr. Aashish Priye, who did the prior simulation and experiment work. I also thank Dr. Victor Ugaz, Dr. Catharina Laporte, Dr. Jose Contreras Naranjo, and Annabelle Aymond for helpful comments.
I thank Dr. Victor Ugaz for advising and providing me the opportunity to conduct my research and interests in his lab, and Dr. Aashish Priye, who did the prior simulation and experiment work. I also thank Dr. Victor Ugaz, Dr. Catharina Laporte, Dr. Jose Contreras Naranjo, and Annabelle Aymond for helpful comments.
Yuncheng Yu ‘18Yuncheng Yu is a senior chemical engineering major with a minor in mathematics from Harbin, China. Yu is passionate about using interdisciplinary approaches to push the boundaries of human knowledge in hopes of improving daily life. After graduation, Yu plans to pursue a PhD in chemical engineering and intends to work in academia.
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References
1. Oparin, Alexander I. The Origin of Life. Translated by Sergius Morgulis. New York City: The Macmillan Company, 1938. 2. Miller, Stanley L. “A Production of Amino Acids under Possible Primitive Earth Conditions.” Science 117 (1953): 528–529. 3. Cristina Luiggi. “Life on the Ocean Floor, 1977,” The Scientist. http://www.the-scientist.com/?articles. view/articleNo/32523/title/Life-on-the-Ocean- Floor--1977/. 4. Martin, William, John Baross, Deborah Kelley, and Michael J. Russell. “Hydrothermal Vents and the Origin of Life.” Nature Reviews Microbiology 6 (2008): 805–814. doi:10.1038/nrmicro1991. 5. Dodd, Matthew S., Papineau Dominic, Tor Grenne, et al. “Evidence for Early Life in Earth’s Oldest Hydrothermal Vent Precipitates.” Nature 543 (2017): 60–64. doi:10.1038/nature21377. 6. Priye, Aashish, Yuncheng Yu, Yassin A. Hassan, and Victor M. Ugaz. “Synchronized Chaotic Targeting and Acceleration of Surface Chemistry in Prebiotic Hydrothermal Microenvironments.” Proceedings of the National Academy of Sciences USA 114 (2017): 1275–1280. doi:10.1073/pnas.1612924114. |