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Themed Issue Commemorating Prof. David Deamer's 80th Birthday

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A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Origin of Life".

Deadline for manuscript submissions: closed (15 November 2019) | Viewed by 81241

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Dr. Bruce Damer

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1. Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
2. BIOTA Institute, Boulder Creek, CA 95006, USA
Interests: origins of life; nonenzymatic polymerization; lipid biophysics; astrobiology; biosignature detection; Archean geology; space mission design; computational simulation
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Dear Colleagues,

Taken at Shaw River, Pilabara, Western Australia, Summer 2015. Credit: Tara Djokic

Research on how and where the origin of life might have occurred on the Earth some four billion years ago is slowly undergoing a paradigm shift. It is becoming increasingly clear that fresh water hydrothermal conditions may be more conducive than salty sea water for processes leading to the emergence of evolving protocell populations. Central to that shift has been the work of Professor David Deamer, who is now a Research Professor in the Department of Biomolecular Engineering at the University of California, Santa Cruz. Throughout his academic career, Deamer has had unusually broad research interests, primarily focusing on membrane biophysics and nucleic acid chemistry but also exploring the burgeoning field of astrobiology.

Over thirty years ago, Deamer reported that amphiphilic compounds present in a certain class of ancient meteorites can assemble into membranous boundaries required for the origin of primitive cellular life (Nature, 1985). Curious about how membranes could have interacted with other compounds in the prebiotic environment, Deamer began to explore prebiotic analogue sites such as the fresh water hot springs and pools associated with volcanic land masses like Iceland, Hawaii and Kamchatka, where he observed that the hydrothermal water in such sites undergoes endless cycles of evaporation and rehydration.

Deamer decided to simulate wet-dry cycles in the laboratory in order to investigate what happens when mixtures of membrane-forming amphiphilic compounds like fatty acids and phospholipids are exposed to these conditions. He discovered that the amphiphiles assemble into multilayered films on mineral surfaces during evaporation, and that other solutes become organized and concentrated between the layers. This includes nucleotides, the monomers of nucleic acids, which go on to form RNA-like polymers when ester bonds are synthesized between the monomers. When the films were rehydrated, the polymers are encapsulated within self-assembled vesicles. In collaboration with other researchers, these experimental foundations have been expanded into a full hypothesis that was published in Life and other scientific journals, and as a cover article in Scientific American (August 2017).

Even the most basic research can lead to valuable applications, and research on the origin of life is no exception. For instance, in 1989 Deamer was wondering how nutrients might have been transported across the membranes of protocells. One possibility is that some of the polymers might form channels through the membrane, perhaps even large enough to accommodate a long nucleic acid molecule. From other work, Deamer knew that ionic current through a channel could be modulated by molecules passing through, and proposed that the modulations might be a way to determine the base sequence in the nucleic acid. The idea was patented in 1998, then licensed to a company that developed it into a commercial nanopore sequencing device. Deamer plans to use the device in his latest research, which will test whether wet-dry cycles not only synthesize polymers resembling RNA and DNA, but may also drive molecular functions like replication and transcription. If this is possible, it will provide yet another piece to the biogenesis puzzle.

If there is one statement that sums up Prof. Deamer’s career it might be this: We are discovering that self-assembly, a biophysical process, was probably the key to life emerging in the chaotic conditions of the prebiotic Earth. The chemical reactions that are the foundation of metabolism, growth and replication could only begin after molecular systems were contained in membranous compartments. Vast numbers of such compartments, each different from all the rest, were the first populations of protocells capable of undergoing the selection and evolutionary processes that led to the origin of life.

Detailed history (from Wikipedia) mainly focused on his work on nanopore sequencing: https://en.wikipedia.org/wiki/David_W._Deamer

The journal is pleased to be publishing a commemorative issue in honor of Professor David Deamer for his outstanding contributions in the fields of the origins of life and genetics on the occasion of his 80^th birthday in 2019.

This Special Issue of Life welcomes submission of unpublished manuscripts of original work or reviews on previous work. We plan to receive submissions now or up until the deadline (21 April 2019).

Dr. Bruce Damer
Guest Editor

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

membrane biophysics
origins of life
nonenzymatic polymerization
meteoritic delivery of organics
astrobiology
nanopore sequencing
others TBD

Published Papers (14 papers)

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Editorial

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9 pages, 2385 KiB

Open AccessEditorial

Exploring the Kamchatka Geothermal Region in the Context of Life’s Beginning

by Vladimir N. Kompanichenko

Life 2019, 9(2), 41; https://doi.org/10.3390/life9020041 - 16 May 2019

Cited by 6 | Viewed by 4374

Abstract

This article is a brief review of research in the Kamchatka geothermal region initiated by David Deamer and the author in 1999. Results obtained over the last 20 years are described, including a seminal experiment in which biologically important organic compounds were dispersed in a hot spring to determine their fate. Other investigations include ionic and organic composition of hydrothermal water, the source of hydrothermally generated oil, and pressure–temperature oscillations in hydrothermal systems. The relation of these results to research on the origin of life is discussed. Full article

(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)

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14 pages, 8028 KiB

Open AccessEditorial

David Deamer: Five Decades of Research on the Question of How Life Can Begin

by Bruce Damer

Life 2019, 9(2), 36; https://doi.org/10.3390/life9020036 - 02 May 2019

Cited by 3 | Viewed by 7698

Abstract

In commemoration of his 80th birthday, this interview article engages David Deamer in some personal and scientific insights into his fifty year quest surrounding the question of “how can life begin” on the Earth or other worlds. Full article

(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)

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Graphical abstract

Research

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15 pages, 618 KiB

Open AccessArticle

A Polyaddition Model for the Prebiotic Polymerization of RNA and RNA-Like Polymers

by Alex Spaeth and Mason Hargrave

Life 2020, 10(2), 12; https://doi.org/10.3390/life10020012 - 02 Feb 2020

Cited by 5 | Viewed by 4582

Abstract

Implicit in the RNA world hypothesis is that prebiotic RNA synthesis, despite occurring in an environment without biochemical catalysts, produced the long RNA polymers which are essential to the formation of life. In order to investigate the prebiotic formation of long RNA polymers, we consider a general solution of functionally identical monomer units that are capable of bonding to form linear polymers by a step-growth process. Under the assumptions that (1) the solution is well-mixed and (2) bonding/unbonding rates are independent of polymerization state, the concentration of each length of polymer follows the geometric Flory-Schulz distribution. We consider the rate dynamics that produce this equilibrium; connect the rate dynamics, Gibbs free energy of bond formation, and the bonding probability; solve the dynamics in closed form for the representative special case of a Flory-Schulz initial condition; and demonstrate the effects of imposing a maximum polymer length. Afterwards, we derive a lower bound on the error introduced by truncation and compare this lower bound to the actual error found in our simulation. Finally, we suggest methods to connect these theoretical predictions to experimental results. Full article

(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)

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9 pages, 6085 KiB

Open AccessArticle

Silica Precipitation in a Wet–Dry Cycling Hot Spring Simulation Chamber

by Andrew Gangidine, Jeff R. Havig, Jeffrey S. Hannon and Andrew D. Czaja

Life 2020, 10(1), 3; https://doi.org/10.3390/life10010003 - 14 Jan 2020

Cited by 5 | Viewed by 4191

Abstract

Terrestrial hot springs have emerged as strong contenders for sites that could have facilitated the origin of life. Cycling between wet and dry conditions is a key feature of these systems, which can produce both structural and chemical complexity within protocellular material. Silica precipitation is a common phenomenon in terrestrial hot springs and is closely associated with life in modern systems. Not only does silica preserve evidence of hot spring life, it also can help it survive during life through UV protection, a factor which would be especially relevant on the early Earth. Determining which physical and chemical components of hot springs are the result of life vs. non-life in modern hot spring systems is a difficult task, however, since life is so prevalent in these environments. Using a model hot spring simulation chamber, we demonstrate a simple yet effective way to precipitate silica with or without the presence of life. This system may be valuable in further investigating the plausible role of silica precipitation in ancient terrestrial hot spring environments even before life arose, as well as its potential role in providing protection from the high surface UV conditions which may have been present on early Earth. Full article

(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)

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16 pages, 6959 KiB

Open AccessArticle

Prebiotic Chemistry that Could Not Not Have Happened

by Steven A. Benner, Hyo-Joong Kim and Elisa Biondi

Life 2019, 9(4), 84; https://doi.org/10.3390/life9040084 - 14 Nov 2019

Cited by 29 | Viewed by 5939

Abstract

We present a direct route by which RNA might have emerged in the Hadean from a fayalite–magnetite mantle, volcanic SO₂ gas, and well-accepted processes that must have created substantial amounts of HCHO and catalytic amounts of glycolaldehyde in the Hadean atmosphere. In chemistry that could not not have happened, these would have generated stable bisulfite addition products that must have rained to the surface, where they unavoidably would have slowly released reactive species that generated higher carbohydrates. The formation of higher carbohydrates is self-limited by bisulfite formation, while borate minerals may have controlled aldol reactions that occurred on any semi-arid surface to capture that precipitation. All of these processes have well-studied laboratory correlates. Further, any semi-arid land with phosphate should have had phosphate anhydrides that, with NH₃, gave carbohydrate derivatives that directly react with nucleobases to form the canonical nucleosides. These are phosphorylated by magnesium borophosphate minerals (e.g., lüneburgite) and/or trimetaphosphate-borate with Ni²⁺ catalysis to give nucleoside 5′-diphosphates, which oligomerize to RNA via a variety of mechanisms. The reduced precursors that are required to form the nucleobases came, in this path-hypothesis, from one or more mid-sized (10²³–10²⁰ kg) impactors that almost certainly arrived after the Moon-forming event. Their iron metal content almost certainly generated ammonia, nucleobase precursors, and other reduced species in the Hadean atmosphere after it transiently placed the atmosphere out of redox equilibrium with the mantle. In addition to the inevitability of steps in this path-hypothesis on a Hadean Earth if it had semi-arid land, these processes may also have occurred on Mars. Adapted from a lecture by the Corresponding Author at the All-Russia Science Festival at the Lomonosov Moscow State University on 12 October 2019, and is an outcome of a three year project supported by the John Templeton Foundation and the NASA Astrobiology program. Dedicated to David Deamer, on the occasion of his 80th Birthday. Full article

(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)

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11 pages, 1699 KiB

Open AccessArticle

Detection of Biological Bricks in Space. The Case of Adenine in Silica Aerogel

by Aline Percot, Emilie-Laure Zins, Amélie Al Araji, Anh-Tu Ngo, Jacques Vergne, Makoto Tabata, Akihiko Yamagishi and Marie-Christine Maurel

Life 2019, 9(4), 82; https://doi.org/10.3390/life9040082 - 26 Oct 2019

Cited by 3 | Viewed by 3608

Abstract

Space missions using probes to return dust samples are becoming more frequent. Dust collectors made of silica aerogel blocks are used to trap and bring back extraterrestrial particles for analysis. In this work, we show that it is possible to detect traces of adenine using surface-enhanced Raman spectroscopy (SERS). The method was first optimized using adenine deposition on glass slides and in glass wells. After this preliminary step, adenine solution was injected into the silica aerogel. Finally, gaseous adenine was successfully trapped in the aerogel. The presence of traces of adenine was monitored by SERS through its characteristic bands at 732, 1323, and 1458 cm⁻¹ after the addition of the silver Creighton colloid. Such a method can be extended in the frame of Tanpopo missions for studying the interplanetary transfer of prebiotic organic compounds of biological interest. Full article

(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)

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16 pages, 2676 KiB

Open AccessArticle

The Oxygen Release Instrument: Space Mission Reactive Oxygen Species Measurements for Habitability Characterization, Biosignature Preservation Potential Assessment, and Evaluation of Human Health Hazards

by Christos D. Georgiou, Christopher P. McKay, Richard C. Quinn, Electra Kalaitzopoulou, Polyxeni Papadea and Marianna Skipitari

Life 2019, 9(3), 70; https://doi.org/10.3390/life9030070 - 27 Aug 2019

Cited by 1 | Viewed by 3706

Abstract

We describe the design of an instrument, the OxR (for Oxygen Release), for the enzymatically specific and non-enzymatic detection and quantification of the reactive oxidant species (ROS), superoxide radicals (O₂^•−), and peroxides (O₂²⁻, e.g., H₂O₂) on the surface of Mars and Moon. The OxR instrument is designed to characterize planetary habitability, evaluate human health hazards, and identify sites with high biosignature preservation potential. The instrument can also be used for missions to the icy satellites of Saturn’s Titan and Enceladus, and Jupiter’s Europa. The principle of the OxR instrument is based on the conversion of (i) O₂^•− to O₂ via its enzymatic dismutation (which also releases H₂O₂), and of (ii) H₂O₂ (free or released by the hydrolysis of peroxides and by the dismutation of O₂^•−) to O₂ via enzymatic decomposition. At stages i and ii, released O₂ is quantitatively detected by an O₂ sensor and stoichiometrically converted to moles of O₂^•− and H₂O₂. A non-enzymatic alternative approach is also designed. These methods serve as the design basis for the construction of a new small-footprint instrument for specific oxidant detection. The minimum detection limit of the OxR instrument for O₂^•− and O₂²⁻ in Mars, Lunar, and Titan regolith, and in Europa and Enceladus ice is projected to be 10 ppb. The methodology of the OxR instrument can be rapidly advanced to flight readiness by leveraging the Phoenix Wet Chemical Laboratory, or microfluidic sample processing technologies. Full article

(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)

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20 pages, 2391 KiB

Open AccessArticle

Survival of RNA Replicators Is Much Easier in Protocells Than in Surface-Based, Spatial Systems

by Vismay Shah, Jonathan de Bouter, Quinn Pauli, Andrew S. Tupper and Paul G. Higgs

Life 2019, 9(3), 65; https://doi.org/10.3390/life9030065 - 07 Aug 2019

Cited by 14 | Viewed by 3614

Abstract

In RNA-World scenarios for the origin of life, replication is catalyzed by polymerase ribozymes. Replicating RNA systems are subject to invasion by non-functional parasitic strands. It is well-known that there are two ways to avoid the destruction of the system by parasites: spatial clustering in models with limited diffusion, or group selection in protocells. Here, we compare computational models of replication in spatial models and protocells as closely as possible in order to determine the relative importance of these mechanisms in the RNA World. For the survival of the polymerases, the replication rate must be greater than a minimum threshold value, k_min, and the mutation rate in replication must be less than a maximum value, M_max, which is known as the error threshold. For the protocell models, we find that k_min is substantially lower and M_max is substantially higher than for the equivalent spatial models; thus, the survival of polymerases is much easier in protocells than on surfaces. The results depend on the maximum number of strands permitted in one protocell or one lattice site in the spatial model, and on whether replication is limited by the supply of monomers or the population size of protocells. The substantial advantages that are seen in the protocell models relative to the spatial models are robust to changing these details. Thus, cooperative polymerases with limited accuracy would have found it much easier to operate inside lipid compartments, and this suggests that protocells may have been a very early step in the development of life. We consider cases where parasites have an equal replication rate to polymerases, and cases where parasites multiply twice as fast as polymerases. The advantage of protocell models over spatial models is increased when the parasites multiply faster. Full article

(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)

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Review

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34 pages, 3537 KiB

Open AccessReview

Factoring Origin of Life Hypotheses into the Search for Life in the Solar System and Beyond

by Alex Longo and Bruce Damer

Life 2020, 10(5), 52; https://doi.org/10.3390/life10050052 - 27 Apr 2020

Cited by 16 | Viewed by 11499

Abstract

Two widely-cited alternative hypotheses propose geological localities and biochemical mechanisms for life’s origins. The first states that chemical energy available in submarine hydrothermal vents supported the formation of organic compounds and initiated primitive metabolic pathways which became incorporated in the earliest cells; the second proposes that protocells self-assembled from exogenous and geothermally-delivered monomers in freshwater hot springs. These alternative hypotheses are relevant to the fossil record of early life on Earth, and can be factored into the search for life elsewhere in the Solar System. This review summarizes the evidence supporting and challenging these hypotheses, and considers their implications for the search for life on various habitable worlds. It will discuss the relative probability that life could have emerged in environments on early Mars, on the icy moons of Jupiter and Saturn, and also the degree to which prebiotic chemistry could have advanced on Titan. These environments will be compared to ancient and modern terrestrial analogs to assess their habitability and biopreservation potential. Origins of life approaches can guide the biosignature detection strategies of the next generation of planetary science missions, which could in turn advance one or both of the leading alternative abiogenesis hypotheses. Full article

(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)

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10 pages, 1311 KiB

Open AccessReview

Lipid-Assisted Polymerization of Nucleotides

by Felix Olasagasti and Sudha Rajamani

Life 2019, 9(4), 83; https://doi.org/10.3390/life9040083 - 05 Nov 2019

Cited by 9 | Viewed by 4204

Abstract

In addition to being one of the proponents of the “Lipid World hypothesis”, David Deamer, together with other colleagues, pioneered studies involving formation of RNA-like oligomers from their ‘non-activated’, prebiotically plausible monomeric moieties. In particular, the pioneering work in this regard was a publication from 2008 in Origins of Life and Evolution of Biospheres, The Journal of the International Astrobiology Society, wherein we described the formation of RNA-like oligomers from nucleoside 5’-monophosphates. In that study, we had simulated a terrestrial geothermal environment, a niche that is thought to have facilitated the prebiotic non-enzymatic synthesis of polynucleotides. We showed that a mixture of lipids and non-activated mononucleotides resulted in the formation of relatively long strands of RNA-like polymers when subjected to repeated cycles of dehydration and rehydration (DH-RH). Since 2008, terrestrial geothermal niches and DH-RH conditions have been explored in the context of several other prebiotic processes. In this article, we review the work that we and other researchers have carried out since then in this line of research, including the development of new apparatus to carry out the simulation of prebiotic terrestrial geothermal environments. Full article

(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)

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12 pages, 1114 KiB

Open AccessReview

Twenty Years of “Lipid World”: A Fertile Partnership with David Deamer

by Doron Lancet, Daniel Segrè and Amit Kahana

Life 2019, 9(4), 77; https://doi.org/10.3390/life9040077 - 20 Sep 2019

Cited by 15 | Viewed by 6046

Abstract

“The Lipid World” was published in 2001, stemming from a highly effective collaboration with David Deamer during a sabbatical year 20 years ago at the Weizmann Institute of Science in Israel. The present review paper highlights the benefits of this scientific interaction and assesses the impact of the lipid world paper on the present understanding of the possible roles of amphiphiles and their assemblies in the origin of life. The lipid world is defined as a putative stage in the progression towards life’s origin, during which diverse amphiphiles or other spontaneously aggregating small molecules could have concurrently played multiple key roles, including compartment formation, the appearance of mutually catalytic networks, molecular information processing, and the rise of collective self-reproduction and compositional inheritance. This review brings back into a broader perspective some key points originally made in the lipid world paper, stressing the distinction between the widely accepted role of lipids in forming compartments and their expanded capacities as delineated above. In the light of recent advancements, we discussed the topical relevance of the lipid worldview as an alternative to broadly accepted scenarios, and the need for further experimental and computer-based validation of the feasibility and implications of the individual attributes of this point of view. Finally, we point to possible avenues for exploring transition paths from small molecule-based noncovalent structures to more complex biopolymer-containing proto-cellular systems. Full article

(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)

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21 pages, 4371 KiB

Open AccessReview

Investigating Prebiotic Protocells for a Comprehensive Understanding of the Origins of Life: A Prebiotic Systems Chemistry Perspective

by Augustin Lopez and Michele Fiore

Life 2019, 9(2), 49; https://doi.org/10.3390/life9020049 - 07 Jun 2019

Cited by 53 | Viewed by 8449

Abstract

Protocells are supramolecular systems commonly used for numerous applications, such as the formation of self-evolvable systems, in systems chemistry and synthetic biology. Certain types of protocells imitate plausible prebiotic compartments, such as giant vesicles, that are formed with the hydration of thin films of amphiphiles. These constructs can be studied to address the emergence of life from a non-living chemical network. They are useful tools since they offer the possibility to understand the mechanisms underlying any living cellular system: Its formation, its metabolism, its replication and its evolution. Protocells allow the investigation of the synergies occurring in a web of chemical compounds. This cooperation can explain the transition between chemical (inanimate) and biological systems (living) due to the discoveries of emerging properties. The aim of this review is to provide an overview of relevant concept in prebiotic protocell research. Full article

(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)

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Other

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8 pages, 5687 KiB

Open AccessCommentary

A Constructive Way to Think about Different Hydrothermal Environments for the Origins of Life

by Arthur Omran and Matthew Pasek

Life 2020, 10(4), 36; https://doi.org/10.3390/life10040036 - 09 Apr 2020

Cited by 12 | Viewed by 4639

Abstract

The question of where life originated has been contentious for a very long time. Scientists have invoked many environments to address this question. Often, we find ourselves beholden to a location, especially if we think life originated once and then evolved into the myriad forms we now know today. In this brief commentary, we wish to lay out the following understanding: hydrothermal environments are energetically robust locations for the origins and early evolution of life as we know it. Two environments typify hydrothermal conditions, hydrothermal fields on dry land and submarine hydrothermal vents. If life originated only once, then we must choose between these two environments; however, there is no reason to assume life emerged only once. We conclude with the idea that rather than having an “either or” mind set about the origin of life a “yes and” mind set might be a better paradigm with which to problem solve within this field. Finally, we shall discuss further research with regards to both environments. Full article

(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)

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16 pages, 2368 KiB

Open AccessConcept Paper

Polyesters as a Model System for Building Primitive Biologies from Non-Biological Prebiotic Chemistry

by Kuhan Chandru, Irena Mamajanov, H. James Cleaves II and Tony Z. Jia

Life 2020, 10(1), 6; https://doi.org/10.3390/life10010006 - 19 Jan 2020

Cited by 27 | Viewed by 7597

Abstract

A variety of organic chemicals were likely available on prebiotic Earth. These derived from diverse processes including atmospheric and geochemical synthesis and extraterrestrial input, and were delivered to environments including oceans, lakes, and subaerial hot springs. Prebiotic chemistry generates both molecules used by modern organisms, such as proteinaceous amino acids, as well as many molecule types not used in biochemistry. As prebiotic chemical diversity was likely high, and the core of biochemistry uses a rather small set of common building blocks, the majority of prebiotically available organic compounds may not have been those used in modern biochemistry. Chemical evolution was unlikely to have been able to discriminate which molecules would eventually be used in biology, and instead, interactions among compounds were governed simply by abundance and chemical reactivity. Previous work has shown that likely prebiotically available α-hydroxy acids can combinatorially polymerize into polyesters that self-assemble to create new phases which are able to compartmentalize other molecule types. The unexpectedly rich complexity of hydroxy acid chemistry and the likely enormous structural diversity of prebiotic organic chemistry suggests chemical evolution could have been heavily influenced by molecules not used in contemporary biochemistry, and that there is a considerable amount of prebiotic chemistry which remains unexplored. Full article

(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)

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