David Deamer
University of California, Santa Cruz, Biomolecular Engineering, Faculty Member
- David Deamer is a Research Professor of Biomolecular Engineering at the University of California, Santa Cruz. Deamer ... moreDavid Deamer is a Research Professor of Biomolecular Engineering at the University of California, Santa Cruz. Deamer received his undergraduate degree in Chemistry from Duke University in 1961, and PhD in Physiological Chemistry at the Ohio State University School of Medicine, 1965. Over his scientific career, Deamer has maintained a central focus on biological and synthetic membranes. In 1989, Deamer proposed the idea that it may be possible to sequence a DNA molecule by passing it through a nanoscopic pore embedded in a lipid bilayer membrane. Deamer, Daniel Branton, (Harvard University), and John Kasianowitz (NIST) demonstrated the feasibility of this concept in 1996. Collaborative work with Mark Akeson at UC Santa Cruz demonstrated proof of principle in 1999 when it was shown that a nanopore could distinguish between sequences of adenine and cytosine in RNA. In 2014, Oxford Nanopore Technology developed and distributed the MinION device which utilizes nanopore sequencing concepts. In a second research area, Deamer investigates how primitive amphiphilic compounds could have encapsulated polymer systems to give rise to the first living cells. In 1985 he showed that lipid-like compounds in carbonaceous meteorites can self-assemble into membranous vesicles, making it plausible that such vesicles were present on the prebiotic Earth. Deamer was awarded a Guggenheim Fellowship in 1986 to work with Murchison meteorite samples at the Australian National University, Canberra. He is currently using nanopore biosensors to detect nucleic acid polymers synthesized in a robotic device that simulates prebiotic conditions. Deamer is the author or co-author of 200 research papers and review articles, and the author/editor of 12 books, including Origins of Life (2010), co-edited with Jack Szostak, and First Life (2011) published by UC Press. His research has been featured in NOVA and National Geographic programs related to artificial life and the origin of life.edit
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Genetics professor Michelle Murphy loses her husband under mysterious circumstances and without warning, while their brilliant eight-year-old daughter Avalon, adopted in Kazakhstan, stubbornly believes she is a mutant. As if this were not... more
Genetics professor Michelle Murphy loses her husband under mysterious circumstances and without warning, while their brilliant eight-year-old daughter Avalon, adopted in Kazakhstan, stubbornly believes she is a mutant. As if this were not enough, she soon finds herself thrown into the middle of a quickly thickening plot, where the legacy of Genghis Khan meets the hunt for FOXP5, a genetic transcription factor that could herald the dawn of new human species. Initially caught helplessly between well-meaning fellow scientists, the government, and more sinister agents, Michelle eventually takes control with the help of a host of unlikely heroes and finds the courage to confront the decision of whether to save human lives or humanity. The scientific and technical aspects underlying the plot in particular aspects of FOX proteins, genetic mutations, viruses, and cancer as well as the relation between intelligence and cortical complexity are introduced and discussed by the authors in an ext...
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Two processes required for life's origin are condensation reactions that produce essential biopolymers by a nonenzymatic reaction, and self-assembly of membranous compartments that encapsulate the polymers into populations of... more
Two processes required for life's origin are condensation reactions that produce essential biopolymers by a nonenzymatic reaction, and self-assembly of membranous compartments that encapsulate the polymers into populations of protocells. Because life today thrives not just in the temperate ocean and lakes but also in extreme conditions of temperature, salinity, and pH, there is a general assumption that any form of liquid water would be sufficient to support the origin of life as long as there are sources of chemical energy and simple organic compounds. We argue here that the first forms of life would be physically and chemically fragile and would be strongly affected by ionic solutes and pH. A hypothesis emerges from this statement that hot springs associated with volcanic land masses have an ionic composition more conducive to self-assembly and polymerization than seawater. Here we have compared the ionic solutes of seawater with those of terrestrial hot springs. We then describe preliminary experimental results that show how the hypothesis can be tested in a prebiotic analog environment.
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We present a testable hypothesis related to an origin of life on land in which fluctuating volcanic hot spring pools play a central role. The hypothesis is based on experimental evidence that lipid-encapsulated polymers can be synthesized... more
We present a testable hypothesis related to an origin of life on land in which fluctuating volcanic hot spring pools play a central role. The hypothesis is based on experimental evidence that lipid-encapsulated polymers can be synthesized by cycles of hydration and dehydration to form protocells. Drawing on metaphors from the bootstrapping of a simple computer operating system, we show how protocells cycling through wet, dry, and moist phases will subject polymers to combinatorial selection and draw structural and catalytic functions out of initially random sequences, including structural stabilization, pore formation, and primitive metabolic activity. We propose that protocells aggregating into a hydrogel in the intermediate moist phase of wet-dry cycles represent a primitive progenote system. Progenote populations can undergo selection and distribution, construct niches in new environments, and enable a sharing network effect that can collectively evolve them into the first microbial communities. Laboratory and field experiments testing the first steps of the scenario are summarized. The scenario is then placed in a geological setting on the early Earth to suggest a plausible pathway from life's origin in chemically optimal freshwater hot spring pools to the emergence of microbial communities tolerant to more extreme conditions in dilute lakes and salty conditions in marine environments. A continuity is observed for biogenesis beginning with simple protocell aggregates, through the transitional form of the progenote, to robust microbial mats that leave the fossil imprints of stromatolites so representative in the rock record. A roadmap to future testing of the hypothesis is presented. We compare the oceanic vent with land-based pool scenarios for an origin of life and explore their implications for subsequent evolution to multicellular life such as plants. We conclude by utilizing the hypothesis to posit where life might also have emerged in habitats such as Mars or Saturn's icy moon Enceladus.
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waters, H. Schmidt, W. Vercoutere, D. Deamer, A.R. Hawkins, R. C. Quinn, A. S. Burton, and C. P. McKay, NASA Postdoctoral Program (Kathryn.f.bywaters@nasa.gov), University of California, Santa Cruz (hschmidt@soe.ucsc.edu;... more
waters, H. Schmidt, W. Vercoutere, D. Deamer, A.R. Hawkins, R. C. Quinn, A. S. Burton, and C. P. McKay, NASA Postdoctoral Program (Kathryn.f.bywaters@nasa.gov), University of California, Santa Cruz (hschmidt@soe.ucsc.edu; deamer@soe.ucsc.edu), NASA Ames Research Center (wenonah.a.vercoutere@nasa.gov; chris.mckay@nasa.gov; richard.c.quinn@nasa.gov), Brigham Young University (Hawkins@ee.byu.edu), NASA Johnson Space Center (aaron.burton@nasa.gov)
Research Interests: Materials Science, Chemistry, RNA, Nanotechnology, DNA, and 5 morePolymer, Molecule, Polyelectrolyte, Nucleic Acid, and Nanopore
FOR LIFE BEYOND EARTH. M. Van Kranendonk, R. Baumgartner, E. Boyd, S. Cady, K. Campbell, A. Czaja, B. Damer, D. Deamer, T. Djokic, M. Fiorentini, A. Gangidine, J. Havig, A. Mulkidjanian, S. Ruff, P. Thordarson, Australian Centre for... more
FOR LIFE BEYOND EARTH. M. Van Kranendonk, R. Baumgartner, E. Boyd, S. Cady, K. Campbell, A. Czaja, B. Damer, D. Deamer, T. Djokic, M. Fiorentini, A. Gangidine, J. Havig, A. Mulkidjanian, S. Ruff, P. Thordarson, Australian Centre for Astrobiology, University of New South Wales Sydney, Kensington, NSW 2052, Australia, m.vankranendonk@unsw.edu.au, Montana State University, Pacific Northwest National Laboratory. University of Auckland, University of Cincinnati, University of California at Santa Cruz, University of Western Australia, University of Minnesota, Osnabrueck University, Germany, Arizona State University.
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A personal narrative is presented which explores the author's experience of navigating through the dense forests of northwestern Australia with his friend guided by dim light from a Global Positioning System (GPS) screen.
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Biomarkers collected from past and present life on Earth are a central guide in the development of flight-ready technologies designed to search for life on other planets and moons. Data from numerous laboratory and field studies have... more
Biomarkers collected from past and present life on Earth are a central guide in the development of flight-ready technologies designed to search for life on other planets and moons. Data from numerous laboratory and field studies have revealed the importance of incorporating capabilities that minimize the risk of false negatives or false positives during life detection missions. Biomolecules are the most unambiguous and information-rich of all known biosignatures. Indeed, the identification in a sample of biopolymers akin to DNA, RNA or proteins, would be difficult to refute as a successful life detection experiment. In the case of Mars, the search for biomolecules is inescapable, but few technological solutions exist for in situ identification. Thus, our work has focused on the development of technologies designed to detect biochemical polyelectrolyte molecules, which have been argued to be a universal signature for life due to their ability to store information while reducing their...
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Polymerization of nucleotides and amino acids to form large, complex, and potentially functional products was an early and essential event on the paths leading to life's origin. The standard Gibbs energies of the condensation... more
Polymerization of nucleotides and amino acids to form large, complex, and potentially functional products was an early and essential event on the paths leading to life's origin. The standard Gibbs energies of the condensation reactions are uphill, however, and at equilibrium will yield only declining sequences of small, nonfunctional oligomers. Geochemically produced condensing agents such as carbonyl sulfide, cyanamide, and polyphosphates have been proposed to invert the unfavorable condensation Gibbs energies and thereby activate exergonic condensation. We argue, however, that although activators may provide modest yields of oligomers, the inherently episodic nature of their sources throttles their effectiveness, and the fundamental hydrolytic instabilities of oligonucleotides and peptides ultimately prevail to yield decreasing product sequences. Notably, the Gibbs energy governing oligomer formation is antientropic. Accordingly, we propose that declining progression can be surmounted in evaporating pools in which a favorable entropy change is produced when high surface/volume ratios concentrate reactants at the air/water interface in continuous cycles of wetting and drying. The severely reduced configurational freedom of the solutes then inverts the antientropic nature of the condensation reactions, pivoting them to exergonic states and thus to the production of ascending sequences of complex polymeric products.
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Research Interests: Thermodynamics, Chemistry, Organic Chemistry, Water, Kinetics, and 15 moreSelf Assembly, Chemical Evolution, Medicine, Biological Sciences, Temperature, Biogenesis, Glycerol, Dehydration, Environmental Conditions, Surface Active Agents, Osmotic Stress, Quntitative Thin Layer Chromatography, Hydrolysis, Elevated Temperature, and Organic Compound
<p><b>A</b> Schematic of out-of-plane structure of the lipid/AMP complex. The lamellar spacings determined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062810#pone-0062810-g004"... more
<p><b>A</b> Schematic of out-of-plane structure of the lipid/AMP complex. The lamellar spacings determined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062810#pone-0062810-g004" target="_blank">Figure 4</a> all fall on a master curve. The thickness of a single AMP layer, Δd, is determined by the slope to Δd = 2.67 Å. <b>B-D</b> show proposed AMP in-plane crystal structures and the resulting diffraction pattern (black) compared against the peak locations in our in-plane data (blue). <b>B</b> A herringbone structure would be geometrically favorable due to the shape of AMP. The diffraction pattern, however, does not agree with our experimental data. <b>C</b> The chevron pattern is also a favorable structure for the packing of ’v’ shaped molecules, however the diffraction pattern that would be produced from this structure is not consistent with the experiential data. <b>D</b> The tetragonal 2-dimensional unit cell with lattice parameters of a = 6.25 Å and b = 4.8 Å gives the most plausible structure of the AMP molecules. <b>E</b> Molecular representation of the crystalline AMP between the stacked DMPC bilayers; in-plane representation below. The molecular coordinates for the DMPC bilayer were taken from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062810#pone.0062810-deGroot1" target="_blank">[<i>29</i>]</a>. Molecular structure files of the structures in <b>D</b> and <b>E</b> are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062810#pone.0062810.s001" target="_blank">Structure Files S1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062810#pone.0062810.s002" target="_blank">S2</a>.</p
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<p>In the 3∶1 fit in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062810#pone-0062810-g003" target="_blank">Figure 3</a> <b>A</b>, the planar structure (as in all... more
<p>In the 3∶1 fit in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062810#pone-0062810-g003" target="_blank">Figure 3</a> <b>A</b>, the planar structure (as in all other AMP/DMPC samples) was found to coexist with another structure. The new crystal structure is compatible with AMP molecules oriented perpendicular to the existing structure. <b>A</b> The coexistence of two crystal structures as viewed in the plane of the bilayers. A unit cell is drawn for clarity. <b>B</b> Crystal structures as viewed from out of the plane of the lipid bilayers. A molecular structure file of the structures is provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062810#pone.0062810.s003" target="_blank">Structure File S3</a>.</p
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Most experimental results that guide research related to the origin of life are from laboratory simulations of the early Earth conditions. In the laboratory, emphasis is placed on the purity of reagents and carefully controlled... more
Most experimental results that guide research related to the origin of life are from laboratory simulations of the early Earth conditions. In the laboratory, emphasis is placed on the purity of reagents and carefully controlled conditions, so there is a natural tendency to reject impurities and lack of control. However, life did not originate in laboratory conditions; therefore, we should take into consideration multiple factors that are likely to have contributed to the environmental complexity of the early Earth. This essay describes eight physical and biophysical factors that spontaneously resolve aqueous dispersions of ionic and organic solutes mixed with mineral particles and thereby promote specific chemical reactions required for life to begin.
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The author wishes to add the following information to the acknowledgements section of his paper published in Life [...]
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Research Interests: Sociology, Geology, Geochemistry, Astrobiology, Mars, and 4 moreMedicine, Exobiology, Life, and Biogenesis
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The earliest forms of life would likely have a protocellular form, with a membrane encapsulating some form of linear charged polymer. These polymers could have enzymatic as well as genetic properties. We can simulate plausible prebiotic... more
The earliest forms of life would likely have a protocellular form, with a membrane encapsulating some form of linear charged polymer. These polymers could have enzymatic as well as genetic properties. We can simulate plausible prebiotic conditions in the laboratory to test hypotheses related to this concept. In earlier work we have shown that mononucleotides organized within a multilamellar lipid matrix can produce oligomers in the anhydrous phase of dehydrationrehydration cycles [1]. If mononucleotides are in solution at millimolar concentrations, then oligomers resembling RNA are synthesized and exist in a steady state with their monomers [2]. We have used conventional and novel techniques to demonstrate that secondary structures stabilized by hydrogen bonds may be present in the condensation products produced in dehydrationrehydration cycles that simulate hydrothermal fields that were present on the early Earth. Gel electrophoresis data corroborates the presence of 200-base pair ...
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This chapter describes recent studies in which nucleic acid oligomers are synthesized in simulated hydrothermal field conditions using cycles of dehydration and rehydration to promote ester bond synthesis. Such conditions involve elevated... more
This chapter describes recent studies in which nucleic acid oligomers are synthesized in simulated hydrothermal field conditions using cycles of dehydration and rehydration to promote ester bond synthesis. Such conditions involve elevated temperatures and acidic pH ranges that are also conducive to depurination of nucleotides. For this reason it is important to establish the extent to which depurination occurs and whether this limits yields of oligomers. Here we review condensation reactions that occur in mixtures of AMP and UMP undergoing multiple dehydration cycles in acidic conditions, and report new results related to depurination under the same conditions. Although depurination could be detected, the reaction was inhibited by the presence of a phospholipid. Furthermore, a fraction of the original AMP remains in subsequent cycles, suggesting that depurination does not proceed to completion. We conclude that even though decomposition of mononucleotides occurs in hydrothermal cycling, purine nucleotides will continue to be available to participate in polymerization.
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It is possible that the transition from abiotic systems to life relied on RNA polymers that served as ribozyme-like catalysts and for storing genetic information. The source of such polymers is uncertain, but previous investigations... more
It is possible that the transition from abiotic systems to life relied on RNA polymers that served as ribozyme-like catalysts and for storing genetic information. The source of such polymers is uncertain, but previous investigations reported that wet–dry cycles simulating prebiotic hot springs provide sufficient energy to drive condensation reactions of mononucleotides to form oligomers and polymers. The aim of the study reported here was to verify this claim and visualize the products prepared from solutions composed of single mononucleotides and 1:1 mixture of two mononucleotides. Therefore, we designed experiments that allowed comparisons of all such mixtures representing six combinations of the four mononucleotides of RNA. We observed irregular stringy patches and crystal strands when wet-dry cycling was performed at room temperature (20 o C). However, when the same solutions were exposed to wet–dry cycles at 80 o C, we observed what appeared to be true polymers. Their thickness...
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Publisher Summary This chapter describes the properties and preparation of lipid vesicles from the simplest kinds of amphiphilic compounds. It addresses issues of stability, permeability, and encapsulation of macromolecules and shows how... more
Publisher Summary This chapter describes the properties and preparation of lipid vesicles from the simplest kinds of amphiphilic compounds. It addresses issues of stability, permeability, and encapsulation of macromolecules and shows how such vesicles can be used to encapsulate functional enzymes. The chapter also describes how these vesicles are related to naturally occurring substances, particularly the vesicular membranes that are produced from ancient organic compounds present in carbonaceous meteorites. Self-reproduction is an essential property of living systems. When a primitive cell was able to replicate its encapsulated macromolecular components, an increase of its membrane area was necessary to accommodate the internal growth. To model this evolutionary step, fatty acid vesicle systems have been designed successfully, using anhydride derivatives as a source of additional membrane amphiphiles. The prebiotic availability of fatty acids or their precursors and their properties of encapsulation, high permeability, and membrane growth make them ideal model systems for investigating primitive forms of life.
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Nutrient transport, polymerization and expression of genetic information in cellular compartments are hallmarks of all life today, and must have appeared at some point during the origin and early evolution of life. Because the first... more
Nutrient transport, polymerization and expression of genetic information in cellular compartments are hallmarks of all life today, and must have appeared at some point during the origin and early evolution of life. Because the first cellular life lacked membrane transport systems based on highly evolved proteins, they presumably depended on simpler processes of nutrient uptake. Using a system consisting of an RNA polymerase and DNA template entrapped in submicrometre-sized lipid vesicles (liposomes), we found that the liposome membrane could be made sufficiently permeable to allow access of ionized substrate molecules as large as nucleoside triphosphates (NTPs) to the enzyme. The encapsulated polymerase transcribed the template-specific base sequences of the DNA to the RNA that was synthesized. These experiments demonstrate that units of genetic information can be associated with a functional catalyst in a single compartment, and that transcription of gene-sized DNA fragments can be...
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Research Interests: Chemistry, Water, RNA, Origins of Life, Catalysis, and 15 moreKinetics, Carbon, Biological Sciences, Biogenesis, Shell Half-Life, Amino Acids, Gas Chromatography/mass Spectrometry, Amino Acid Profile, Carboxylic Acids, Meteoroids, Hydrolysis, Hydrogen-Ion Concentration, Organic Compound, ribonucleic acid, and purines
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The self-assembly of simple amphiphiles like fatty acids into cell-like membranous structures suggests that such structures were available on prebiotic Earth to support the origin of cellular life. However, the composition of primitive... more
The self-assembly of simple amphiphiles like fatty acids into cell-like membranous structures suggests that such structures were available on prebiotic Earth to support the origin of cellular life. However, the composition of primitive membranes remains unclear because the physical properties of the aqueous environment in which they assembled are relatively unconstrained in terms of temperature, pH, and ionic concentrations. It seems likely that early membranes were composed of mixtures of various amphiphiles in an aqueous medium warmed by geothermal activity prevalent in the Archean era. To better understand the properties of mixed bilayers formed by binary mixtures of single-chain amphiphiles under these conditions, we conducted stability experiments, using membranes composed of various fatty acids having hydrocarbon chain length between 8 and 18 carbons, in mixtures with their glycerol monoacyl amphiphile derivatives (GMAs). The parameters investigated were critical vesicle concentration (CVC), encapsulation, and temperature-dependent stability. We found that hydrocarbon chain length and the presence of GMAs were major factors related to membrane stability. As chain length increased, GMA additions decreased the CVC of the mixtures 4- to 9-fold. Encapsulation ability also increased significantly as a function of chain length, which reduced permeation of small marker molecules. However, long exposures to temperatures in excess of 60 degrees C resulted in a total release of encapsulated solutes and extensive mixing of the membrane components between vesicles. We conclude that GMAs can significantly increase the stability of mixed amphiphile membranes, but further studies are required to establish model membranes that are stable at elevated temperatures.