Henderson Cleaves

• PhD
• Tokyo Institute of Technology

α-hydroxy acids (αHAs), simple and prebiotically plausible organic monomers, were likely present in various environments on and off Earth and could have played a role in directing the emergence of the first homochiral living systems. Some αHAs, which could have been of varying chirality, can undergo dehydration polymerization into polyesters, which...

Many non-natural amino acids can be incorporated by biological systems into coded functional peptides and proteins. For such incorporations to be effective, they must not only be compatible with the desired function but also evade various biochemical error-checking mechanisms. The underlying molecular mechanisms are complex, and this problem has be...

Molecular assembly indices, which measure the number of unique sequential steps theoretically required to construct a three-dimensional molecule from its constituent atomic bonds, have been proposed as potential biosignatures. A central hypothesis of assembly theory is that any molecule with an assembly index ≥15 found in significant local concentr...

Physical laws—such as the laws of motion, gravity, electromagnetism, and thermodynamics—codify the general behavior of varied macroscopic natural systems across space and time. We propose that an additional, hitherto-unarticulated law is required to characterize familiar macroscopic phenomena of our complex, evolving universe. An important feature...

The search for definitive biosignatures—unambiguous markers of past or present life—is a central goal of paleobiology and astrobiology. We used pyrolysis–gas chromatography coupled to mass spectrometry to analyze chemically disparate samples, including living cells, geologically processed fossil organic material, carbon-rich meteorites, and laborat...

We report the co-polymerization of glycol nucleic acid (GNA) monomers with unsubstituted and substituted dicarboxylic acid linkers under plausible early Earth aqueous dry-down conditions. Both linear and branched co-polymers are...

Synthesis of polyester gels via dehydration of α‐hydroxy acids is a plausible route to form primitive functional polymers. α‐Hydroxy acid polyester gels assemble into membraneless droplets upon rehydration in aqueous media that can segregate and compartmentalize early biomolecules. However, conditions for polyester synthesis and microdroplet assemb...

Phosphorus (P) is a crucial structural component of living systems and central to modern bioenergetics. P cycles through terrestrial geochemical reservoirs via complex physical and chemical processes. Terrestrial life has altered these fluxes between reservoirs as it evolved, which is why it is of interest to explore planetary P flux evolution in t...

Using high‐resolution atomic force microscopy (AFM) with CO‐functionalized tips, we atomically resolved individual molecules from Murchison meteorite samples. We analyzed powdered Murchison meteorite material directly, as well as processed extracts that we prepared to facilitate characterization by AFM. From the untreated Murchison sample, we resol...

“Prebiotic soup” often features in discussions of origins of life research, both as a theoretical concept when discussing abiological pathways to modern biochemical building blocks and, more recently, as a feedstock in prebiotic chemistry experiments focused on discovering emergent, systems-level processes such as polymerization, encapsulation, and...

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Searching for life in the Universe depends on unambiguously distinguishing biological features from background signals, which could take the form of chemical, morphological, or spectral signatures. The discovery and direct measurement of organic compounds unambiguously indicative of extraterrestrial (ET) life is a major goal of Solar System explora...

Nucleic acid segregation and compartmentalization were likely essential functions that primitive compartment systems resolved during evolution. Recently, polyester microdroplets generated from dehydration synthesis of various α-hydroxy acids (αHA) were suggested as potential primitive compartments. Some of these droplets can differentially segregat...

The chemical space of prebiotic chemistry is extremely large, while extant biochemistry uses only a few thousand interconnected molecules. Here we discuss how the connection between these two regimes can be investigated, and explore major outstanding questions in the origin of life.

Prebiotic chemists often study how modern biopolymers, e.g., peptides and nucleic acids, could have originated in the primitive environment, though most contemporary biomonomers don’t spontaneously oligomerize under mild conditions without activation or catalysis. However, life may not have originated using the same monomeric components that it doe...

While tensions may lie between science and policy, we argue that dissemination and public engagement are key in alleviating those perceived tensions. Science being valued by society results in fact-based policy-making being demanded by constituents. Constituents’ demands will yield representatives who are familiar with the scientific process and re...

Significance RNA may have been the original polymer to arise spontaneously on the early Earth through natural geochemistry. Although direct physical evidence regarding early Earth’s geochemistry is extremely limited, complex chemical reaction networks are thought to have played an important role in chemical evolution. The present study demonstrates...

Selective binding of aqueous-phase amino acids to mineral surfaces is regarded as a plausible first step in oligopeptide formation on early Earth. To clarify the strength and underlying mechanism of amino acid binding to pyrite surfaces, we measured the unbinding (pull-off) force of ten amino acids and two oligo-peptides from water-pyrite interface...

How the transition of disorganized, inanimate matter to organized, living systems took place on our planet and might have occurred on other bodies of our solar system or elsewhere in the universe is one of the fundamental questions studied in the field of astrobiology. The only instance of life known so far is the terrestrial one, and all living or...

Biology encodes hereditary information in DNA and RNA, which are finely tuned to their biological function and modes of biological production. The central role of nucleic acids in biological information flow makes them key targets of pharmaceutical research. Indeed, other nucleic acid-like polymers can play similar roles to natural nucleic acids bo...

Life uses a common set of 20 coded amino acids (CAAs) to construct proteins. This set was likely canonicalized during early evolution; before this, smaller amino acid sets were gradually expanded as new synthetic, proofreading and coding mechanisms became biologically available. Many possible subsets of the modern CAAs or other presently uncoded am...

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we pr...

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we pr...

Significance The prebiotic milieu was likely heterogeneous, consisting of a large number of chemicals and their associated reactions, including those not only of biological compounds, but also nonbiological compounds. Although origins of life research has focused primarily on biological molecules, the nonbiological molecules which were also present...

Microbial life permeates Earth's critical zone and has likely inhabited nearly all our planet's surface and near subsurface since before the beginning of the sedimentary rock record. Given the vast time that Earth has been teeming with life, do astrobiologists truly understand what geological features untouched by biological processes would look li...

The search for life in the universe is a major theme of astronomy and astrophysics for the next decade. Searches for technosignatures are complementary to searches for biosignatures, in that they offer an alternative path to discovery, and address the question of whether complex (i.e. technological) life exists elsewhere in the Galaxy. This approac...

Contribution to the DLR-IMF-ATP Annual Report 2017

The chemistry occurring in the universe generates a huge variety of organic compounds abiotically. Significant progress has been made in understanding the types and distributions of these compounds in various planetary, asteroidal, cometary, nebular, and molecular cloud environments. One of the most exciting recent discoveries was the detection of...

Since its inception six decades ago, astrobiology has diversified immensely to encompass several scientific questions including the origin and evolution of Terran life, the organic chemical composition of extraterrestrial objects, and the concept of habitability, among others. The detection of life beyond Earth forms the main goal of astrobiology,...

Since its inception six decades ago, astrobiology has diversified immensely to encompass several scientific questions including the origin and evolution of Terran life, the organic chemical composition of extraterrestrial objects, and the concept of habitability, among others. The detection of life beyond Earth forms the main goal of astrobiology,...

A theoretical and experimental characterization of N(1)‐(2′,3′‐dihydroxypropil)thymine (DHPT), a potential prebiotic nucleoside analogue of 5‐methyluridine, is performed. A proposed methodology based on a solvation method was used to study conformational transformations of the different low‐energy conformers of DHPT according to time‐dependent IR s...

Nucleobases are nitrogen heterocycles that are key structural components of biological nucleic acids. Some theories for the origins of life suggest a role for environmentally supplied organic compounds, including nucleobases, as part of a primordial RNA or pre-RNA world. Over the last 65 years, many potentially prebiotic synthetic mechanisms have b...

The standard alphabet of the 20 genetically encoded amino acids is considered to have been selected during early evolution from a larger pool of α-amino acids based on its coverage of the chemical space. Chemical space is here defined by charge, size and hydrophobicity, leading to 6-tuples representing coverage, which is composed of range and evenn...

We studied the radiolysis of a wide variety of N-heterocycles, including many of biological importance, and find that the majority are remarkably stable in the solid-state when subjected to large doses of ionizing gamma radiation from a ⁶⁰ Co source. Degradation of N-heterocycles as a function of dose rate and total dose was measured using high-per...

It is widely believed that the origin of life depended on environmentally driven complexification of abiotically produced organic compounds. Polymerization is one type of such complexification, and it may be important that many diverse polymer sequences be produced for the sake of selection. Not all compound classes are easily polymerized under the...

Nitrogen is the major component of Earth's atmosphere and plays important roles in biochemistry. Biological systems have evolved a variety of mechanisms for fixing and recycling environmental nitrogen sources, which links them tightly with terrestrial nitrogen reservoirs. However, prior to the emergence of biology, all nitrogen cycling was abiologi...

Workshop on a Cosmic Perspective of Earth: A Planet Permeated and Shaped by Life—Implications for Astrobiology; Tokyo, Japan, 13–15 September 2017

The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, and penta-Gly, with a natural pyrite surface was directly measured using the force mode of an atomic force microscope (AFM). In recent years, selective activation of abiotically formed amino acids on mineral surfaces, especially that of pyrite, has been p...

Water creates special problems for prebiotic chemistry, as it is thermodynamically favorable for amide and phosphodiester bonds to hydrolyze. The availability of alternative solvents with more favorable properties for the formation of prebiotic molecules on the early Earth may have helped bypass this so-called "water paradox". Formamide (FA) is one...

The formation of compartments, through which an internal environment is separated from its surrounding medium, is essential for all modern life. Compartmentalisation enables specific molecules to be concentrated, thus facilitating biochemistry. The existence of individuals also facilitates competition for survival, and provides a driving force for...

Contribution to the DLR-IMF-ATP Annual Report 2016

The reverse tricarboxylic acid (rTCA) cycle has been explored from various standpoints as an idealized primordial metabolic cycle. Its simplicity and apparent ubiquity in diverse organisms across the tree of life have been used to argue for its antiquity and its optimality. In 2000 it was proposed that chemoinformatics approaches support some of th...

The origins of life bring into stark relief the inadequacy of our current synthesis of thermodynamic, chemical, physical and information theory to predict the conditions under which complex, living states of organic matter can arise. Origins research has traditionally proceeded under an array of implicit or explicit guiding principles in lieu of a...

The origin of life is typically understood as a transition from inanimate or disorganized matter to self-organized, ‘animate’ matter. This transition probably took place largely in the context of organic compounds, and most approaches, to date, have focused on using the organic chemical composition of modern organisms as the main guide for understa...

Biological information storage for life as we know it is carried out by the nucleic acids DNA and RNA. However, these may be optimized end-states for life on Earth, or there may be other types of molecules which are similarly capable of carrying out these functions, perhaps used in alien biochemistries or in earlier biochemical states. A number of...

Alfonso Luis Herrera (1868–1942) was a Mexican biologist, and significant as the principal promoter of Darwinian thought in that country. However, Herrera’s thinking went beyond the evolution of living beings, and extended to the question of the origin of life itself and the place of living phenomena in the larger context of the cosmos. Perhaps mor...

Rationale: Spark discharge experiments, like those performed by Stanley Miller in the 1950s, generate complex, analytically-challenging mixtures that contain biopolymer building blocks. Recently, α-amino acids and α-hydroxy acids (AHAs) were subjected to environmental cycling to form simple depsipeptides (peptides with both amide and ester linkage...

Thioesters and thioacetic acid (TAA) have been invoked as key reagents for the origin of life as activated forms of acetate analogous to acetyl-CoA. These species could have served as high-energy group-transfer reagents and allowed carbon insertions to form higher molecular weight compounds such as pyruvate. The apparent antiquity of the Wood-Ljung...

From a geochemical perspective, significant amounts of pure formamide (HCONH2) would have likely been rare on the early Earth. There may have been mixed formamide-water solutions, but even in the presence of catalyst, solutions with >20 weight% water in formamide would not have produced significant amounts of prebiotic compounds. It might be feasib...

At the time before ∼3.5 Ga that life originated and began to spread on Earth, Mars was a wetter and more geologically dynamic planet than it is today. The Argyre basin, in the southern cratered highlands of Mars, formed from a giant impact at ∼3.93 Ga, which generated an enormous basin approximately 1800 km in diameter. The early post-impact enviro...

Self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N9-(2,3-dihydroxypropyl)adenine (DHPA)...

Contents 1. Introduction 1.1. A workshop and this document 1.2. Framing origins of life science 1.2.1. What do we mean by the origins of life (OoL)? 1.2.2. Defining life 1.2.3. How should we characterize approaches to OoL science? 1.2.4. One path to life or many? 2. A Strategy for Origins of Life Research 2.1. Outcomes—key questions and investigati...

Astrobiology is an interdisciplinary scientific field not only focused on the search of extraterrestrial life, but also on deciphering the key environmental parameters that have enabled the emergence of life on Earth. Understanding these physical and chemical parameters is fundamental knowledge necessary not only for discovering life or signs of li...

This special section presents contributed short papers from the 2nd Annual Earth-Life Science Institute International Symposium, which was convened at the National Institute of Informatics in Chiyoda-ku, Tokyo, from March 24th to 26th, 2014. The meeting was attended by about 200 scientists and featured 34 invited speakers from seven countries. Pres...

Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a central role as the intermediary carrier of genetic information in transcription and translation. If RNA was involved in the origin of life, it should have a facile prebiotic synthesis. A wide variety of such syntheses have been explored. However, to date...

Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties...

The geologic history of the multi-ringed Argyre impact basin and surroundings has been reconstructed on the basis of geologic mapping and relative-age dating of rock materials and structures. The impact formed a primary basin, rim materials, and a complex basement structural fabric including faults and valleys that are radial and concentric about t...

Saitta and Saija (1) claim that ab initio simulations of the 1953 Miller experiment (2) provide new insights into the mechanism of prebiotic synthesis of glycine (Gly) and, by implication, other molecules in this classic experiment. However, decades of research into prebiotic amino acid formation in such experiments conflict with their conclusions....

Ribonucleic Acid (RNA) is one of the two nucleic acids used by extant biochemistry, and plays a central role as the intermediary carrier of genet-ic information in transcription and translation. If RNA was involved in the origin of life, it should have a facile prebiotic synthesis. A wide variety of such syntheses have been explored. However, to da...