Uniting the conceptual foundations of the physical sciences and biology, this groundbreaking multidisciplinary book explores the origin of life as a planetary process. Combining geology, geochemistry, biochemistry, microbiology, evolution and statistical physics to create an inclusive picture of the living state, the authors develop the argument that the emergence of life was a necessary cascade of non-equilibrium phase transitions that opened new channels for chemical energy flow on Earth. This full colour and logically structured book introduces the main areas of significance and provides a well-ordered and accessible introduction to multiple literatures outside the confines of disciplinary specializations, as well as including an extensive bibliography to provide context and further reading. For researchers, professionals entering the field or specialists looking for a coherent overview, this text brings together diverse perspectives to form a unified picture of the origin of life and the ongoing organization of the biosphere.

'It is happily no longer axiomatic that a biophysicist is a physiologist who can fix his own amplifier. Fortunately, physicists are still drifting into biology and bringing new ideas. Please dear colleagues, do take the time to learn biochemistry.' Harold Morowitz provides a personal perspective on working at the interface between the physical and biological sciences.

ComplexityVolume 18, Issue 5 p. 5-6 The Simply Complex From simplicity to complexity: The size of the genomes of human pathogens Harold J. Morowitz, Corresponding Author Harold J. Morowitz Harold J. Morowitz, Vijayasarathy Srinivasan, and Eric Smith are at Krasnow Institute for Advanced Study, George Mason University, Fairfax, VirginiaCorrespondence to: Harold J. Morowitz; Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia. E-mail: [email protected]Search for more papers by this authorVijayasarathy Srinivasan, Vijayasarathy Srinivasan Harold J. Morowitz, Vijayasarathy Srinivasan, and Eric Smith are at Krasnow Institute for Advanced Study, George Mason University, Fairfax, VirginiaSearch for more papers by this authorEric Smith, Eric Smith Harold J. Morowitz, Vijayasarathy Srinivasan, and Eric Smith are at Krasnow Institute for Advanced Study, George Mason University, Fairfax, VirginiaSearch for more papers by this author Harold J. Morowitz, Corresponding Author Harold J. Morowitz Harold J. Morowitz, Vijayasarathy Srinivasan, and Eric Smith are at Krasnow Institute for Advanced Study, George Mason University, Fairfax, VirginiaCorrespondence to: Harold J. Morowitz; Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia. E-mail: [email protected]Search for more papers by this authorVijayasarathy Srinivasan, Vijayasarathy Srinivasan Harold J. Morowitz, Vijayasarathy Srinivasan, and Eric Smith are at Krasnow Institute for Advanced Study, George Mason University, Fairfax, VirginiaSearch for more papers by this authorEric Smith, Eric Smith Harold J. Morowitz, Vijayasarathy Srinivasan, and Eric Smith are at Krasnow Institute for Advanced Study, George Mason University, Fairfax, VirginiaSearch for more papers by this author First published: 30 May 2013 https://doi.org/10.1002/cplx.21447Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume18, Issue5May/June 2013Pages 5-6 RelatedInformation

AstrobiologyVol. 13, No. 8 ReflectionThe Death of John F. Kennedy and the Birth of the NASA Theoretical Biology ProgramHarold MorowitzHarold MorowitzSearch for more papers by this authorPublished Online:14 Aug 2013https://doi.org/10.1089/ast.2013.6140AboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"The Death of John F. Kennedy and the Birth of the NASA Theoretical Biology Program." , 13(8), pp. 790–791FiguresReferencesRelatedDetails Volume 13Issue 8Aug 2013 InformationCopyright 2013, Mary Ann Liebert, Inc.To cite this article:Harold Morowitz.The Death of John F. Kennedy and the Birth of the NASA Theoretical Biology Program.Astrobiology.Aug 2013.790-791.http://doi.org/10.1089/ast.2013.6140Published in Volume: 13 Issue 8: August 14, 2013Online Ahead of Print:July 30, 2013PDF download

AstrobiologyVol. 12, No. 8 ReflectionMars MissionsHarold MorowitzHarold MorowitzSearch for more papers by this authorPublished Online:12 Sep 2012https://doi.org/10.1089/ast.2012.8808AboutSectionsView articleView Full TextPDF/EPUB ToolsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Mars Missions." , 12(8), p. 717FiguresReferencesRelatedDetails Volume 12Issue 8Aug 2012 InformationCopyright 2012, Mary Ann Liebert, Inc.To cite this article:Harold Morowitz.Mars Missions.Astrobiology.Aug 2012.717-717.http://doi.org/10.1089/ast.2012.8808Published in Volume: 12 Issue 8: September 12, 2012Online Ahead of Print:August 13, 2012PDF download

AstrobiologyVol. 12, No. 2 ReflectionThe Planetary Biology Subcommittee Versus Richard M. NixonHarold MorowitzHarold MorowitzSearch for more papers by this authorPublished Online:10 Feb 2012https://doi.org/10.1089/ast.2011.1204AboutSectionsView articleView Full TextPDF/EPUB ToolsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"The Planetary Biology Subcommittee Versus Richard M. Nixon." , 12(2), p. 167FiguresReferencesRelatedDetails Volume 12Issue 2Feb 2012 InformationCopyright 2012, Mary Ann Liebert, Inc.To cite this article:Harold Morowitz.The Planetary Biology Subcommittee Versus Richard M. Nixon.Astrobiology.Feb 2012.167-167.http://doi.org/10.1089/ast.2011.1204Published in Volume: 12 Issue 2: February 10, 2012Online Ahead of Print:January 11, 2012PDF download

The word ontology has an extended usage in Philosophy and in this context it is defined in “The Oxford English Dictionary” as “that branch of metaphysics concerned with the nature or essence of being or existence,” with references going back to 1663. Thus, when I was handed my diploma many years ago, under the teaching of Brand Blanshard I had accepted that definition with the further refinement from a 1903 article by F.C.S. Schiller (Humanism i.9) noting that “The effect of what Kant called the Copernican revolution in philosophy is that ontology, the theory of Reality, comes to be conditioned by epistemology, the theory of knowledge.” Thus, metaphysics was presented as a combination of ontology and epistemology, what we know? and how we know it? When I arrived at graduate school and the mentorship of physicist philosopher Henry Margenau these ideas were refined, “We hold with Kant that epistemology must precede ontology and that epistemology denotes the methodology of the cognitive process. The methodology of science involves deliverances of sense as well as rules of correspondence, constructs and principles regulating constructs”1. Note the recurring importance of Kant, who really first codified the epistemology of Newtonian physics (Kritik der reinen Vernunft2) in 1781. Later authors have formed a neo-Kantian tradition altering the a priori features of Kantian epistemology to fit the changing physics. That tradition still persists. I returned to the philosophy of my youth and concern with ontology as a consequence of recent readings and searches for understanding. First, there was the challenging book3, Pauli's Exclusion Principle, “The origin and validation of a scientific principle” by Michela Massimi in 2005. In probing the epistemological roots of exclusion, Massimi emerges as a self-proclaimed neo-Kantian epistemologist along with Ernst Cassirer, Michael Friedman, G. Buchdahl, Henry Margenau, and others. The second book is (Ref.4) “Philosophical Foundations of Neuroscience” by Bennett and Hacker, 2003. It also probes deeply into the theory of knowledge. Other works such as “The Mystery of Consciousness” by John Searle, 19975, raise some of the same issues. In re-examining these philosophical matters, I was immediately struck with the fact that I had been reading about ontology and about ontologies for the last 20 years in a very different sense from my metaphysical past. Ontology has gotten to be a very frequently used word in the information sciences and computer sciences. The new usage as noted by Tom Gruber in 2001 is “An ontology is a description (like a formal specification of a program) of the concepts and relationships that can formally exist for an agent or community of agents. The definition is consistent with the use of ontology as a set of concept definitions, but more general. And it is a different sense of the word than its use in philosophy.” Thus, one can have ontologies of linguistics, genomics, cultural heritage, and almost any domain for which data bases exist. In the earlier usage of ontology, only the singular of the noun may be used if we are to assume that there is only one reality. Aside from the many world view of quantum mechanics and the windowless monads of Leibniz, most philosophies accept a single reality. Therefore, I think that the word “ontology” should be reserved for metaphysics with firm ties to epistemology and a new noun should be developed that includes any data set but is not intended for commitments to reality. Failure to make the distinction leads to a kind of computer modeling where the results are regarded as metaphysical realities as distinguished from the simple consequences of the model to be tested and if possible to be tested by the falsify–verify criteria of experimental science. They can then be incorporated or rejected as part of the relevant paradigm. The one science where the epistemology ontology approach in the tradition of Kant has been worked out in some detail is physics as thoroughly examined in the previously cited Margenau book, “The Nature of Physical Reality.” This is not a prescriptive approach in the tradition of Karl Popper's philosophy of science, but emerges as a descriptive work on the set of metaphysical rules that are followed by physicists in order for the constructs of physics to emerge with the appropriate ontological status. This is carried through in some detail for mechanics, thermodynamics, statistical mechanics, and the exclusion principle. Margenau reserves some doubts as to whether the approach is appropriate to the biological and social sciences. When viewing consciousness he notes, “the problem falls within the province of introspective psychology where the methods of natural science have not come as yet to full fruition.” This leaves an opening for new approachs since “the immediately given” that is a feature of Margenau's epistemology is itself related to consciousness. This is of course one of the great outstanding problems of contemporary philosophy of science. Margenau's book ends with the Pauli exclusion principle introducing some of the same issues considered by Massimi. Again, let's note that the very idea of the plural of ontology deprives philosophy of its search for deep understanding of a unifying reality and allows the information sciences to be rather cavalier in converting the vast array of available data into principles that are supposed to constitute the route to scientific understanding. Such supposed principles may or may not be based on an underlying reality. It all leads to a less than humble attitude about what we really know.

The concept of autotrophy depends on the growth media for pure cultures supplying a single one carbon source for anabolism. Secondary carbon compounds added to the medium as chelators and/or vitamins confuse the meaning. This note suggests a clarification of definition suitable for contemporary biochemical studies of true autotrophs.

AstrobiologyVol. 11, No. 9 ReflectionLife on VenusHarold MorowitzHarold MorowitzPublished Online:17 Nov 2011https://doi.org/10.1089/ast.2011.9270AboutSectionsView articleView Full TextPDF/EPUB ToolsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Life on Venus." , 11(9), pp. 931–932AbstractWhile the surface conditions of Venus make the hypothesis of life there implausible, the clouds of Venus are a different story altogether. As was pointed out some years ago1, water, carbon dioxide and sunlight—the prerequisites for photosynthesis—are plentiful in the vicinity of the clouds. Since then, good additional evidence has been provided that the clouds are composed of ice crystals at their tops2,3, and it seems likely that there are water droplets toward their bottoms4. Independent evidence for water vapour also exists5. The temperature at the cloud tops is about 210°K, and at the cloud bottoms is probably at least 260–280°K (refs. 4 and 6). Atmospheric pressure at this temperature level is about 1 atm.7. The observed planetary albedo falls steeply in the violet and ultra-violet8, which accounts for the pale lemon yellow colour of Venus. The albedo decline would not be expected for pure ice particles, and must therefore be caused by some contaminant. Dust, ozone, C3O2 and other gases may possibly explain these data but, whatever the explanation, the ultra-violet flux below the clouds is likely to be low. If small amounts of minerals are stirred up to the clouds from the surface, it is by no means difficult to imagine an indigenous biology in the clouds of Venus. What follows is one such speculation.FiguresReferencesRelatedDetailsCited ByHypothetical signs of life on Venus: revising results of 1975—1982 TV experiments1 December 2018 | Uspekhi Fizicheskih Nauk, Vol. 189, No. 04 Volume 11Issue 9Nov 2011 InformationCopyright 2011, Mary Ann Liebert, Inc.To cite this article:Harold Morowitz.Life on Venus.Astrobiology.Nov 2011.931-932.http://doi.org/10.1089/ast.2011.9270Published in Volume: 11 Issue 9: November 17, 2011Online Ahead of Print:November 7, 2011PDF download

On my fourth reading of Moby Dick; or, The Whale— many readings are of course required to plumb the depths of such a leviathan of a novel—I became impressed with the extraordinary amount of biological information lurking within this vast maritime novel resonating with human psychopathology and shrouded with strange metaphysical intent. Yet on inspection, 17 of the 135 chapters deal primarily with the anatomy, physiology, ecology, metabolism, and ethology of the sperm whale, Physeter macrocephalus, and various assorted cetaceans as well as seals, squid, sharks, albatrosses, and other marine birds. To place the life sciences in temporal context, we note that Charles Darwin returned to England from the voyage of the Beagle just 9 years prior to Herman Melville leaving New Bedford on the whaleship Acushnet, which he deserted 18 months later. Melville’s classic Moby Dick nevertheless appeared in 1851, some 8 years before Charles Darwin’s paradigmshattering The Origin of Species by Means of Natural Selection. Melville noted “A whaleship was my Harvard and my Yale College.” Yet he must have majored in literature, as noted by his dedication “In Token of my admiration for his genius, This book is inscribed to NATHANIEL HAWTHORNE.” However, at the very least he minored in biology. For Darwin, the Beagle was clearly his graduate school that eventually led to a better understanding of the evolution of whales from land mammals as well as to the foundations of evolutionary biology. While Melville was at sea, Julius Mayer, as ship’s physician on a round trip from Rotterdam to Jakarta, was developing the theory of conservation of energy. For Mayer, a three-masted ship was the locus of his postdoctoral fellowship. His research paper “On the Quantitative and Qualitative Determination of Forces” led to a better understanding of the energetics of the burning of oil, including whale oil. There seems to be something about long sailing trips in the mid 1800s that was propaedeutic to great intellectual productivity. The first formal discussion of biology occurs in Chapter XXXII, “Cetology.” Here we find Melville, the sailor, boldly at odds with academic zoologists and taxonomists. In 1735, Carl Linnaeus first published a generalized work on taxonomy, Systema Naturae. In the 10th edition of that work, Linnaeus recognized that cetaceans were mammals distinct from the fish taxa. This was not a new finding. Aristotle in History of Animals, some 2200 years earlier had noticed the difference between members of the whales and porpoises and the other marine inhabitants, the fish. He based this distinction on the cetaceans having the mammalian properties of being warm-blooded, breathing air through lungs, and feeding the young through mammary glands. Melville, through his spokesman Ishmael, strongly disagreed and was willing to place the anecdotal knowledge of a seaman against the formal knowledge of academics. He insists that a whale is “a spouting fish with a horizontal tail.” Understanding the formalism of taxonomy, he develops a classification system based entirely on size, while ignoring the biologists’ distinction between the suborders Odonticeti (toothed whales) and Mysteceti (baleen whales). He ignores the taxonomic distinction in his cetology in spite of chapters LXXIV, “The Sperm Whale’s Head,” and LXXV, “The Right Whale’s Head.” In these two chapters he goes to great pains to detail the very considerable anatomical and dental differences leading to very distinct life styles. In spite of being aware of these great differences from personal observation, sailor Melville continues to group the sperm whale and the right whale together in his suborder “The Folio Whale” based on size alone. A subtheme of Melville’s cetology is the deckhand with his arms deep in spermaceti teasing the professors sitting in libraries of dubious knowledge or in laboratories too small to accommodate even the tenth part of a whale’s head. In any case there is an underlying lack of confidence in the professoriate by the man of the sea. Received 28 February 2011; accepted 1 March 2011. * E-mail: morowitz@gmu.edu Reference: Biol. Bull. 220: 83–85. (April 2011) © 2011 Marine Biological Laboratory

WHILE the surface conditions of Venus make the hypothesis of life there implausible, the clouds of Venus are a different story altogether. As was pointed out some years ago1, water, carbon dioxide and sunlight—the prerequisites for photosynthesis—are plentiful in the vicinity of the clouds. Since then, good additional evidence has been provided that the clouds are composed of ice crystals at their tops2,3, and it seems likely that there are water droplets toward their bottoms4. Independent evidence for water vapour also exists5. The temperature at the cloud tops is about 210° K, and at the cloud bottoms is probably at least 260–280° K (refs. 4 and 6). Atmospheric pressure at this temperature level is about 1 atm.7. The observed planetary albedo falls steeply in the violet and ultra-violet8, which accounts for the pale lemon yellow colour of Venus. The albedo decline would not be expected for pure ice particles, and must therefore be caused by some contaminant. Dust, ozone, C3O2 and other gases may possibly explain these data but, whatever the explanation, the ultra-violet flux below the clouds is likely to be low. If small amounts of minerals are stirred up to the clouds from the surface, it is by no means difficult to imagine an indigenous biology in the clouds of Venus. What follows is one such speculation.

The assumption that all biological catalysts are either proteins or ribozymes leads to an outstanding enigma of biogenesis-how to determine the synthetic pathways to the monomers for the efficient formation of catalytic macromolecules in the absence of any such macromolecules. The last 60 years have witnessed chemists developing an understanding of organocatalysis and ligand field theory, both of which give demonstrable low-molecular-weight catalysts. We assume that transition-metal-ligand complexes are likely to have occurred in the deep ocean trenches by the combination of naturally occurring oceanic metals and ligands synthesized from the emergent CO(2), H(2), NH(3), H(2)S, and H(3)PO(4). We are now in a position to investigate experimentally the metal-ligand complexes, their catalytic function, and the reaction networks that could have played a role in the development of metabolism and life itself.

All extant life forms depend, directly or indirectly, on the autotrophic fixation of the dominant elements of the biosphere: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. We have earlier presented the canonical network of reactions that constitute the anabolism of a reductive chemoautotroph. Separating this network into subgraphs reveals several empirical generalizations: (1) acetate (acetyl-CoA), pyruvate, phosphoenol pyruvate, oxaloacetate, and 2-oxoglutarate serve as universal starting points for all pathways leading to the universal building blocks—20 amino acids and 4 ribonucleotide triphosphates; (2) all pathways are anabolic; (3) all reactions operate by complete utilization of outputs with no molecules left behind as waste, ensuring conservation of information; (4) the core metabolome of 120 compounds is acidic, consisting of compounds containing phosphoric or carboxylic acid or both; and (5) the core network is both brittle—vulnerable to a single break—and robust—having persisted for 4 billion years. Preliminary analysis of the chemical reactions and resultant structures reveals (a) a sparseness among possible molecular structures; (b) subdomains in the network; and (c) restriction of anabolism to a small set of rudimentary organic reactions with limited diversity in chemical mechanisms. These generalizations have implications for biogenesis and trophic ecology.

As the frontiers of knowledge have advanced, scientists have resolve one creation question after another. We now have a pretty good understanding of the origin of the Sun and the Earth, and cosmologists can take us to within a fraction of a second of the beginning of the universe itself. We know how life, once it began, was able to proliferate and diversify until it filled (and in many cases created) every niche on the planet. Yet one of the most obvious big ques tions?how did life arise from inorganic matter??remains a great unknown. Our progress on this question has been impeded by a formidable cogni tive barrier. Because we perceive a deep gap when we think about the differ ence between inorganic matter and life, we feel that nature must have made a big leap to cross that gap. This point of view has led to searches for ways large and complex molecules could have formed early in Earth's history, a daunting task. The essential problem is that in modern living systems, chemical reactions in cells are mediated by pro tein catalysts called enzymes. The in formation encoded in the nucleic acids DNA and RNA is required to make the proteins; yet the proteins are required to make the nucleic acids. Furthermore, both proteins and nucleic acids are large molecules consisting of strings of small component molecules whose synthesis is supervised by proteins and nucleic acids. We have two chickens, two eggs,