The Principles of Life

superior insights into the nature of life

Criteria of life

The chemoton theory

Relevance of Chemoton model and criteria of life

• Robert Shapiro (2007) 'A simpler origin of life', Scientific American, June 2007, pp. 24-31.
  Shapiro refers to the definitions of life in the Encyclopeadia Britannica and uses the thermodynamic rather than the genetic definition because the origin of a genetic system is too improbable. The thermodynamic definition is: "a localized region that increases in order (decreases in entropy) through cycles driven by an energy flow" and he gives five common requirements:
  1. a boundary is needed to separate life from nonlife
  2. an energy source is needed to drive the organization process
  3. a coupling mechanism must link the release of energy to the organization process that produces and sustains life
  4. a chemical network must be formed to permit adaptation and evolution
  5. the network must grow and reproduce
  I note the lack of a clear distinction between definition of life and origin of life hypotheses. Furthermore, if (4) is required to create a complex cell, in other words: evolution, how could that be done without a genetic system? Usually, one requires the ability to evolve, not evolution itself. A system incapable of evolution, could still be alive. Again, a confusing mixture of definition of life and origin of life. Shapiro adds to requirement 5 that "a system of reproduction must eventually develop" (my emphasis). Question: is the system alive before that event? If so, requirement 5 must be dropped from the definition of life. Apart from these remarks, the article is recommended very much (regrettably, it is not freely available online).
  
• Pier Luigi Luisi (2006) The Emergence of Life. From chemical origins to synthetic biology.
  Chapter 2 is devoted to the definition of life. Preferred definition of life is autopoiesis (chapter 8). Includes a comparison with Gánti's chemoton model p.177. Info: research issues.
• Kevin W. Plaxco & Michael Gross (2006) Astrobiology: A Brief Introduction.
  This introduction to astrobiology appropriately starts with the question: What is Life?. Their working definition of life is: "Life is a self-replicating chemical system capable of evolving such that its offspring might be better suited for survival". Gánti would absolutely agree with including 'chemical system', but self-replication and evolution are potential life criteria (B1 and B2). Interestingly, the authors note that self-replication is not necessary for a specimen to be alive (non-reproducing individuals exist!), so self-replication cannot be a litmus test for life. However, self-replication must be applicable to most individuals of a species. Their justification is that all non-reproducing individuals originated from reproducing individuals. Furthermore, they note that evolution acts on the level of populations. Remarkably, the authors state 'the fragile state of chemical disequilibrium we call life' on page 173, but chemical disequilibrium is not in their definition of life. They sum up 5 requirements for the origin and survival of life: 1) suitable atoms, 2) abundance of suitable atoms, 3) a solvent (water), 4) energy, and 5) time. Remarkably, metabolism is not part of their definition, although metabolism is perfectly and uniquely applicable to a potential living individual. Even the more remarkable, because the Viking spacecraft on Mars used radioactive markers to detect carbon-based metabolism (p.221). Please note, that membranes are absent from their definition. Indeed, they claim that replicating and evolving RNA molecules are 'organisms' (p.122). On the other hand, they claim that membranes are 'the key step in creating cellular life' (p.139). Yet, they are aware that even 'RNA-organisms' need to be enclosed by something. Here we see that Gánti's boundary should be included in the definition of life too. Conclusion: their initial definition is incomplete. However, a satisfactory definition can be reconstructed from their book. They do not mention Gánti. Knowing Gánti's definition would have been useful for constructing a working definition of life.   [ 6 Jul 06 ]
• Schulze-Makuch & Irwin (2006) Life in the Universe. Expectations and Constraints.
  (Advances in Astrobiology and Biogeophysics. Chapter 2: Definition of Life. No Gánti. No index.)
• Radu Popa (2004) Between Necessity and Probability: Searching for the Definition and Origin of Life. [ Springer info. Contents of the book]
  Popa discusses Gánti's chemoton model in the appendix: "The chemoton model proposed by Tibor Gánti (1971) is one of the most elaborate models of primitive life". Popa discusses nine other theories of the origin of life in the appendix. Astrobiology adds an extra dimension to the definition of life. First: the definition of life is no longer of secondary importance, but a core question to be solved in order to detect life on other planets. Secondly, the definition must be free of earth-bound specifics according to Popa. DNA, proteins, lipids, Carbon and water may all be necessary for life on earth, but may not be necessary for life on other planets. DNA does not mean life, only complex chemistry. Lovelock is absent! (detect life via the composition of the atmosphere). See also: (29) [ 11 June 04 ]
• Stephen Stearns & Rolf Hoekstra (2005) Evolution, an introduction.
  This evolution textbook contains a short section on the origin of life. The authors recognize the importance of defining life, but only give a rough characterization: "a living thing should have metabolism - a coordinated system of chemical reactions contributing to its maintenance, a system that imports energy to maintain order - and hereditary replication - a system of copying in which the new structure resembles the old." (p.357). What is wrong with this definition? (1) the definition ignores the fact that all life is cellular (Gánti's boundary); (2) non-reproducing individuals (mules, sterile individuals, non-dividing cells) are alive; (3) no distinction between absolute and potential life criteria, which explains error 2. For a textbook aimed at students taking a first course in evolution it is really a missed opportunity to teach deep insights into the nature of life. Please note that according to their definition viruses are not alive because of the lack of metabolism.   [ 1 Oct 05 ]
• Christian de Duve (2002) Life Evolving - Molecules, Mind, and Meaning.
  De Duve is the 1974 winner of the Nobel Prize in Physiology/Medicine. This magnificent book written for a wider audience has high educational value. There is no explicit definition of what life is, and no distinction between relative and absolute life criteria, despite the fact that the first two chapters are about the What Is Life? question. Of course all the ingredients of the definition are present. His implicit definition of Life is: "Life Is What Is Common To All Living Beings", which has the advantage that it enables the exclusion of a lot of characteristics not common to all life. For example characteristics which are not common to plants and animals (photosynthesis), single-cellular and multi-cellular organisms (lung, brain), prokaryotes and eukaryotes (nucleus), etc. The disadvantage is that this definition is more a task than a result. He elaborates this in subsequent chapters. The central characteristic of life is the ability to 'follow a blueprint'. Additionally, a self-building property. Life's requirements are: raw materials, energy and catalysis. On the whole this is a descriptive approach and this blocks the development of the concept 'minimal life'. He summarises: life is one, life is chemistry, central role of RNA. At the same time catalysis (enzymes) are central to life. He clearly has the knowledge, but just does not produce a compact and complete definition.
  About the origin of life: ATP preceded RNA; RNA preceded DNA and proteins. Proteins were invented by RNA. No metabolism without enzymes, so metabolism is relatively late in the origin of life. The advantages of Gánti's explicit definition are: clarity, completeness, compactness and sophistication.   [4 Apr, 15 May 04]
• Franklin Harold (2001) The Way of the Cell.
  This book deserves a separate review. Harold asks the same question as Gánti and Schrödinger: What is Life? The goal of his book is to identify the essential features that distinguish living organisms from other things. His definition is a combination of (1) Lynn Margulis' autopoietic system and (2) John Maynard Smith's systems capable of evolving: "Life is the property of autopoietic systems capable of evolving by variation and natural selection." The word 'capable' here is crucial: does 'capable' mean that autopoietic systems incapable of evolution are not alive? That seems wrong, because a living cell that (a) is incapable of multiplication or (b) is incapable of evolution is still separated from all physical and chemical systems in a crucial way. Here comes Gánti's distinction between absolute and potential life criteria to the rescue. 'Multiplication' and 'evolution' are not part of his absolute life criteria. From the point of view of the origin of life and discriminating life from physical and chemical systems, autopoietic systems are sufficient as a definition of life. From the point of view of populating a planet one needs reproduction (cell division) and from the point of view of 'adaptation'and 'diversity' one needs the most inclusive definition of life (Harold's evolving autopoietic systems).   [15 Jan 2005]
• Stuart Kauffman (2000) Investigations.
  "I may have stumbled on the proper definition of life itself", "What must a physical system be to be an autonomous agent?". There are similarities (autocatalysis, work) between Investigations, and Gánti's The Principles of Life. I prefer the latter because of its clarity. Kauffman has a completely different style of writing, often leaving the reader astounded and confused.
• Iris Fry (2000) The Emergence of Life on Earth: A Historical and Scientific Overview.
  Fry is pessimistic about the possibility of a definition of life. The definition will either be too narrow (exclude dormant seed) or too wide (include automobiles and flames). However, the problem of dormant seed can be solved by recognising different states of life (Gánti: 'potential living but not dead'). Automobiles do consume fuel and excrete waste products, but they do not use the energy and molecules to maintain their own structure (self-repair). So automobiles can easily be excluded from the definition. Despite her pessimism, she gives the next page a definition that excludes flames and automobiles: "Every living system is organized in a much more complex way than any ordered physical system. The unique character of this complexity lies in the ability of an organism to maintain and reproduce its organization according to specific internal instructions, or information." Fry does not distinguish between real and potential life criteria (Gánti). She is not clear about whether or not evolution (as the capacity for evolution or being the result of evolution) must be included in the definition of life. Watching a chemist-philosopher wrestling with life criteria, convinces me that Gánti's distinction between actual and potential life criteria is certainly a conceptual breakthrough.   [25 Apr 04]
• Christopher Wills & Jeffrey Bada (2000) The Spark of Life. Darwin and the Primeval Soup.
  The title of this book is somewhat misleading, because the book is about the origin of life and is strong in education, science and the key figures in the history of biology. The authors are aware that a definition of life is mandatory. However, they define 'proto-bionts' instead. "Protobionts are certainly not living cells as we know them and probably had few of the characteristics of living cells today". Protobionts are defined as having (1) replication, (2) survival under savage conditions, (3) draw energy from the environment to make energy-rich compounds for the replication process, (4) death. The problem with this definition is that it looks like a definition of (minimal) life, but it is presented as a definition of 'proto-life'. Interestingly, the authors remark that Oparin, the famous Russian origin-of-life researcher, later in his life recognised the importance of membranes for life. Just as Gánti did.
• Lynn Margulis and Dorion Sagan (2000) What is Life?
  Margulis recognises metabolism as the primary characteristic of life, but later mentions membranes as primary for the origin of life (following Morowitz). Viruses are not living, but can mutate and evolve (in perfect accord with Gánti) (she does not note the paradoxical combination of not-living and evolving). A reason is that 'viruses lack sufficient genes and proteins to maintain themselves' (p.18). But that means that genes are important for autopoiesis (=self-maintenance) and that is nowhere explicitly stated. "Replication is not nearly as fundamental a characteristic of life as is autopoiesis". This is also in complete accord with Gánti. She mentions as an example a sterile mule, who cannot reproduce but is alive (p.18). She overlooks the fact that the mule is the product of reproduction, so it owes its existence to reproduction. Furthermore, all the body cells of the mule originated by (asexual) reproduction. So, reproduction is still important, although in another way. "The first autopoietic system, which may have lacked both DNA and RNA, was almost certainly a cell." (p.86). Prophetic remark, but no further details. All the ingredients of the definition and the origin of life are there, but not as clearly and systematically organised as in Gánti's book. The frequently used word 'autopoiesis' is not explained in this book, but in Slanted Truths, chapter 20, page 268, there is a list of 6 properties of autopoietic systems. 'Heredity' or 'reproduction' are not among those 6 properties. Nucleic acids are mentioned, but not what they are doing in the cell. No distinction between absolute and potential life criteria, which could help to include heredity, mutation and evolution as a optional life criteria. What is Life? is a reprint from the 1995 edition. Therefore, Gánti is not mentioned. [ upd 25 Jul 2006 ]
• Freeman Dyson (1999) Origins of Life, second edition.
  Dyson defines life as a dual structure: metabolism (proteins) and replication (DNA). He forgets Gánti's third subsystem: membrane (lipids). He 'agrees' with Gánti about the primacy of metabolism. It is useful to read Dyson together with Gánti. The thing I like in Gánti is his attention to the definition of life, which is absent in Dyson.
• Paul Davies (1999) The Fifth Miracle. The Search for the Origin and Meaning of Life.
  Physicist Paul Davies wrote an excellent book about the origin of life for the general reader (biologist and nonbiologist). He is the first author I encountered who presented explicit life criteria. He lists no less than ten: Autonomy, Reproduction, Metabolism, Nutrition, Complexity, Organization, Growth and development, Information content, Hardware/software entanglement, and Permanence and change. Davies makes no distinction between absolute and potential life criteria. One criterion is clearly missing: Gánti's boundary system (membrane), although he knows that life is cellular (Oparin).
• John Maynard Smith, Eörs Szathm\E1ry (1999) The Origins of Life. From the Birth of Life to the Origin of Language.
  In this superb book, the authors present two definitions of life. The first is: "Entities are alive if they have the 3 properties multiplication, variation and heredity (or are descended from such entities)". This definition misses metabolism, moreover a single cell can not have 'variation'. So, this definition fails. The second definition is in terms of metabolism and misses the hereditary component. They end up with the dual nature of life: metabolism and information (just as Dyson, who is mentioned also). The first chapter closes with a page long description of Gánti's contribution. That is unique, because in 1999 no English translation of Gánti's work was available (Szathm\E1ry is Hungarian). All other books about the origin of life do not mention Gánti.
• Ernst Mayr (1997) This is Biology - The Science of the Living World
  Ernst Mayr started his career as an evolutionary biologist and evolved into a historian and philosopher of biology. In this book, he devoted (only) two pages to the distinguishing characteristics of life, but they are instructive. His purpose is to get a list of phenomena that are specific to living beings. He arrives at 'properties' and 'capacities', which are based on those properties. For example, a property is 'evolved programs', and a capacity is 'capacity for evolution'. The distinction properties/capacities is clearly similar if not identical to Gánti's real/potential life criteria distinction. Interestingly, Mayr describes 'evolved programs' as the product of 3.8 billion years of evolution, which is correct, but obviously does not apply to the first forms of life! Furthermore, including evolution ('evolved programs') both in properties and in capacities seems problematic. Apparently, the definition of life depends on whether one describes current life, current + extinct life, or 'essential life'. Remarkably, Mayr lists metabolism as a capacity and not as a property (because of viruses?). Metabolism in Gánti's system is a real (or absolute) life criterion. There are some inconsistencies and redundancies in Mayr's system, but it is interesting to compare his system with Gánti's system. [17 Apr 2004]
• Stuart Kauffman (1995) At Home in the Universe. The Search for the Laws of Self-Organization and Complexity
  (review). There is a similarity between Kauffman's ideas about the origin of life and those of Gánti. On theoretical grounds, Kauffman believes that autocatalytic sets can originate without a genome ("metabolism-first and genes-later" view of the origin of life). Gánti's believes that highly specific enzymes must be later additions to life-like chemical systems ("metabolism-first and enzymes+genes later"). Kauffman's sets can be enzymatic or non-enzymatic. Kauffman believes that specificity arises statistically as an effect of a great number of proteins with random specificity. It is unclear whether Kauffman's autocatalytic sets can be non-enzymatic. According to Gánti non-enzymatic catalysis is not an option because they are out of control of the proto-cell. They are not copied and multiplied as cells divide (pers.comm.). So the question remains whether auto-catalysis based on enzymes is feasible. Kauffman writes fascinatingly, but he uses the abstract language of a physicist and often of a poet. Gánti has an analytic approach.
• James Lovelock (1995) The Ages of Gaia. A biography of our living earth
  Gaia theory says that the earth is a living superorganism. Lovelock recognises the need for a definition of the concept 'life'. Lovelock observes that the Dictionary of Biology has no entry for 'life'! In general biologists avoided the question, he says. However, I disagree that no one has yet succeeded in defining life. Lovelock did not know Gánti's definition. Lovelock attempts to define life, but misses the dual nature of life (metabolism-heredity). On the other hand he quotes Schrödinger's definition: living systems have boundaries and are open systems at the same time. This is a dual nature from another perspective. In the context of thermodynamics: life is a self-organising system characterised by an actively sustained low entropy. Because Lovelock overlooks the importance of 'minimal life' in defining life, he fails to give a thorough and satisfactory definition. A probable cause is his focus on planetary biology and symbiosis (life exists in communities and collectives). The lack of a good definition of minimal life prevents a good understanding of problems inherent in the origin of life. For example when discussing the origin of life, he states "The first living cells may have used as food the abundant organic chemicals lying around; also the dead bodies of the less successful competitors..." (p.72). However, by definition, the first forms of life could not have used dead bodies. [9 May 04]
• Mark A. Ludwig (1993) Computer viruses, Artificial Life and Evolution
  Although physicist and anti-Darwinist Mark Ludwig is sceptical about the possibility to give a list of defining characteristics of life, he presents a list used by artificial life researchers: 1) the ability to reproduce, 2) emergent behavior, 3) metabolism, 4) ability to function under perturbations of the environment and interact with the environment, 5) ability to evolve. This list is a mix of real life criteria (#3,#4) and potential life criteria (#1,#5) according to G\E1nti's life criteria. That explains his problems. Ludwig states that the approach of refusing to call something alive unless it can evolve is rather blind (I agree). He claims that evolution cannot be used as a dividing line between life and non-life (I agree), but he does so for the wrong reasons (creationist argument: it cannot be observed). The correct reason is that living individuals have the potential to reproduce and evolve (#1,#5), but need not actually do it. That's why reproduction and evolution are potential life criteria. Remarkably, Ludwig claims that computer viruses can be designed to show Darwinian evolution (I agree). Because Ludwig does not make the important step of discriminating between the non-overlapping units of life and units of evolution, he is driven to the conclusion that from a mechanical perspective, it seems safe to say that computer viruses have a fairly strong claim to "life" (I disagree). In the G\E1nti definition neither biological nor computer viruses are alive. Furthermore, Ludwig does not distinguish between the properties self-reproduction and information system. This prevents him making an information subsystem a primary life criterion. Secondly, it prevents him from moving self-reproduction from primary to secondary criterion of life. (review) [5 Dec 05]
• Harold Morowitz (1992) Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis
  Lynn Margulis (2000) gives a description of Morowitz theory. According to Morowitz, neither DNA nor RNA alone is enough to form life. Membranes arose before proteins and nucleic acids. A membrane represents the transition from nonlife to life. All forms of metabolism and the synthesis of proteins and nucleic acids evolved only after membranes enclosed the precursors of cells. A non-aqueous barrier was necessary to separate the cell from its surroundings. There seems to be a problem with this scenario. If a membrane must be produced before any metabolism is in place, then the suitable lipids must be produced abiotically. Can they be produced without enzymes? Morowitz is an important and original researcher in the origin of life field and although I do not know enough details, his views seem to show great similarity with Gánti. [11 Apr 04]
• Hubert Yockey (1992) Information theory and molecular biology
  Obviously, for Yockey, information is a very important defining characteristic of life. Otherwise he would not have written such a book. But how important? "The essential difference between living and non-living matter is that the formation and function of important biological molecules is governed by genetic messages. No trace of a comparable specification by sequences or of a code between sequences exists in non-living matter" (Prologue). This is based on Mayr (1988). I summarised this view as "Information is the essence of life" in a review of his book. Yockey does not discuss the matter further (there is no chapter or paragraph devoted to the question). This is not a complete definition of life. It seems that viruses are living according to this definition. [12 June 04]
• Robert Shapiro (1986) Origins. A Skeptic's Guide to the Creation of Life on Earth
  A very useful book, but also lacks an explicit discussion of the definition of life. On page 132 I noticed components of life: 'the membrane, the energy-generating system, the genetic system, the vital catalysts', but I don't know whether Shapiro discussed them earlier in the context of the definition of life. Note that the first 3 are identical to the 3 components of Gánti's chemoton model. The following quote from Shapiro shows an implicit definition of life and one that is clearly opposed to Gánti's definition: "It becomes important, then, to find the simplest possible self-reproducing, or replicating, system, for this would be the first living thing (emphasis added). (this is according to the 'naked gene' theory of the origin of life). Again, I notice a similarity between Gánti and Kauffman: both oppose the 'naked gene theory'.
• John Maynard Smith (1986) The Problems of Biology
  This is one of his first books for the general reader. Concise and well written. A beautiful opening chapter 'the definition of life'. An indispensable topic if one wants to introduce readers to biology. Scientists like Tibor Gánti brought the subject to a superior level of sophistication, but what JMS has to tell us, is still of great value. His definition is "entities with the properties of multiplication, variation, and heredity are alive, and entities lacking one or more of those properties are not". Fire consumes external energy, continuously changes its internal substance (metabolism), can multiplicate itself and it varies, but since it lacks heredity, it is not alive. Therefore it can not evolve by natural selection and cannot acquire organs to keep it going. Adaptation is all about organs that help an organism to survive. Any adequate theory of evolution must explain adaptation. I think a definition of life does not need to explain life. It is necessary and sufficient that it includes all living objects and excludes all non-living objects. Fire has no parts that help it survive, so it can be rejected whether or not is has heredity. [27 May 04]
• Francis Crick (1981) Life Itself. Its Origin and Nature
  Chapter four of this book, 'The general nature of life', contains a concise and splendid description of the nature of life with an unsurprising emphasis on replication. The result is that metabolism and membranes become almost accessories. However, Crick has a very good reason why life needs membranes: cells with useful genes are able to prevent that other cells take advantage of their genes. Unlike Gánti, Crick does not distinguish between life as such and life capable of evolution. According to Crick's definition of life, chemical systems without an informational subsystem or with 100% accurate (error-free) replication, would not be living systems.

       Notes  

1. God could have created every individual directly and without the capacity for reproduction. Two effects of reproduction destroy perfect design: recombination and mutation. Recombination creates new combinations and mutation mutates what is perfect and this means less perfect. God could prevent hereditary diseases, congenital defects, spontaneous abortion, ageing, etc by creating each individual directly. Evolution would not be possible, but then, who needs evolution when one is directly created by God? See Swinburne review ('Four ways to create life').
2. God could have created every individual without death and ageing. "Cell aging and death is not an obligatory attribute of life on earth" (W.R. Clark, 1996). But then evolution would not be possible, because death is a necessary condition for evolution on a finite planet. But who needs evolution if one is directly created by God and if one is immortal?
3. Paley's watch has an internal structure, but does not carry internal information about its construction! That's why it cannot reproduce itself. See Swinburne review.
4. If one equals 'life' with 'information', then creating life equals the creation of information. William Dembski, Hubert Yockey and Periannan Senapathy fall in this trap. However, Tibor Gánti shows that information is only one of the 3 subsystems of living systems. Information is meaningless without the other two subsystems. Manfred Eigen (1996) Steps towards Life, also has an information-centred approach to the origin and evolution of life, but mentions the importance of compartments.
5. If reproduction would be included in the absolute definition of life, then homosexual and all other non-reproducing individuals would not be alive. See review of Bagemihl.
6. Szathmáry is co-author with John Maynard Smith of the important The Origins of Life. From the Birth of Life to the Origin of Language (see review).
7. Periannan Senapathy constructed a theory which is based on the idea that single-celled as well as multicellular organisms could originate directly from non-living materials. This is rejected by every biologist.
8. Kim Sterelny and Paul Griffiths (1999) Sex and Death. An Introduction to Philosophy of Biology, chapter 15 "What is Life?". Gánti is not mentioned (of course), and there is nothing similar to Gánti's life criteria, which is a serious omission for a philosophy of biology textbook.
9. JMS's definition: "Entities are alive if they have the properties of multiplication, variation, and heredity or are descended from such entities" is indeed a mix of 'life' and 'evolution'.
10. Jens Burmeister in Brack (1998) The Molecular Origins of Life confuses 'life' and 'evolving system' and produces an implicit definition of life: "In general, an evolving system is able to metabolize, to self-replicate, and to undergo mutations. Thus self-replication is one of the three criteria that enable us to distinguish non-living from living systems." (p.295). He switches, without noticing, from 'evolving systems' to 'living systems'. An organism without mutations is not alive? That is why we need explicit definitions!
11. There is a snag. The basic cell membrane alone would have been useless. Surrounding a self-replicating molecule with a lipid bilayer would prevent dispersal of most of the products of any reaction; but it would also prevent access to essential raw materials. Real cell membranes contain a host of pumps, channels, gates and pores. Ian Glynn (1999) An Anatomy of Thought, p.78
12. The famous HeLA-cell line, a human tumor cell line, kept growing indefinitely. William R. Clark (1996) Sex and the Origin of Death, pp 93-97.
13. In 2002, human genome sequencer Craig Venter announced his plan to build an artificial cell with a minimal genome based on modern genes. According to Koonin, the minimal set of genes will number about 600 (Nature 19 Feb 2004). Building artificial life would be a huge success, a milestone in the origin-of-life-research, but how does a minimal set of 600 genes arise? Gánti could bridge the gap between life-with-a-minimal-genome and life-without-a-genome.
14. Christopher Langton in Artificial Life (1989), p.21. There is also a scientific journal Artificial Life. See also: The Digital Life Laboratory for a description of digital life.
15. John Maynard Smith said about Eörs Szathmáry: "he really knows molecular biology and chemistry".
16. A possible exception are the Chlamydiae (Eubacteria) because they have no energy metabolism at all, and depend on their hosts for ATP. So if the production of ATP is an essential property of life, then Chlamydiae are not living! See: Peter Skelton (1993) Evolution. A Biological and Palaeontological approach, page 881.
17. Steen Rasmussen, Liaohai Chen, David Deamer, David C. Krakauer, Norman H. Packard, Peter F. Stadler, and Mark A. Bedau, "Transition fron nonliving to living matter", Science. (see website: protocells).
18. "Whether or not these digitals are truly alive is ultimately of no concern to us as researchers: We use them because we are interested in complicated and vexing questions of evolutionary biology, and digitals offer us the possibility to attack them." quoted from Artificial Life.
19. Nature News item: Giant virus qualifies as 'living organism'. About a giant virus which qualifies as living organism, because it can reproduce independently and make its own proteins. So far this is an exceptional virus. It does not mean that all viruses are alive. Nature online 14 Oct 2004. See also: Didier Raoult et al (2004) The 1.2-megabase Genome Sequence of Mimi virus, Science 19 Nov 2004. The Mimivirus has 911 genes, which is an extremely high number for a virus. Further reading: Helen Pearson (2008) 'Virophage' suggests viruses are alive, Nature, 7 Aug 2008. The name of the virus is Acanthamoeba polyphaga mimivirus and it can be infected by a small virus, a 'Virophage'. "It crossed the imaginary boundary between viruses and cellular organisms." (Eugene Koonin). I would like to know whether the virus has a metabolism (produces ATP). Raoult, Koonin and their colleagues report the isolation of a new strain of giant virus from a cooling tower in Paris, which they have named mamavirus because it seemed slightly larger than mimivirus.
20. Philip Ball (2004) "Artificial cells take shape", Nature 6 Dec 2004, writes: "These synthetic cells are not fully alive, because they cannot replicate or evolve." They may not be alive, but for other reasons. Being able to divide is a potential and not an absolute life criterion. Apart from this mistake, the article is useful. [ 10 Dec 2004 ]
21. Louis P. Villarreal (2004) Are viruses alive?, Scientific American, December 2004, pp 77-81. The article is useful, but I have a few comments. Villarreal does not mention the important insight of The Principles of Life that viruses have the contradictory properties of not being alive, and the ability to evolve. Furthermore, Gánti's definition of life could clarify his discussion of viruses far more than the confusing quotes accompanying the article. Regrettably, Villarreal fails to point out that the strongest argument for the connection of viruses with 'the web of life' is that viruses have the same genetic code as all forms of life on earth. Interestingly, Villarreal wrote a book about the role of viruses in evolution: Viruses and the Evolution of Life (2004) [ 11 Dec 2004 ]
22. Eörs Szathmary (2005) In search of the simplest cell, Nature, 433, 469-470, 3 Feb 2005. Szathmary recognises the following approaches to the minimal-cell-problem: top-down, bottom-up, RNA-based, lipid-based, theoretical, experimental. Top-down approaches [stripping] seem to point to a minimum genome size of slightly more than 200 genes.
23. Later I kindly received from professor Gánti what seems to be the first book in the English language: The Principle of Life published in 1987 in Budapest (sixth edition). I guess it was not distributed widely. The first (1971), second (1978), third (1979), and fourth (1983) edition were published in Hungarian (Az Elet Principuma) and the fifth edition (1986) in Polish. The English edition is still worth reading: it was aimed at the wider public.[ 18 Feb 2005 ]
24. David L Chandler (2005) Robotic rover detects life in the driest desert, NewScientist, 16 March 2005.
25. Saul Griffith, Dan Goldwater, Joseph M. Jacobson (2005) Self-replication from random parts, Nature, 437, 636 (29 September 2005). doi:10.1038/437636a. Editor's Summary.
26. However, if enzymes and genetic code are not necessary, then there is no point at all in having an information system (like DNA). If it is not controlling the synthesis of proteins, then what is it doing?
27. Prions could be defined as self-reproducing proteins. Prions could evolve if copy errors occur. Artificial Life is potentially evolving non-biological 'life'.
28. Nick Lane (2005) writes: "the enzyme reaction is catalysed by the mineral [iron, sulphur, manganese, copper, magnesium, and zinc], not the protein, which improves the efficiency rather than the nature of the reaction", Power, Sex, Suicide p.95.
29. Radu Popa (2002) A hierarchical model of the emergence of life as a both probabilistic and deterministic conjecture, poster presented at Second Astrobiology Science Conference, April 7 - 11, 2002. Contains advanced definition of life.
30. Philip Ball (2008) 'Genome stitched together by hand' , Published online 24 January 2008 Nature.
    "The genome of the pathogenic bacterium Mycoplasma genitalium has been stitched together from scratch, creating a full set of instructions to make a living thing in the lab."
31. Ann Pearson (2008) 'Biogeochemistry: Who lives in the sea floor?', News and Views, Nature 454, 952-953 (21 August 2008) Published online 20 August 2008.
    Archaea and Bacteria in the seafloor ('deep biosphere') live at the limits of energetic viability. "Part of the problem lies in the distinction between 'living' cells, total cells (including inert or dead cells), and/or cells that are in between, persisting in an undefined degree of stasis. This leads to ambiguity about what should or should not be counted. (...) The fluorescent stains acridine orange and DAPI detect all cells - alive or dead - that contain any remnant of DNA." A method is to detect ribosomal RNA (rRNA) or intact polar lipids (IPLs) of cell membranes (both are proxies for live cells). (...) Polar lipids are presumed to reflect living biomass, because their labile (often phosphate-containing) head groups are quickly lost after cell death. (...) It is therefore reasonable that in a sub-seafloor world, where it has been estimated that cell turnover times could be centuries or longer, organisms with honed strategies to conserve energy would dominate. (...) For microbes, the boundary between alive and dead is fuzzy, and the extent to which any category of biomolecule can define it remains unclear."