The riddle of “life,” a biologist’s critical view

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Naturwissenschaften (2009) 96:1–23 DOI 10.1007/s00114-008-0422-8 REVIEW The riddle of “life,” a biologist’s critical view Heinz Penzlin Received: 5 March 2007 / Revised: 17 June 2008 / Accepted: 24 June 2008 / Published online: 2 September 2008 # Springer-Verlag 2008 Abstract To approach the question of what life is, we first have to state that life exists exclusively as the “being-alive” of discrete spatio-temporal entities. The simplest “unit” that can legitimately be considered to be aliv

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  REVIEW The riddle of  “ life, ” a biologist ’ s critical view Heinz Penzlin Received: 5 March 2007 /Revised: 17 June 2008 /Accepted: 24 June 2008 / Published online: 2 September 2008 # Springer-Verlag 2008 Abstract To approach the question of what life is, we first have to state that life exists exclusively as the “  being-alive ” of discrete spatio-temporal entities. The simplest  “ unit  ” that can legitimately be considered to be alive is an intact  prokaryotic cell as a whole. In this review, I discusscritically various aspects of the nature and singularity of living beings from the biologist  ’ s point of view. In spite of the enormous richness of forms and performances in the biotic realm, there is a considerable uniformity in thechemical “ machinery of life, ” which powers all organisms.Life represents a dynamic state; it is performance of asystem of singular kind: “ life-as-action ” approach. All “ life-as-things ” hypotheses are wrong from the beginning. Life isconditioned by certain substances but not defined by them.Living systems are endowed with a power to maintain their inherent functional order (organization) permanentlyagainst disruptive influences. The term organization inher-ently involves the aspect of functionality, the teleonomic, purposeful cooperation of structural and functional ele-ments. Structures in turn require information for their specification, and information presupposes a source. Thissource is constituted in living systems by the nucleic acids.Organisms are unique in having a capacity to use, maintain,and replicate internal information, which yields the basisfor their specific organization in its perpetuation. Theexistence of a genome is a necessary condition for life andone of the absolute differences between living and non-livingmatter. Organization includes both what makes life possibleand what is determined by it. It is not something “ implanted ” into the living beings but has its srcin and capacity for maintenance within the system itself. It is the essence of life.The property of being alive we can consider as an emergent  property of cells that corresponds to a certain level of self-maintained complex order or organization. Keywords Livingstate.Vitalorganization.Metabolism.Self-maintenance.Autonomy.Emergence Introduction The bondage of biology to the physical sciences haslasted more than half a century. It is now time for  biology to take her right full place as an exact independent science: to speak her own language andnot that of other sciences. Haldane (1922)Living matter exists in a wondrous array of emergent  products, perhaps 10 to 20 million different species or evenmore  —  nobody really knows the exact number. Life is soubiquitous in our world, so evident that we fail to evenwonder at its existence. We take it for granted that a human being composed of an estimated 10 billion (10 13 !) tissuecells of about 350 different types and another 30 billion blood cells should develop from a relatively unstructuredseminated egg cell  —  and this, fortunately, with a remark-ably low rate of error. And nevertheless, embryogenesisdoubtlessly belongs to the most amazing and puzzling phenomena to be found in our natural world. What causesall the cells to differentiate in the way that they do so a  Naturwissenschaften (2009) 96:1  –  23DOI 10.1007/s00114-008-0422-8H. PenzlinInstitut für Allgemeine Zoologie und TierphysiologieFriedrich-Schiller-Universität Jena,Erbertstrasse 1,07745 Jena, GermanyH. Penzlin ( * )Leo-Sachse-Strasse 10,07749 Jena, Germanye-mail: penzlin-jena@t-online.de  healthy child with a head, trunk, arms, and legs, with a brain, heart, and all the other organs comes into being and begins to speak and to think? There is probably no one who better recognizes how remarkable “ life ” actually is than thedevelopmental biologist.Two hundred years ago, Treviranus, Lamarck, and othersintroduced the term “  biology ” to describe the sciencedealing with living beings. In the light of the multiple andheterogeneous questions it asks and approaches it takes, theterm “ life sciences ” is more usual nowadays. Strictlyspeaking, despite generations of trying, the subject matter of life sciences is as yet still undefined. My centralintention in this review therefore is not to try to define “ life, ” which is probably a hopeless undertaking, but toattempt to work out what living entities are and todemonstrate that living beings are distinct from non-livingentities not only in their degree of complexity but fundamentally, in principle. Organisms have propertiesand facilities, which are unique to them and only to them. “ Life ” means “ being-alive ” of discrete entities:organisms Life exists exclusively as the “  being-alive ” of somethingTo approach to the question of what life is, we first have tostate that life exists exclusively as the “  being-alive ” of discrete entities, which we call “ living creatures ” or  “ organisms. ” No life exists outside and independently of organisms; no independent  “ agent  ” makes inorganic matter alive. Life always means “  being alive. ” There is no entity “ life, ” which we can make the object of our science.Therefore, biology is not the “ science of life ” but the “ science of living entities ” in all their forms, aspects, andhierarchical levels. We can consider the living entities ashighly complex systems and “ life ” as the specific perfor-mance of these systems. This underlines the absolutenecessity of systems thinking in General Biology.The negation of a “ vital agent  ” independent fromorganisms is not a trivial step by any means. It implicatesa fundamental point of view in the discussion of the problem of life. Many cultural groups, philosophies, andreligions, for example, believed and believe in a vital agent,which also exists and acts outside of and independentlyfrom organisms. For Plato for instance, as already men-tioned, the soul is a distinct non-material entity, which bonds to certain objects and induces in them animate behavior. However, daily experience teaches us that such aduality does not exist. Life exists  —  as already mentioned  —  only as “  being-alive ” of highly complex, dynamic systemswith the fundamental property to autonomously maintainand replicate their internal organization. Each organismexists as a single, unique, spatiotemporally restricted entitywith a beginning and an end. Under present conditions onEarth, no organism comes into being spontaneously out of non-living matter. In every case, living entities derive fromliving entities: omne vivum e vivo (Lorenz Oken). Eachorganism has a unique, non-repeatable history. Becauseorganisms derive from other organisms (ancestors) and produce yet other organisms (descendents), a continuoussuccession of generations connects each present organismwith life ’ s srcin on earth.Cells as “ elementary organisms ” Despite the tremendous diversity of living forms in our world, scientists in nineteenth century discovered that all present-day living organisms are made up of one, some,thousands, millions, or billions of cells. The entiremetabolism takes place in cells, and all cells are derivedfrom the division into two of previously existing cells: Omnis cellula e cellula (Rudolf Virchow). Life is cellactivity  —  its uniqueness is the uniqueness of the cell.There are only two different types of cells (Fig.1), the primitive prokaryotic cell (protocyte) of the archaea and bacteria and the essentially more complex eukaryotic cell(eucyte) of all the other organisms (protista, fungi, plants,and animals). The latter is about a thousand-fold morevoluminous and more complex than the protocyte. Nointermediate forms exist between these two types of cellsthat would guide a gradual evolutionary inference betweenthe prokaryotic and eukaryotic state. The protocyte has nomembrane-bounded organelles. Its genome consists in theminimum case of a single, double-stranded, closed loop of DNA. In contrast, the eucyte contains organelles surrounded by double membranes, a nucleus with its contiguousendoplasmatic reticulum, a Golgi apparatus, and flagellawith a 9-+2-pattern of microtubule arrangement. During theinterphase, their hereditary material is concentrated in a set of complex chromosomes inside the cell nucleus.The whole cell is the most elementary unit that canmaintain life; it is the least complex thing that properlylives. When protozoan cells divide into two halves, onecontaining the nucleus and the other without, only the first can maintain life. A nucleus-less Amoeba is still able to eat and digest for some time. Later on, this capacity disappears,and the protozoan rejects the undigested food. Only cellfragments with an intact nucleus are able to regenerate thelost parts. The physiologist Ernst von Brücke characterizedthe cell as an “ elementary organism ” (Brücke1851), andmany influential biologists (Walter Flemming 1882, E. B.Wilson 1907, Frederick Gowland Hopkins 1913, andothers) agree with him that life should be considered asthe activity  —  or ensemble of activities  —  of whole cells andnothing less. This conclusion expresses on the cellular level 2 Naturwissenschaften (2009) 96:1  –  23  the holistic concept once formulated by Kant for theorganism as a whole. Below the cellular level, noindependent life is possible. Although some organelles,such as mitochondria and chloroplasts, undergo replication,this requires the functioning of the integrated cell. In tryingto define the essence of the living state (not of organisms!)fundamental for  all  living entities, we may confineourselves to considering life at its cellular level. When thefirst multicellular organisms appeared, life had alreadyexisted approximately 2.8 Ga. About three quarters of evolution up to now has taken place on a cellular level or,in other words, was cell evolution 1 .Viruses are the most abundant biological entities on our  planet (Breitbart and Rohwer 2005). There are 10 31  –  10 32 virus particles in the biosphere; this is at least one order of magnitude more than the number of host cells! Virus particles (virions) indeed contain genetic information (DNAor RNA), but they are incapable of growth or division bythemselves. They lack the machinery to generate energy or to synthesize their own proteins. They are obligate parasitesand depend on the host cell ’ s ribosomes to synthesize their own proteins. Therefore, extant viruses are not truly alive.They were generally considered to be fragments of livingentities that have lost their capacity for autonomousexistence, but we must own up to the fact that we reallyhave no sound knowledge of how the entire domain of viruses is organized, what the srcins of viruses are, andhow they evolve (Bamford et al.2005). Recently, Koonin et al. (2006) proposed an alternative hypothesis to thescenarios that describe viruses originating as genes that have escaped from cellular organisms. In their concept of an ancient virus world, “ the principal lineages of virusesand related selfish agents emerged from a primordial poolof primitive genetic elements, the ancestors of both cellular and viral genes. ” In the opinion of these authors, theemergence of substantial genetic diversity antedates theadvent of fully fledged cells. To explain the crucial step of compartmentalization in the primordial pool, a highlyspeculative model has been elaborated (Koonin and Martin2005). The assumption of a non-cellular  “ last universalcommon ancestor  ” of the three domains Bacteria, Archaea,and Eukaryotes, as favoured in this scenario, remains atopic of controversial discussion (e.g. Gogarten and Taiz1992).Last vital units below the cell level?  —“ life-as-things ” hypothesesThe assumption that single substances are the primaryvehicles of life has a long tradition beginning with the pre-Socratic philosophers. In the Middle Ages and earlyRenaissance, life was sometimes identified as a fluidsubstance known as liquor vitae . Felix Dujardin ’ s “ living jelly ” or  “ sarcode ” was later succeeded by the more generalterm “  protoplasm ” which was considered by many as the 1 This cell-as-elementary-organism theorem is not inconsistent withthe well-known fact that the totipotency of the zygote gets lost in thedescendants of the zygote during the ontogenesis of a multicellular organism. The cells become determined and differentiate into specifictypes of cells. This differentiation usually results from the differentialexpression of genes in the cell, i.e., from the differential regulation of transcription, posttranscriptional events, or translation but not from aloss of DNA or irreversible changes in the genome. It is onlyirreversible in certain types of cells. In many cases, differentiation isreversible under the right environmental circumstances. Transdiffer-entiation of one differentiated cell type into another type has beenshown to occur for instance during regeneration and in cells in tissueculture. Eukaryotic cellProkaryotic cell Fig. 1 Diagrams of thelarger and more complicatedeukaryotic (animal) cell ( left  )and the simpler prokaryotic cell( right  ). Only the eukaryotic cellshave a separate compartment (nucleus) that contains their DNA (left figure after Storchand Welsch2005, right figureafter Kaplan1972) Naturwissenschaften (2009) 96:1  –  23 3  material basis of life until well into the twentieth century.In the second half of the nineteenth century under theinfluence of the blossoming discipline of organic chemis-try, the notion of  “ last units of life ” below the cellular levelwas widespread among theoretical biologists: “  physiologicalentities ” (Spencer), “ lebendiges Eiweiß ” (Pflüger 1875), “ Bioblasts ” (O. Hertwig1906), “ Biophors ” (Weismann1892), “ Protomers ” (Heidenhain1894), or  “ Biogens(Verworn1903). All these “ life-as-things ” hypotheses baseon the effort to “ explain ” the specific properties and performances of living systems in terms of mysterious units,molecules, or aggregates of molecules. Nowadays, it is clear that no single molecule, no singlecomponent of the cell per se is alive. Chemists have learnedto synthesize any protein or any nucleotide sequence but, indoing so, have never created “ life. ” The “  birth ” of life onearth did not coincide with the first appearance of a certain protein molecule as the physicist Pascual Jordan believed. Neither is it true that life began with the appearance of thefirst nucleic acid strand in the primeval soup, which was ableto replicate and to mutate and thus became the subject of selection, as Kuhn and Waser (1982) once stated. If that werethe case, scientists would have succeeded in making artificiallife in a test tube many times over. We have to accept that life is the performance of complex internally organizedsystems and as such necessarily began as a minimal integralmultimolecular system. Translation and replication areconsequences of the total functioning of the whole.The role and importance of DNA is frequently exagger-ated. It is often uncritically elevated to the “ vital principle, ” the “ thread of life. ” What we must bear in mind, however,is that the DNA double helix can only fulfill its centralfunction inside a living cell. Replication requires not just energy but also the presence of several protein enzymes andsome complex precursors. The same is true of thetranscription of information from DNA to RNA and of the translation of the RNA sequence into the proper sequence of amino acids in the polypeptide chain. Trans-lation requires highly specific aminoacyl synthetases toattach the correct amino acid to the correct transfer RNA(tRNA), thus permitting the synthesis of polypeptide chainswith the “ right  ” amino acid sequence. This sequencedetermines at a given pH and temperature the three-dimensional structure (tertiary structure) of the polypeptidechain, which is accountable for the function of this protein. No one molecule, including DNA, catalyses its ownformation. There is no such thing as a “ genobiosis ” (Kaplan1972) on the level of genes! Numerous efforts (Joyce andOrgel1986; Joyce1987) “ to find an enzyme-free polynu-cleotide system able to undergo replication cycles bysequentially and correctly adding the proper nucleotide tothe newly synthesized strand have not yet succeeded ” (Kaufmann1996).Scientists who pretend that the riddle of life has beensolved by modern molecular biology are quite simpledeluded. Claims such as “ genes have created us body andmind; so when we know exactly what the genes look like,we will know what it is to be human, ” are absurd, asLowentin (1992) pointed out in his readable polemic. Lifecannot be associated with a single substance. All “ life-as-things ” views or positions are wrong from the beginning.Life is conditioned by certain substances but not defined bythem. It is in no way a “ thing ” ; on the contrary, it is action,it is dynamic, it is the performance of certain naturalsystems, which we call “ alive ” : “ life-as-action ” approach. “ Minimal ” cellsOver the last few years, much theoretical and experimentalwork has been done to determine the minimum set of genesnecessary and sufficient to maintain a functioning cellunder ideal conditions, i.e., in the presence of unlimitedamounts of all essential nutrients and in the absence of anyadverse factors, including competition. Morowitz (1967)calculated that the minimal cell may be about one tenthsmaller than Mycoplasma genitalium , the organism with thesmallest known genome size. The wall-less Mycoplasma has a cell diameter of 250 nm. That means that, in the caseof an intracellular pH value of 7.0, on average, only two protons can exist simultaneously in its plasma.  M. genitalium and Buchnera sp. (Shimkets1998) do not represent a type of ancestral cell but evolved from moreconventional progenitors by a process of massive genomereduction in connection with their life style (Islas et al.2004): M. genitalium is an obligate parasite in the humanurogenital system and Buchnera sp. an endosymbiont.Their life styles permit the direct import of severalmetabolites and essential compounds from the host and,consequently, the withdrawal of some synthesis activities.It is probably not wrong to suppose that the largelyunredundant genome of  M. genitalium comes close to theminimal gene set essential for maintaining life. The genomeof  M. genitalium consists of one circular double strand of DNA and has 580,074 base pairs (580 kb). Out of 487 protein-coding genes, Glass et al. (2006) identified only100 nonessential genes. The remaining 387 protein-codinggenes plus three phosphate-transporting genes and 43RNA-coding genes constitute the set of genes essential for the existence of this individual. Genes for electron transport and the citrate cycle are missing. Only one gene (enzyme)exists for the synthesis of amino acids. Gil et al. (2004), onthe basis of their work with Buchnera sp. and other organisms, proposed a protein-coding gene core of just 206 for a minimal bacterial gene set (Table1). Resultsobtained by other authors are close to those presented byGil and his co-workers. Two hundred to 300 genes are 4 Naturwissenschaften (2009) 96:1  –  23
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