This is a very densely written, and important book. It has taken me
          several months to read, on and off, and I am sure I've missed some of
          the points. But I have taken away much of interest. The theme is that
          biology is not merely a consequence of physics, but has a
          fundamentally important extra property: that of symbolic
          relationships. The title comes from the idea of relationships: a
          boat remains a boat if one (or indeed all) of its planks are replaced,
          even with planks made from different material: it is not a function of
          the objects that make it up, but of the relationships
          between those objects.
         p174.
          What makes the Delphic boat float is the
          nature of the relationship between its planks, not their
          physicochemical nature. Whether they are made of oak or pine or
          aluminum or steel is irrelevant to their function.  
        
        
         p280.
          Our priority should be studying the
          relationships that make up life, rather than remaining at the level of
          the objects themselves; and we should do this by looking into the
          nature of whatever it is that gives these relationships their
          permanence.  
        
        The "symbolic" part is that in biology, those
          relationships can be arbitrary (for example,
          the
            genetic code). They are consistent with the laws of physics, of
          course, but in some sense independent of them. The encoding, the
          symbols used, could have been different, and so are not deducible
          from, or reducible to, physics. Indeed, they have more in common with
          ideas of computation, or information processing, and Danchin pursues
          the relationship between cellular mechanisms and Turing Machines to a
          sophisticated level.
        
        The book is divided into five hefty chapters. The first two give the
          biological background of the various genome sequencing achievements,
          probably in more detail than you want unless you are a
          genome-sequencer. I would probably have given up sometime before
          chapter three (starting on p109), had I not been reading this because
          I'd read a shorter, fascinating paper by Danchin, and wanted to delve
          deeper. In summary, the first two chapters say that the genome is very
          complicated, very detailed, very big, that it has structure, but that
          structure is very messy, and that nearly everything you think you know
          about it (from kindergarten "Ladybird" biology to
          undergraduate studies) is untrue, by being highly and selectively
          oversimplified. Then we get on to the interesting stuff. Not that it
          gets any easier going, mind you. But stick with it; it's well worth
          the journey.
        
        Danchin reiterates that biology cannot be understood and explained
          in terms of outdated mechanical physical concepts.
         p109.
          life ... is not a mechanical process,
          and that even if we do not deny its deterministic character, what we
          can know about it does not enable us to predict its future.
          Life is simply the one material process that has discovered that the
          only way to deal with an unpredictable future is to be able to produce
          the unexpected itself. 
        
        Physics is about identical objects, but by the time biology is
          reached,  distinguishability, identity, relationships become key.
         pp246-9.
          Generally speaking, it is fairly easy to
          build up a picture of the physical world, and to explain it in terms
          of a combination of simple principles 
, because physics is
          concerned with reproducible objects that cannot normally be
          distinguished from each other as individual entities. ...
          
    
          
    Chemistry is more complex than physics,
          and begins when atoms combine. 
          
    In chemistry, two individual examples of
          the same object are usually indistinguishable when they are observed
          under similar conditions. However, there is one particular
          characteristic, quite rare in physics but almost universal in
          chemistry, which clearly illustrates the importance of the
          relationships between the parts that make up the object in question.
          There are structures that are identical in every respect but their
          symmetry, and the link between chemistry and biology was formed after
          a distinct bias was observed in the symmetries of chemical products
          produced by living things. ...
          
    ...
          
    ... It is impossible to distinguish
          between two atoms of the same object, in the same state, but it is
          possible to distinguish between two individuals of the same species. A
          species is a population of individuals, a class of objects each with
          its own identity. This is true even for microbes like bacteria: a look
          at the way they swim will show that two individual bacteria, which
          look the same and are genetically identical, can very often be
          distinguished by their behavior. It is also true of cells, the "atoms"
          or units of life. 
        
        Biology are characterised not just by the (individual) objects
          involved, but by the relationships between those objects.
         p131.
          ... in biology. No object exists in
          isolation---or if such objects do exist, it is less important to know
          them, because their isolation means that they have little to
          contribute to the phenomenon being studied. It is precisely
          relationships between objects that are at the heart of life. So we
          know in advance that, among the things we need to discover, there are
          relationships that have a particular form, whose implementation
          enables vital functions to be expressed, such as the regulation of
          gene expression. Of course we do not know exactly what these
          relationships are a priori, but we know that they do exist. We
          do not know what form they take, but we know that they demand a
          certain proximity between objects, whether in terms of space or time
          or other forms of mediation. 
        
        Once we realise that relationships are key, we can use this to make
          progress. We can exploit the structure of the relationships to
          investigate new possibilities, via (abstract) neighbourhoods of
          related objects.
         pp130-1.
          Effective as it is, this
          hypothetico-deductive method has the drawback of being able to refine
          only knowledge that we already have, without giving us a way of
          forming hypotheses that are both new and pertinent. How can we find
          original ideas, but with an originality that is not alien to what we
          are studying? ... How can we advance inductively, how can we explore
          upstream, and not downstream as with deduction?
          
    ... We will consider only one approach,
          because it is particularly effective in the case of genomes: that of
          induction by exploring the neighborhood of the objects we want
          to consider. The idea behind this approach is that each object exists
          in relationship with other objects. ...
        
        Here, Danchin takes the fundamental object to be the gene.
          Neighbourhoods are then "similar" genes. Importantly, 
          similarity can be defined in a diverse range of abstract spaces. This
          is where biological intuition and knowledge can pays off: by focussing
          investigation in biologically "meaningful" such spaces.
         pp132-4.
          Inductive exploration consists in
          finding all the neighbors of each given gene, as a starting
          point.
          
"Neighbor" is to be understood here in the broadest
          possible sense. It is not only a geometrical or structural notion.
          Each neighborhood will have its own particular light to throw on the
          gene of interest, and will provide clues for researching its function.
          ... One natural kind of neighborhood is proximity on the chromosome.
          ...
          
    The evolution of species proceeds by
          variation on ancestral themes. Consequently, many genes are descended
          from common ancestors, and just as children look like their parents,
          so genes, or more often their products, have points of resemblance.
          This is a rewarding kind of neighborhood to consider. ...
          
    There are many other ways of finding
          neighborhood. In particular, a gene may have been studied by
          researchers in laboratories all over the world. For one reason or
          another, the gene may have properties that have made these researchers
          associate them with other genes, so it is worth looking for a gene's
          neighbors in the sense that it is mentioned in their company in the
          scientific literature. ...
          
    A gene's similarity with others can also
          come from similar physicochemical characteristics of their products
          ... Similarities can be local rather than global, .... Similarity
          might also be a matter of the absence, rather than the presence, of
          certain motifs ... Giving free rein to the imagination can help us
          discover other kinds of neighborhood ... Neighborhood can be
          structural, if the products of different genes share the same cell
          compartment ... But there are also kinds of functional neighborhood.
          As the molecules involved in metabolism undergo interconversions,
          there are enzymes that are neighbors because they use the same
          substrate, produce the same product, or follow one another in a
          metabolic pathway.
          
    Finally there are more complex kinds of
          neighborhood, and studying these can bring particularly rewarding
          results. To take up the example ... of bias in the use of the genetic
          code, we find, for instance, that two genes can be neighbors because
          they use the code in the same way. It is interesting to study all the
          genes surrounding a given gene, in the cloud of points that describes
          the use of the genetic code in all the genes in that organism. When
          this is done, we begin to discover some very unexpected properties of
          genome texts. 
        
        This emphasis on relationships requires experimental setups where
          they can be investigated: setups where only the objects can be
          investigated are inadequate.  In particular, spatial and structural
          relationships need to be considered. This has consequences:
         p137.
          the genome text and its meaning are
          closely connected with an architecture, which is real even if it is
          minuscule. One consequence of the domination of biology by
          biochemistry, which favors the study of objects in isolation, has been
          to encourage an image of the cell as a miniature test tube. In this
          view, the concentration of molecules is seen as uniform, and the
          standard thermodynamic approach is normally used to measure the course
          of biochemical reactions, as if that were what happened in the cell.
          But this is very misleading.  
        
        The existence of spatial cellular architecture has consequences on
          the structure of the genome:
         p151.
          there is a map of the cell in the
          chromosome. Genes are not randomly distributed in the genome text;
          their position relates to their mode of expression, depending on the
          nature of the environment, and to the location of their products in
          the different cell compartments.  
        
        The existence of temporal cellular architecture also has important
          consequences:
         pp156-7.
          Up to now I have spoken only of the
          spatial organization of the cell, and of its very probable strong
          connection with the spatial organization of the genome. But of course
          we must add the time dimension to this. ... It takes a certain amount
          of time to transcribe or to translate a gene. ... Clearly, adding a
          section to be transcribed introduces a timing element, which can have
          an important effect on the cell's dynamics, simply because of its
          length, without the corresponding nucleotides' necessarily having
          any particular meaning. ... comparison of related genomes should
          reveal regions where the length is preserved, although the
          sequence is not. 
        
        If this book were only about the importance of relationships and
          functions, it would be interesting. But there is an additional crucial
          component. Not only should we think in terms of functions, but there
          is a level of indirection, a symbolic nature, to the
          way the material objects represent the functionality.
         p110.
          life's exploration of reality has been
          based on symbolic transposition. Unlike physical or chemical objects,
          biological objects are more than just a site where actions occur; they
          represent functions. Very often they no longer correspond to
          them directly. ... The nucleic acids and the proteins, which
          are the very foundation of the objects, relationships, and processes
          that make up life, are made from completely different chemicals from
          each other, and the DNA of a gene that codes for the synthesis of an
          enzyme has absolutely no biochemical connection with that enzyme's
          function or shape. 
        
        
         pp123-4.
          I would like to reemphasize the
          arbitrary character of the association between a function and the
          control of its expression. This is a first level of an aspect we
          normally call "symbolic," when we are talking about human
          communication. This arbitrary, symbolic character allows the cell to
          manipulate associations situated at a high hierarchical level, between
          apparently unrelated functions. Life has made systematic use of this
          remarkable phenomenon. This is what makes it possible to introduce
          relationships between physical parameters, as well as chemical ones,
          into gene expression. ... This symbolic aspect is typical of the most
          important biological functions.
          
     
 This model evokes a way of
          representing the world that is profoundly different from the way we
          usually account for the physical world. It adds abstract symbolic
          relationships to the objects of chemistry and physics. The difficulty
          of understanding this symbolic aspect explains why biology in general
          and what we call "molecular" biology in particular are the
          subject of so much misinterpretation and misunderstanding. 
        
   
        
        It is this symbolic abstraction that makes life not deducible
          from physics (although it is consistent with physics). It
          is more than mere physics. He has disparaging things to say about the
          current enthusiasm for self-organised complexity:
         p174.
          What governs life is 
 absolutely
          not outside physics---it respects all its laws; but a law such as the
          genetic code cannot be simply an automatic consequence of the
          laws of physics. This is what I am summarizing when I say that it
          cannot be reduced to physics.
          
    
 many modern thinkers 
 want
          life to be in itself an unavoidable consequence of things. This
          creates a very strong tendency to attempt to represent life not just
          as a possible and predictable result, but as an inevitable, logically
          derived consequence of the laws of physics. This reduction of life to
          the physicochemical world has culminated in studies which postulate
          more or less elaborate connections between various dynamics of simple
          physical systems, and which are summed up by an expression that is as
          fashionable as it is vague and inappropriate, self-organization.
          By sheer tricks of language and abuse of metaphor, the authors of
          these studies seek to "explain" life in terms of the complex
          behavior of oscillating chemical reactions, or the spontaneous
          appearance of organized structures on different levels. This painfully
          reductionist attitude completely fails to recognize what is the basis
          of life, symbolic abstraction. The objects that make
          biological functions happen often have no mechanical relationship with
          them; they are only their mediator, their symbol. 
        
        
        He really doesn't like complexity theory, and the physical
          kind of dynamical systems resulting in catastrophes, bifurcations and
          oscillations. It's not enough:
         p240.
          We can only be astonished that,
          confronted by the marvelous variety and sheer gratuity of
          insect forms, scientists have not more often been inspired to explore
          the mode and timing of their production by starting from reality
          itself, rather than by hiding it under a veneer of simplistic,
          reductionist ideas.  
        
        Clearly reality lies between "just complex physics" and "arbitrary
          symbolic representation". The chosen symbols cannot be totally
          arbitrary: they need to (and do) obey laws of physics. But
          self-organised complexity shows us that those  laws are potentially
          richer (and more structured) than realised. Physics permits,
          constrains, determines certain classes of symbols, but does
          not constrain the actual ones chosen. Even this constrained space is
          vast, and the realised actuality is just a small, arbitrary subset of
          this.
        
        So if  physics doesn't determine the symbols used, what chooses
          them? It's that novel law that appears at the level of  biology:
          evolution.
         pp175-6.
          The complementarity that exists between
          the material world produced by physics and the symbolic world produced
          by natural selection can be explained by the logic underlying the
          self-reference or recursiveness produced by the genetic code. The laws
          of physics and natural selection operate as complementary constraints:
          the laws of physics describe the unchanging part of phenomena, those
          properties that living organisms cannot in principle dominate or
          control. The theory of evolution through natural selection seeks to
          explain the way in which living organisms do, however, progressively
          improve their control over those laws.  
        
        This evolved symbolic mediation allows a relationship between one
          kind of regime and a completely different one:
         p284.
          The role of the coding process is to
          make the transfer from a chemical world in which, broadly speaking,
          the objects (in this case segments of DNA) can be regarded as
          exploring only one dimension of space, to a world in which other
          objects, proteins, explore it in three dimensions, or even four if we
          include time, because proteins can change their shape.  
        
        How does this "accidental" relationship arise?
         pp309-10.
          the idea of a cause-effect relationship
          between the structure of biological objects and their function is so
          well established that it motivates the work of hundreds of thousands
          of scientists around the world. But I have tried to show that the
          causal relationship between the architecture of biological objects and
          their function is often arbitrary and accidental. ...
          
    
 adaptation occurs a posteriori,
          and not a priori, because there is no final cause. The living
          being that survives a critical situation did not know in advance what
          would save it, but, having found the solution, and because it has
          survived, it passes that solution on to its descendants, thus
          preserving and multiplying it. Such a solution is always some way of
          establishing a link or relationship between processes, events, or
          objects. The link is part of a structure, but it was the function that
          revealed it, so it is the function that ensures that the structure is
          retained. Function does not create structure, but discovers it when it
          is needed.  
        
        So the laws of physics are important in biology, but not always in
          the same way they are in the domain of physics itself. For example,
          that old bugaboo,  the second law of thermodynamics and the increase
          of entropy, looks different through the lens of biology, where a
          statistically "representative" ensemble is neither
          realisable (because of the size of the state space) nor explored
          (because of the selective effect evolution).
         p191.
          an increase in entropy, in accordance
          with the Second Law of Thermodynamics, simply means that objects will
          spontaneously explore all the environment accessible to them
          ... In this context, irreversibility 
 is simply the expression
          of the fact that the total "space" of states and positions
          available to the objects considered can only increase, in the absence
          of any ad hoc constraint ...
          
    However, we must insist that not
          everything is possible, because time is also a crucial
          consideration. It is meaningless to consider states that are
          theoretically possible but are inaccessible for lack of time. Once the
          number of objects considered is over a certain minimum, the number of
          possible states is so vast that they cannot all be explored. This is a
          fundamental flaw in the statistical model, right from the outset, and
          it is important to bear this in mind when considering what happens in
          real cases, but unfortunately this is almost never done. Entropy is
          therefore nothing but a measure of the extent to which everything that
          can be occupied is actually occupied, and an increase in entropy only
          accounts for the exploration of all this new space (perhaps we should
          say its creation, to mark the fact that it represents a
          transition from a virtual state to a real state, since the nature of
          the initial space was different from the nature it acquires when
          explored, because of the possibility of new interactions). 
        
        
        Having made the point that biology adds a layer of symbolic
          functionality and control on top of physics, he draws the analogy with
          computation, or information processing, that also has these two
          layers. (He is emphasising here that the functionality needs to be
          considered in addition to the physical implementation; ironically in
          computation the functionality is primary, and the fact of a physical
          implementation is often neglected.)
         pp212-3.
          Turing's 
 approach distinguishes
          between symbolic processes, which control the interactions between
          objects, and the physicochemical nature of the underlying processes.
          Provided that the machine can actually exist as a material reality,
          its physical nature is not important, so long as it can establish the
          necessary relationships between the strings of symbols. This duality
          of the symbolic and the physical nature of things is a characteristic
          feature of living organisms: they are compatible with physics, but
          they cannot be deduced a priori from its laws. ... Physics
          represents the inevitable and universal constraints on things, whereas
          life will always try to take control.  
        
        Danchin makes the point that the physicochemical nature of the
          underlying processes can be separated from the symbolic processes both
          in biology and in computation. Laughlin
          points out that when (emergent) properties are  insensitive to the
          substrate (as in this case) you can't draw conclusions about the
          substrate from them. So we shouldn't expect to be able to draw
          conclusions about the biochemical substrate from observing the
          biological processes. Which is good -- it explicitly admits the
          possibility of life based on other substrates.
        
        So this control layer is (somewhat) independent of the underlying
          laws of physics. We design  this control into our computers;
          life evolves this control:
         p219.
          It is precisely because the cell
          functions using just local, basic operations (of the type
          connect/disconnect, or presence/absence) that life is possible without
          there being any external causality. ... It is the result of
          the succession of a very large number of simple events, which became
          organized essentially because this worked. The only systems
          (organisms) that have survived are those which were able to bring
          together relationships that were locally extremely simple and
          probable, and to combine them in the structured way we know today.
          Selection by existence (which is merely a principle of
          stability) is an infinitely powerful way of discovering precisely what
          is stable enough over time to be able to survive in a given
          environment. One property of the stability principle is systematic
          evolution toward ever-increasing control over the unavoidable physics
          of the world. And the object of biology is to discover the principles
          of this evolution toward increasing stability. 
        
        One mistake people often make when pursuing the computational
          analogy is to assume that the program is all there is -- an approach
          that developmental biologist Jack Cohen
          for one strongly decries. Danchin does not make this mistake, but
          explicitly brings in the role of the environment, providing data, and
          providing the context where the symbols gain their  meaning:
         p270.
          there is no one-to-one correspondence
          between a gene and its expression. In particular, a gene may or may
          not be expressed, depending on the cell's environment. This is obvious
          in multicellular organisms such as mammals---a skin cell does not
          express the same proteins as a brain cell, and when it divides it
          produces more skin cells, not neurons, despite the fact that both of
          them must have the same DNA content, and therefore the same genetic
          program. This same program can thus produce different outcomes,
          demonstrating that the external environment is an intrinsic part of
          the way the program is expressed, because it contains the data
          that determine the outcome. A cell can be defined as a machine that
          puts the genetic program into operation according to the data
          provided by its environment. 
        
        
         p176.
          The laws specific to biology are able to
          exist because of a particular aspect of their role: they do not affect
          the nature of physical and chemical objects, but govern the
          relationships that exist between certain objects. These objects have a
          meaning, which is connected to their function in the
          physicochemical processes of life. This gives them an original order
          of abstraction, quite distinct from what physics tells us: .... This
          space-time plan, this program that links together the material objects
          of physics in order to compose a living organism, is an abstraction.
          However, it cannot be regarded as arbitrary or as existing in itself,
          without the material support of the physicochemical objects of life.
          The links in question are not just any links; they have original
          properties which we must try to understand. They are the result of a
          continuing selection, in the normal course of an evolutionary
          process that can be measured by the survival and existence of the
          organisms in question.  
        
        Danchin takes the computational analogy further than most. For
          example, he considers the Kolmogorov (algorithmic) complexity of the
          genome, and what it might tell us:
         p224.
          compress the sequence 
 to
          understand how the sequence has been generated in the course of
          evolution. A genome is not a random piece of DNA, but the result
          of evolution through duplication, recombination, mutation, and so on,
          and all these processes could be described in terms of algorithms.
           
        
        Here again, time is of crucial importance: an algorithm is no good
          if it takes too long to execute! This relates to a complexity in terms
          of algorithmic, or logical, depth:
         p229-30.
          Given a particular sequence, we will
          want to look for algorithms that will generate it, but we must always
          keep in mind the parallel importance of evaluating the program's run
          time. ...
          
    ... we should never speak of what is
          potential in the same way we do of what is real. It may be
          meaningless to speak of potential, because it may be impossible to
          realize that potential explicitly in the time available. 
        
        Danchin goes all the way to Godel and the Halting Problem:
         p232.
          Although it is not possible to go into
          detail here, the connection between the halting problem and the finite
          character of genome texts, if they are considered as algorithms,
          suggests that their formal properties are worth studying in detail, as
          a source of mathematical conjectures. By the very fact that they
          exist, they prove that it is possible for an algorithm to have a
          critical structure, a critical depth, which is related to
          their capacity to reproduce themselves in a given environment, while
          at the same time producing the machine that runs them. 
        
        It is a real pity he doesn't go into further detail -- it was
          getting interesting!
        
        His dislike of the modern application of physical complexity science
          to biology resurfaces, and he instead describes developmental systems
          in terms of construction via algorithmic description:
         p239.
          Because many reproducible structures
          exist in physics (branching structures, cells, circles, spheres, and
          so on), many thinkers looked to certain physical or mathematical
          principles to explain the genesis of forms in biology. According to
          these ideas, life has simply rediscovered the general principles that
          govern physics 
. This horribly reductionist, Platonist attitude
          prevailed for a long time. It is still sometimes popular among those
          who know nothing of biology, because they fail to understand two vital
          things: first, that the functions which construct, or which ensure
          control, have an essentially symbolic role; second, that the important
          form that is preserved in organisms is not the final shape, but the
          form of the algorithm that constructs it. 
          
...
          
Life certainly uses the principles of physics 
 but just as
          a basic vocabulary, a set of elementary processes, organized into a
          program, not as the main construction principle of life. 
        
        
        Algorithms provide iteration and (spatial and temporal)
          combinatorics, which lead to a biological-style complexity of
          developmental processes:
         p241.
          The processes are all extremely simple
          in themselves, but the way they are strung together is complex,
          because it is compartmentalized in space and time. Although the
          diversity of the control elements is limited, their combinatorial
          possibilities are extremely rich.  
        
        
         p243.
          What preexists is not the organism
          itself, but the preformation of a development algorithm. 
          what heredity passes on is not the form, but its construction program.
          The successive expression of control genes, activated or
          suppressed one after another, enables morphogenesis to take place
          (while respecting and making use of the constraints of physics, of
          course, such as the rules of overall symmetry).  
        
        Messing about with this developmental program can have macroscopic,
          structured effects, such as growing legs where antennae should be.
          Even:
         p244.
          The organization is so hierarchical that
          modifying a single gene, Lim-1, produces animals without a
          head.  
 
        
        Even though all organisms have a control level, it can be more
          sophisticated in sme than in others:
         pp244-5.
          there is a significant difference
          between mammals and insects. In mammals, instead of a single linear
          arrangement corresponding to the layout of the insect, there are four
          linear arrangements, arranged exactly as in the fly, and also
          corresponding to the animal's development from the tail to the head.
          ... This discovery accounts for mammals' greater complexity compared
          to insects: the construction algorithm is produced by the combination
          of four homologous procedures working simultaneously. It also explains
          how the segmented character so visible in insects (mostly at the
          larval stage, of course) is much weaker in mammals. We can also
          definitely see signs of evolution by duplication of the
          genetic program, which suddenly makes new properties appear---the
          effects of duplication are not only quantitative, they also create new
          relationships de facto.  
        
        In programming, it is important to be able to remove old objects as
          well as create new ones. The same is true of the developmental
          approach: scaffolding is erected, then removed:
         p242.
          During this development, certain cells
          are programmed to disappear, leaving room for other cells which are
          differently differentiated, and which could not otherwise have
          developed. It is thus important to note that development includes a
          significant element of absence, as distinct from presence, so
          that a "negative" form plays a role in development that is
          just as important as that of a positive presence.  
      
         
        
        This focus on the processes and relationships between objects within
          the cell leads to a definition of life here in terms of four features:
         p253.
          The processes that make life are metabolism,
          compartmentalization, memory, and manipulation.
          Metabolism and compartmentalization are organized by small molecules
          (comprising a few tens of atoms, with a carbon skeleton), whereas
          memory and manipulation are controlled by nucleic acids and proteins,
          so the scale of their basic components is that of macromolecules  ...
          Two spatial scales are thus interlinked in all living processes, which
          operate on a mesoscopic scale, intermediate between our
          macroscopic world and the microscopic world of atoms. This is the
          scale that is revealed in the geometrical program superimposed on the
          genetic program in the genome.  
        
        This does not fully carry over into the computational analogy:
         p253.
          Reconciling all these processes has
          seemed so difficult that ... at the conceptual level, when comparisons
          have been made between life and Turing machines, the general
          principles for the construction of a self-replicating machine have
          nearly always overlooked the need for compartmentalization and
          metabolism.  
        
        This definition of life might seem to lead to a clear answer to the
          problem of viruses, but it is, of course, never that simple:
         p254.
          This means that organisms such as
          viruses, which do not metabolize, cannot be considered to be
          straightforward living organisms. They must be studied for what they
          are: pure parasites, a memory that perpetuates itself at the expense
          of a genuine life, that of the cell they have infected. Of course they
          are not similar to the usual non-living matter found on the Earth;
          they seem to be artifacts created by life 
 
        
        It might seem that 300-odd pages is a long time to say "life
          has evolved symbolic relationships between its objects, and has an
          algorithmic development program". But there is much more to it
          than that. The thesis  is backed up by detailed biological
          explanations, juicy physics and computational explorations, and
          interesting excursions into the philosophy of science. For example, he
           has some important things to say about the practice of (biological)
          science. In particular, on the important role of  models, theory, and
          abstraction in science, when we need to move beyond "stamp
          collecting", beyond observed phenomena, he says:
         p124.
          It is difficult to connect the text of
          genomes with biological functions. Knowing the text of a gene,
          predicting the sequence of the protein it specifies, visualizing its
          architecture, does not directly give us its function. The best we can
          do is to modify the gene or inactivate it and to study the genetically
          modified organism. But then we are faced with the difficult situation
          of studying phenomena 
 What is the best way forward? How should
          we interpret what we observe, and avoid taking our wishes for reality?
          Unlike in a number of domains of physics, where phenomenology is
          already well established and the theoretical, a priori
          approach is highly developed, we are not in a position to make a model
          of what we want to observe according to the criteria I have outlined.
          First we must observe and account for a phenomenon: growth under
          certain conditions, use of a particular molecule, sensitivity or
          resistance to a particular variation of a physical parameter. Simple
          phenomenology, because of its approach in which observation is only
          very loosely connected to a well-defined and delimited theoretical
          corpus, is on the borderline between science and an unstable form of
          thought, often close to a kind of primitive magic. This is not often
          recognized, but it explains why a large part of scientific work, even
          work that is institutionally recognized, is in fact of very little
          value in advancing scientific knowledge. It also explains the
          existence of many activities in the field of biology that are close to
          ignorance or even fraud. 
        
        This is a passionate book. It is a translation from the French, and
          in the acknowledgements he thanks his translator for
          making the transpositions required by
          the move from a Latin culture to an Anglo-American one. On the
          whole, this succeeds, but I feel there is still a French style peeking
          through in places, particularly in the philosophical stance. This is a
          good thing; it would have been sad to lose this flavour in the
          translation. 
        
        Danchin ends on a slightly depressed note, with references to 9/11,
          and the smallpox virus,  but I think there is optimism in the
          observation:
         p325.
          what we create cannot be reduced to what
          we are
        
        Recommended -- but expect to take some time over it.