Adami, Christoph. 1998. Introduction to Artificial Life, with accompanying CD-ROM package, Springer (Telos)-Verlag, New York, ISBN 0-387-94646-2, 374 pp., $59.95.
The book begins with a Preface written by the author and it is followed by: a section entitled Contents of the CD-ROM; 11 chapters; Appendix (entitled The avida User's Manual with sub-sections A.1 through A.11); a five-page Glossary; References (including nine by the author-- three alone-- totaling 143, and including others such as: Bak, 1996, How Nature Works: The Science of Self-Organized Criticality, Springer-Verlag, NY; Bartel and Szostak, 1993, Science 261: 1411; Kock, Ann. Rev. Microbiol. 50: 317; McKay et al., 1996, Science 274: 924; Morowitz, 1992, Beginnings of Cellular Life, Yale University Press, New Haven, CT; and, Wright and Joyce, 1997, Science 276: 614); and, Index (14 pages). A Registration Card is enclosed since the field is fast-moving and updates and changes are expected. The chapters are: 1. Flavors of Artificial Life; 2. Artificial Chemistry and Self-Replicating Code; 3. Introduction to Information Theory; 4. Statistical Mechanics and Thermo-dynamics; 5. Complexity of Simple Living Systems; 6. Self-Organization to Criticality; 7. Percolation; 8. Fitness Landscapes; 9. Experiments with avida; 10. Propagation of Information; and, 11. Adaptive Learning at the Error Threshold.
The avida software is provided for Windows95/NT and UNIX platforms. "Avida is the name of the Artificial Life 'platform' --- for experiments by the ALife group at Caltech (Pasadena, CA)--- . --- Avida is the result of an attempt to construct the most simple system that displays the basic properties of life. Simply put, avida is a population of self-replicating strings of computer-code subject to random mutations, adapting to a complex information-rich landscape." (See xvii - xviii.)
In the Preface (page vii), Adami asks: " What makes living systems live?" In the following paragraph he points out that the physical world yields to analysis, "because we can deconstruct complex physical systems and study aspects of them in isolation. Such an approach appears to be hopeless as far as living systems are concerned. In almost all cases, a deconstructed living system is no longer alive." What does he mean by "In almost all cases?" I can not be the first to point out that there is no such example of a deconstructed-reconstructed cell (whether at the prokaryotic or eukaryotic cellular level)! In every case, deconstruction of those cells results in their death! But, if you are willing to open your mind to protocells self-assembled from thermal proteins, they can be constructed (self-assembled), deconstructed, and reconstructed (often)!
It is going to be a difficult review since Adami does not cite Sidney W. Fox (and/or associates). Students in the origin-of-life sciences would expect Oparin and Haldane to be cited somewhere in this book (Adami does cite them: Oparin, 1938, The Origin of Life, Macmillan, NY; and, Haldane, 1929, The Origin of Life, Rationalist Annual). Miller also is cited (1953, Science 117: 528). Most students also like to read Miller and Urey, 1959 but it isn't cited. Eigen is cited (seven times, --- three times as sole author---; from 1971 to1989). Where is Orgel's work? Of the many researchers in the field, the contributions by S. W. Fox and the many who have worked with thermal proteins and protocells therefrom could have been a great help to the ALife group, possibly influencing their model. These cells are the "simplest" living cellular units. To be more pointed, these are the simplest units of Domain Protolife.
Adami's model ("the simplest living system") is a "precursor to all living systems here" and it "was replaced by much more complicated ones over three billion years ago." He does not make the hypothesis that pre-prokaryotic cellular life is still being formed by self-assembly. The synthesis of thermal proteins and self-assembly of protocells that exhibit all of the attributes of life should not be set aside by the ALife group. After all, students in introductory biology classes for non-science majors using Enger and Ross, 1997, (Concepts in Biology, eighth edition, WCB Publishers., Dubuque, IA) as their textbook, review the contributions of Oparin and Fox. Of the latter, they say: proteinoid microspheres (protocells) are "double-boundary" structures. These boundaries "exhibit some membranelike characteristics." These protocells "swell or shrink depending upon the osmotic potential in the surrounding solution" --- and "contain some proteinoids that function as enzymes. Using ATP as a source of energy, microspheres can direct the formation of polypeptides and nucleic acids. They can absorb materials from the surrounding medium and form buds, which results in a second generation of microspheres. Given these characteristics, some investigators believe that microspheres can be considered protocells, the first living cells."
The protocells seem to fit Adami's model even if he is not saying so himself. To learn more about the general principles, maybe the protocells of thermal proteins should be used in their studies as a comparison to avida results. Some researchers and/or teachers think that Fox has synthesized artificial cellular life rather than a functional protocell. They do not think of life not described by the five kingdom classification system (life as we know it). I don't expect many in the ALife group are ready to accept protocells as the smallest units of life in Domain Protolife (a life form we are beginning to know).
The Thermal Protein-First Paradigm (Pappelis and Fox) for the origin and early evolution of life [proposed in 1993 at the Illinois State Academy of Science Annual Meeting, on this campus; at the ISSOL meeting in Spain, 1993; at the ACS meeting in San Diego, 1994; at the Centennial Celebration of the Birth of A. I. Oparin (Russian Academy of Sciences, Moscow, 1994), at a similar celebration at the International Centre for Theoretical Physics, Trieste (1994); and, at subsequent meetings at Trieste(1996, 1997)] received strong support from researchers who were familiar with the work Fox and associates (since the 1950, some 380 manuscripts and nine books). The presentations placed a strong emphasis on replacing the old question ---"which came first, proteins or nucleic acids--- the so-called chicken-egg problem of the origin-of-life sciences" (see Eigen's version of this in Adami's book, page 139) and with protocellular evolution (protocells of thermal proteins, having evolved oligo-peptides and oligo-nucleotides, etc. in the metaprotocell phase of protocell evolution, enabled the emergence of prokaryotic cells and, later, eukaryotic cells. Essentially, this is stated in Fox,1988, The Emergence of Life: Darwinian Evolution from the Inside, Basic Books, Inc., Publishers, NY (see also, Pappelis, 1997, Studyguide for History of Biology 315-2: Individualized Learning Program, Southern Illinois University at Carbondale, Carbondale, IL, http://mccoy.lib.siu.edu/projects/bio315.
The "general principles of the living state" sought by Adami are already available and describe protocells of thermal proteins. Could this protocell be the one that Adami seeks-- the "protean cell" that "gave rise to life on earth (the speculative RNA world), putative ancient life on Mars, or those worlds in which information is coded in binary strings compiled to programs that have the ability to self-replicate?" (Page viii.) The Thermal Protein-First Paradigm is proposed as a universal process that gave and gives rise to life. It should be understood that thermal proteins are branched--- not strings.
It is in the next statement that we see the trouble ahead. Adami sent us to read Langton, 1995 (Artificial Life: an Overview, MIT Press, Cambridge, MA). I know the book. That will have to be another book review.
I agree with Adami; what we "see" (attribute exhibited by cells) is life! We assume that these attributes are "rooted" in physical /chemical laws and, thus, can be understood by those who are trained to use methods in these fields. But I disagree with Adami. The "particular" system is not hidden! Nor is it "obscured by the difficulty to perform dedicated experiments." (See Fox, 1995, To cellular life and neurocellular assemblies, in Evolutionary Biochemistry and Related Areas of Physiochemical Biology, B. F. Poglazov, B. I. Kurganov, M. S. Kritsky, and K. L. Gladilin, eds., Bach Institute of Biochemistry and ANKO, Moscow. pp. 161-175; Pappelis and Fox, in the same book, Domain Protolife: The protocell theory, pp. 151-159; and, Fox, 1997 in this web-site, Symposium Article, published in the Harbinger Vol. XV 5/27/97-- My Scientific Discussions of Evolution for the Pope and His Scientists). We have added additional points to these ideas (see recent publications cited on this web site).
Adami (page ix) states that his book "has grown out of lectures given to advanced undergraduate- and graduate-level students in Computation and Neural Systems and in Physics at Caltech since 1995." The course, History of Biology 315-2 at SIUC has emphasized the origin of life for the passed ten years (since S. W. Fox came to this university for a three-month visit in 1988 that lasted into 1993). The students in this course are a mix from biology, chemistry, physics, history, and computer science. Just as one would predict, they take the entire course to review the past 200 years of research in this now fast-moving field. We are very interested in Adami's book, especially the early chapters and the chapter overviews. As for myself, I couldn't put the book down. I was ready to go to Pasadena to ask permission to join the ALive group, and split my time in California with that group and J. W. "Bill" Schopfs seminar group at UCLA (hopefully, also hearing about Jim Lake's progress).
I see (page 1) that the bias in Adami's book is very great! "Scientists have not achieved, or dared to achieve, the construction, or synthesis, of life from the nonliving materials." I am waiting to see our 1997 presentation in print soon (Pappelis, A., S. W. Fox, R. Grubbs, and J. J. Bozzola. 1997. Animate protocells from inanimate thermal proteins: Visualization of the process. Trieste Conference on Chemical Evolution V: Exobiology; Matter, Energy and Information in the Origin and Evolution of Life in the Universe. September 22-26. International Centre for Theoretical Physics, Trieste, Italy). We have two other presentations in that volume (Kluwer Academic Publishers, J. Chela-Flores and F. Roulin, eds.). We also present a new set of terms to describe the transfer of information from thermal proteins to DNA. It should make ALife group members stop for a few moments. I can send these to the ALife group for discussion.
In Box 1.1 (page 5) Definitions of life, Adami presents reasons why the physiological, metabolic, and biochemical definitions alone are not as good as the genetic definition (evolution) as the central defining characteristic of living systems. "An even more general approach is the thermodynamic one, which attempts to define living systems in terms of their ability to maintain low levels of entropy, or disorder, only."
Since thermal proteins in protocells are simultaneously the boundary with wall-membrane structure and functions [such as biochemistry = metabolism using multizymic activities; reproduction by budding, etc.; inheritance; transducer of light to chemical bond energy (ADP + Pi + light yields ATP); and, converter of light energy into membrane potential spike trains], we say that we agree with Adami and his concept: a "best" character must be replaced by the "collected properties" expressed simultaneously. On page 6, Adami has moved to that idea as he states: his "principle abandons the idea of life being a property of any single object." --- " --life is an emergent, rather than atomistic, phenomenon." The thermal protein protocells are of the range Adami expects for cellular life (thanks to his reading of Kock---- 0.3 micron to 10 or more microns). Our concept of what protolife must achieve on Earth (through evolution) is based on the recent work of others; i.e., we accept the minimum number of genes to drive a prokaryotic cell as 256 and propose (in press) how that was achieved through protocellular evolution.
It becomes clear that my students will spend many hours reading this book as an example of a good group being led down a difficult road (trying to understand how the RNA world could lead to cellular life). On page 22, Adami comes to our point we present in the unified theory called Thermal Protein-First Paradigm. His point: "The belief that self replicating RNA may have been encased in simple cell membranes made of lipid bilayers has spawned research in the possibility of simple self-replicating compounds, the 'core-and-shell' self-reproduction approach (Luisi et al., 1994)." In our proposal, the amphiphillic material that is the protocell boundary (wall-membrane) is selectively porous thermal protein that contains chromophores (flavin- and pteridine-like molecules = amino acids rearranged during thermal protein synthesis) that transduce light to chemical bond energy in molecules like ATP. The lipids used by Fox and associates in the protoneuronal studies shows how easy it is to evolve toward a fluid mosaic model membrane, especially since these protocells conduct nonribosomal synthesis of oligo-peptides. The insertion of some of these into the membrane to replace thermal proteins is envisioned as an evolutionary process. The synthesis of oligo-nucleotides by protocells and the coevolution of these yields with oligo-peptides is like the model sought by the ALife group. In our model, the mechanisms of the core-and-shell reproduction system Adami describes are not independent! Time to go to the bench! Also, time to go to the computer. I think Adami would understand that we all come together (eventually) in origin-of-life studies.
The self-ordering of amino acids during copolymerization resulting in thermal proteins has much molecular information to add to the subsequent cellular information (complexity) step during self-assembly of the protocell (spontaneous) when these abiotic macromolecules come into contact with water. This surprising reaction has been known since 1959. Books are now available about self-assembly of other complex molecules but only thermal proteins give rise to protocells.. Adami writes about "evolutionary transitions." We call that molecular diversity and molecular selection (like biological diversity and natural selection). Thermal proteins have mutable side chains and the amino acids do undergo rearrangements during the synthesis of these macromolecules. The thermal proteins would make templates, new catalytic capabilities, etc. for metabolism. The branched thermal proteins may be like Figure 7.4 (page 186) Bethe lattice with x = 3 (or like that with thousands of options)
It is about time to try the avida system and reread the book with great care. Dr. Adami; thanks for the challenge. I still would like to come to Pasadena. I miss the Blue Boy, the San Marino Cafe on Saturday mornings, and weekday breakfasts at Conrad's. And, besides, Dr. Fox did his Ph.D. at Caltech with Dr. T. H. Morgan. For him, it would be like coming home. For me, it would be like coming to a new home.
This illustrated review was prepared by Aristotel Pappelis (Professor, Department of Plant Biology, Southern Illinois University at Carbondale, Carbondale, IL 62901.)