Lie, Wen-Hsiung. 1997. Molecular Evolution. Sinauer Associates, Inc., Publishers, Sunderland, MA, 487 pp., ISBN 0-87893-463-4, $52.95.
The author wrote the Preface and Introduction (Molecular Evolution: A Brief History of the Pre-DNA Era) to his book. "It describes the dynamics of evolutionary change at the molecular level, the driving forces behind the evolutionary process, novel evolutionary phenomena revealed by molecular data, the effect of various molecular mechanisms on the structure of genes and genomes, and the methodology involved in the statistical analysis of molecular data from an evolutionary perspective." The material flows logically and is intended for "advanced students and researchers in molecular evolution or molecular biology."
The chapter titles are: 1. Gene Structure, Genetic Codes, and Mutation; 2. Dynamics of Genes in Populations; 3. Evolutionary Change in Nucleotide Sequences; 4. Estimating the Number of Nucleotide Substitutions Between Sequences; 5. Molecular Phylogenetics: Methods; 6. Molecular Phylogenetics: Examples; 7. Rates and Patterns of Nucleotide Substitution; 8. Molecular Clocks; 9. DNA Polymorphism in Populations; 10. Evolution by Gene Duplication and Domain Shuffling; 11. Concerted Evolution of Multigene Families; 12. Evolution by Transposition and Horizontal Transfer; 13. Genome Organization and Evolution; and, 14. Roles of Mutations and Selection in Molecular Evolution. Answers to Problems (pages 433 - 435) is just that: for problems posed in Chapters 1 through 5. Literature Cited runs from page 437 through 474 (over 1400 citations). The Index runs from page 475 through 487.
This book is essential for students and researchers interested in origin-of-life studies; although that is not the author's purpose. Some researchers propose that aggregations of "metabolically active" carbon-containing chemicals evolved to the point where catalytic proteins were contained and "reproduction" (colloidal fragmentation) occurred. This implied that nucleic acids emerged in the aggregates containing enzymes necessary for their synthesis --- (i.e., the pre-RNA and pre-DNA worlds); others saying that there was no need for enzymes since nucleic acids could arise and evolve without them --- (RNA and DNA worlds). After some time, nucleic acids would become "genetically active" within a cell; mechanism for the evolution of the nucleic acids and the cell being well understood. The cell was generally described as a lipid bilayer. (Now you can understand the need for this book. Is there any chance that such pathways are correct?)
Chemical life evolves to be cellular life. Shades of A. I. Oparin and Miller and Urey!
There are many problems in these proposals. Manuscripts and books attempt to support the generalizations (see Biology 315-2-800, History of Biology: The Origin of and Early Evolution of Life described in this web-site).
In Biology 315-2-800, I present the Thermal Protein-First Paradigm (Pappelis and Fox, 1995 Moscow, 1995 Trieste, and 1996 Trieste; and, Pappelis et al. in press; citations in this web-site). It is a unifying theory for the origin and early evolution of cellular life. Information transfer is traced from amino acids to thermal proteins to protocells (seen as microspheres having semi-selective porous wall-membranes that are simultaneously metabolically active; i.e., thermal proteins are multizymes) and on through oligo-peptides (non-ribosomal synthesis within the protocells) and oligo-nucleotides (synthesized on thermal protein templates within protocells) to protein-poly-nucleotide double-templates that enable their coevolution within protocells. Protocellular RNAs would be expected to form templates for and with DNAs; both RNAs and DNAs evolving. Coordinated gene expression mechanisms --- intracellular mechanisms coupled to mechanisms sensitive to environmental signals --- enable the expression of the attributes of life common to prokaryotic and eukaryotic cells.
How mutations occurred in information transferring thermal-oligo/poly-peptides and thermal proteins (= thermal proteomes) and their information transferring products (oligo/poly-peptides and proteins synthesized on thermal proteome templates = proteomes) in protocells and simple forms of metaprotocells are points of discussion in the course. The nucleic acids that emerged in metaprotocells would be susceptible to types of mutations described in Molecular Evolution.
The author stresses two areas: "the evolution of macromolecules" (includes the rates and patterns of change in DNA and its encoded products during evolutionary time and the mechanisms responsible for such changes); and, "the reconstruction of the evolutionary history of genes and organisms" (molecular phylogeny or phylogenetics). "Traditionally, a third area of study, prebiotic evolution or the 'origin of life' is also included within the framework of molecular evolution." ... (Here is where you come in.) ... "The rules that govern the process of information transfer in prebiotic systems (i.e., systems devoid of replicable genes) are not known at the present time. Therefore, this book will not deal with the origin of life. Interested readers may consult " the following:
Oparin, A. I. 1957. The Origin of Life on Earth. Academic Press, New York.
Eigen, M. and P. Schuster. 1979. Hypercycle: A Principle of Natural Self-Organisation. Springer-Verlag, Heidelberg.
Cairns-Smith, A. G. 1982. Genetic Takeover and Mineral Origins of Life. Cambridge University Press, Cambridge.
Dyson, F. 1985. Origins of Life. Cambridge University Press, Cambridge.
Loomis, W. F. 1988. Four Billion Years: An Essay on the Evolution of Genes and Organisms. Sinauer Associates, Sunderland, MA.
Eigen, M.1992. Steps Toward Life. Oxford University Press, Oxford.
Gesteland, R. F. and J. F. Atkins. 1993. The RNA World. Cold Springs Harbor Laboratory Press, Cold Spring Harbor, NY.
Well! What did I tell you? You need Biology 315-2-800. Where is the information transfer system that existed before prokaryotic and eukaryotic life? O.K. class; all together: How about protocells of thermal proteins --- "devoid of replicable genes" --- and their evolved forms, metaprotocells, with functional peptide and RNA/DNA "genes", but not a sufficient number of DNA "genes" (as in modern genomes) to support prokaryotic life? Pappelis et al 1998 Animate protocells from inanimate thermal proteins: Visualization of the Process, in press (see the recent publication list in this web-site for the exact citation), has reviewed the literature that suggests that the number of modern DNA genes to operate the minimum prokaryotic cell has to be 256 (Mushegian and Koonin 1990, Proc. Natl. Acad. Sci. USA 93: 10268 -10273; and, 1997, J. Mol. Evol. 45: 117 - 118).
The Thermal Protein-First Paradigm proposes animate protocells arise spontaneously (at 60 to 100 degrees C, within a few minutes at 20 degrees C, and within 10 hours at 4 degrees C) from inanimate thermal proteins. These evolve to yield metaprotocells and prokaryotic cells. --- Thus, backtracking sequences in DNAs, RNAs, or proteins from eukaryotic through prokaryotic organisms would bring the researcher doing phylogenetic studies into metaprotocells [the most advanced form being the cenancestor (= a meta-protocellular organism heavily dependent on DNAomes) that emerged from the progenote (= a metaprotocellular organism heavily dependent on RNAomes)]. The progenote emerged from a primitive metaprotocellular organism that was heavily dependent on proteomes (products of nonribosomal oligo/poly-peptide synthesis catalyzed by thermal proteins that make up the protocells). The genetically active molecules in protocells are called thermal proteomes (= thermal peptides and thermal proteins with "genetic" informational units that synthesize proteomes and RNA-DNAomes). The sequence of information transfer is: amino acids to thermal proteins to protocells (thermal proteomes) to metaprotocells (proteomes, RNAomes, proteome-RNA-DNA co-templates, toRNA- DNAome co-templates, to DNA genes), and to prokaryotic cells having DNA genomes. This information transfer system in Domain Protolife involves non-ribosomal peptide synthesis. Ribosomal protein synthesis probably began to evolve in the cenancestor.
Thus, the significance of understanding life from its origin and through its early evolution is continuity: chemical evolution (as proposed by Oparin) linked with biological evolution (called Darwinian evolution). For this kind of understanding, this book will have to studied. We will have to design experiments to prove the pathway of information transfer proposed in the Thermal Protein-First Paradigm. We need to know the appropriate methods to use in such studies. Will the molecular clock hypotheses (discussed in several places in Molecular Evolution) work at that level? We must keep these things in mind as we go. Lets do it. Lets jump into it while excited. Someone in Astrobiology has to check-out the Thermal Protein-First Paradigm at the bench.
The author states: "Chapter 1 provides basic knowledge of molecular biology such as the genomic structure of prokaryotic and eukaryotic genes and genetic codes, and describes some biochemical properties of amino acids and proteins." Many biologists still define a gene as a segment of DNA that codes for a polypeptide primary structure or of various RNAs important to ribosomal protein (poly-peptide) synthesis (hnRNA, mRNA, rRNA, tRNA). Some include the kRNAs [= karyoskeleton or nuclear matrix RNAs; Bhattacharya, Karagiannis, and Pappelis, 1994, Changes in nuclear and nucleolar volumes and nuclear macromolecules associated with selective ribosomal cistron activation by ethylene, Mechanisms if Aging and Development 73: 1 - 7: and, Bhattacharya, Pappelis, Lee, BeMiller, and Karagiannis, 1996, Nuclear (DNA, RNA, histone, and non-histone protein) and nucleolar changes during growth and senescence of May Apple Leaves, Mechanisms of Aging and Development 92: 83 - 99)], snRNAs, and other small cytoplasmic RNAs. The author defines three kinds of genes. They are: protein-coding genes; RNA-specifying genes; and, nontranscribed sequences of regulatory genes (replicator, telomere, segregator, and recombinator genes). The first --- or the first and second types (depending on the researcher) are called structural genes.
In prokaryotic cells, we know of DNA-dependent RNA polymerase. In nuclei of eukaryotic cells, we know of: RNA polymerase I (Pol I) for rRNAs; RNA polymerase II (Pol II) for protein-coding genes; and, RNA polymerase III (Pol III) for small cytoplasmic RNA (scRNA) genes for tRNAs. "The snRNA gene U3 is transcribed by Pol II in vertebrates and lower eukaryotes, but by Pol III in plants (page 9)." Also, the universal genetic code, mutations, crossing-over, gene conversion, deletions, insertions, and hotspots are reviewed .
You should recall the Thermal Protein-First Paradigm when reading Chapter 1 since protocells must transfer information all the way from thermal proteins to DNA genes (from abiotic chemicals through Domain Protolife into Domains Archaea and Bacteria). Mutation in Domain Protolife include changes in side groups of amino acids, changes in amino acids linked by peptide bonds (rearrangements yielding flavin-like and pteridine-like structures embedded in the primary structure of thermal proteins), branching of thermal proteins, and more traditional mutations in nucleic acids evolving in metaprotocells. Also, changes must occur from no regulation of information expression in thermal proteins to coordination of DNAomes in advanced metaprotocells. How many ideas does the author give us is his book?
Jump ahead in the book to page 412, "Figure 13.13 Schematic representations of four possible scenarios for the evolution of introns." There we read that a progenote gives rise to a cenancestor that gives rise to prokaryotes in Domains Archaea and Bacteria. We have already discussed their place in the Thermal Protein-First Paradigm. The author makes no attempt to explain the origin of the progenote. We have discussed that, too.
Intervening sequences (introns) were found in DNA that coded for hnRNAs when we discovered how the information in DNA became information in mRNA. Also, the study of adenovirus (a DNA virus) penetration into a cell revealed that large RNA molecules they formed were subsequently cleaved into smaller mRNAs. the DNA sequences that code for a given molecule of mRNA are not continuous with each other. Sequences destined for retention in mRNAs were named exons.(Do you know what sequences are in cDNA?) Where did introns come from? (See Figure 13.13.)
Gilbert (1978, Nature 271: 501) suggested that "this gene organization could speed up evolution by providing mechanisms for the generation of novel proteins from old ones" (i.e., exon shuffling). Doolittle (1978, Nature 272: 581) and Darnell (1978, Science 202: 1257) "speculated that the 'genes-in-pieces' structure is a primitive form that was present in the genome of the progenote." Blake (1978, Nature 273: 267) "suggested that the 'gene-in-pieces' might imply 'proteins-in-pieces,' that is, exons originally corresponded to structural units of proteins." This is the "introns-early hypothesis." Gilbert (1987, Cold Spring Harbor Symp. Quant. Biol. 52: 901) suggested that "exons are the descendants of ancient minigenes and introns are the descendants of spacers between them." Others presented another view: the introns-late view --- in which early genes had no introns (these evolved with a splicing mechanism in eukaryotes or were transfered into eukaryotes when mitochondria became endosymbionts). (Reading suggested by author = Doolittle and Brown, 1994, Tempo, mode , the progenote, and the universal root. Proc. Natl. Acad. Sci. USA 91: 6721; the progenote "is probably considerably more ancient than the cenancestor").
Do we need to go into the organelle origin of spliceosomal introns (nuclear introns)? Not for Domain Protolife. But what if ribozymes had their origins in the progenote? Could they have been lost as genetic information in organisms of Domains Archaea and Bacteria only to reappear again in organisms of Domain Eucarya? Is that continuity? How did the endosymbionts get introns? Is retropositioning involved? Are spliceosomal introns in eukaryotes degenerate prokaryotic introns (the nuclear origin hypothesis) or did they degenerate in the prokaryotes and then become part of emerging eukaryotes (the prokaryote origin hypothesis).
Do you see where the RNA-first and DNA first hypotheses are going? Where did the information come from? Proteomes? Thermal proteomes? These may be right at the beginning of the introns-early / introns-late controversy. The author presents intron-sliding and the findings that early protists lack introns as other interesting topics for discussion (pages 413 - 414). "To explain the observed intron distribution, the intron-early view would have to postulate the parallel loss of tens of thousands of introns from many different protistan lineages, including complete intron extinction from the several earliest lineages." Are introns junk or selfish DNA? If self-splicing out of RNA occurs, how common is self-splicing into RNA and from there into DNA? "...There is evidence that some transposable elements in maize can be spliced out like an intron (page 418)."
"In conclusion, although the introns-early view was once the prevailing view and has been cited as an established theory in textbooks on molecular and cell biology, it is facing serious challenges. In fact, current evidence seems to be more in favor of the introns-late hypothesis rather than the introns-early hypothesis. However, the controversy is still unsettled and may continue for a long time."
Just as molecular biology completely revolutionized the study of genetics and phylogeny, and has contributed to our understanding of ancient DNA, it is obvious that it is going to play a prominent role in the origin-of-life sciences. Thanks for a great book
This illustrated review was prepared by Aristotel Pappelis (Professor, Department of Plant Biology, Southern Illinois University at Carbondale, Carbondale, IL 62901.)