Once again this year, RNCSE presents a brief summary and a bibliography of recent works, organized to parallel the structure of Of Pandas and People. On each topic there is active and ongoing research in the appropriate sciences as well as a growing bibliography of resources for those interested in specific topics. By contrast, in the 11 years since the publication of the first edition of Pandas and the 6 years in which I have been preparing these summaries, the scientific triviality of the "intelligent design" theory is, and has been, manifest in the lack of any primary research reports based on "intelligent design" in the peer-reviewed scientific literature.
Before investigating the possible origin of life, one ought to know what it is. The difficulties of defining "life" are reviewed by Holmes (1998). Radetsky (1998) and Joyce and Orgel (1998) summarize current ideas about the origin of life.
The Origin of Life
The Space ConnectionStrong polarization of infrared light has been observed in the star-formation regions of the Orion nebula. Such polarization at short wavelengths might result in "left-handed" interstellar organic molecules that could have found their way to earth in comets, meteors, and interplanetary dust. This process would account for one of the most characteristic features of biological molecules — namely the overwhelming preference for "left-handed" over "right-handed" forms of organic compounds associated with all living things on earth (Bailey and others 1998). Recreating the environment of outer space in the lab produces many organic compounds representing some of the key ingredients of life that condense on simulated dust grains, including lipid-like molecules that can form cell-like vesicles (Schueller 1998).
The Martian meteorite still engenders debate (Kerr 1998a; Gibbs 1998). Several new studies (such as Bada and others 1998) indicate that the organic material in the meteorite is the result of terrestrial contamination. Research on the possible extraterrestrial organic materials in other meteorites continues. The Murchison meteorite contains over 70 different kinds of amino acids, many uniquely extraterrestrial (Pizzarello and Cronin 1998). Brainard (1998) speculates that even though Martian microbes may exist, they may be very scarce and hard to find on Mars.
Scientists are also reporting more evidence about the materials and conditions elsewhere in our solar system that could have supported the origin of life. Highly detailed pictures of Europa's surface by the Galileo spacecraft continue to reinforce the hypothesis that a watery ocean is hidden beneath the icy surface (Holden 1998). The paucity of craters on the surface is interpreted as showing that the surface is an active young surface (Kerr 1998b). Other evidence for an ocean is the detection of absorption bands in reflectance spectra indicating hydrated salts on the surface (McCord and others 1998). Evidence for induced magnetic fields is interpreted as evidence for subsurface oceans on both Europa and Callisto (Kivelson and others 1998). Svitil (1998) discusses the possibility of large amounts of methane and other organic compounds on Saturn's moon Titan.
As to the question of whether life could have arisen on planets elsewhere in the universe, astronomers continue to find evidence for extrasolar planets (Semeniuk 1998; Cowen 1998a). Most are inferred from observed wobbles in their stars' paths. Others are inferred from irregularities in a star's dusty disk (Cowen 1998b; Kalas 1998). One has been imaged directly (Leutwyler 1998). The known extrasolar planets now outnumber the planets of the solar system.
ExtremophilesResearchers continue to find organisms in habitats previously thought to be too extreme for life to exist. Priscu and others (1998) describe the microbes existing in Antarctic lake ice. Cary and others (1998) report on tube worms living on the outer walls of deep-sea hydrothermal vents where the temperatures may be as high as 81̊C. General reviews of extremophiles are given by DeLong (1998) and Pain (1998a). Cossins (1998) reviews Michael Gross's book Life on the Edge: Amazing Creatures Thriving in Extreme Environments (1998). Pain (1998b) discusses the microorganisms that live deep in the earth's crust.
Researchers also claim to have found tiny nanobacteria in rocks and in the Martian meteorite. Other workers are skeptical of the existence of these organisms (Vogel 1998). Kajander and Ciftcioglu (1998) report on finding such ultramicroorganisms in biological materials.
Prebiotic ChemistryResearch continues into the production billions of years ago of organic molecules typical of living things on earth. Cleaves and Miller (1998) have demonstrated that many organic polymers and inorganic ions dissolved in the early ocean would act as ultraviolet absorbers, protecting the organic compounds farther below the surface and thus allowing them to accumulate. Canfield (1998) proposes a new model for Proterozoic ocean chemistry in which sulphide, rather than oxygen, is responsible for removing iron from ocean waters. Although there was some oxidation at the earth's surface around 2000 million years before the present (MaBP) ago, aerobic deep-ocean waters did not develop until about 1000 MaBP. Boctor and others (1998) report that nitrogen reduction can be brought about through mineral catalysis under conditions typical of hydrothermal vents.
Nitta and others (1998) report that ribosomal RNA can produce peptide bonds. Similarly, utilizing test-tube evolution, Zhang and Cech isolated a pure RNA pseudo-ribosome that could link amino acids together (Cohen 1998). Carmi and others (1998) report on "deoxyribozimes" (for example, a DNA molecule) that can act as an enzyme and cleave single-stranded DNA oligonucleotides. Unrau and Bartel (1998) report the creation, by test-tube evolution, of an RNA molecule that can synthesize a pyrimidine nucleotide from its phosphate, sugar, and base constituents.
Some theorists favor a high-temperature origin of life near oceanic hydrothermal vents (Balter 1998). Levy and Miller (1998) report that this is unlikely because the nucleotide bases are not sufficiently stable at such high temperatures. Huber and Wachtershauser (1998) claim that amino acids can be activated and condensed into peptides under conditions like those prevailing near vents. Another idea is that mineral surfaces may have aided in the production of polymers (Edwards 1998; Smith 1998; Parsons and others 1998). Along these lines, Luther and others (1998) describe a self-replicating chemical system involving solid support for the chemical templates that can increase the concentration of oligonucleotide analogues exponentially.
Poole and others (1998) describe a Darwinian model for the evolution of life from the late stages of the RNA world through to the emergence of eukaryotes and prokaryotes. In connection with this, Jeffares and others (1998) derive criteria for identifying ribozyme relics of ancient RNA structures in modern microorganisms and creating a model of the last ribo-organism before the advent of protein-directed catalysis.
The Rise of EukaryotesEukaryotes are thought to have arisen from prokaryotes when archaebacteria engulfed eubacteria, which eventually became mitochondria and chloroplasts. Martin and Muller (1998) put forward the hypothesis that this process was not just an accident but the development of a symbiosis: the orginal host was a methanogen that consumed hydrogen and carbon dioxide and produced methane. The symbiont that eventually became the mitochondrion was a bacterium that made hydrogen and carbon dioxide as its waste products.
A rich find of unicellular eukaryotic fossils along with bacteria have been found in 800-Ma-old rocks on Canada’s Victoria Island (Monastersky 1998b). South African researchers have found evidence that primitive unicells may have lived in soil on land 2000–2200 MaBP (Monastersky 1998a). Recent experiments suggest that multicellular colonies may evolve from unicells as a defense against predation. Unicellular predators found the colonies too big to ingest (Blackman 1998).
Genetics and Evolution
MutationCurrent research demonstrates how mutations can produce variations with positive outcomes; mutation is not universally, or even generally, a bad thing. Rainey and Travisano (1998) describe the rapid evolution of an aerobic bacterium when exposed to novel environmental conditions in multiple ecological niches. Boyce (1998) reports that mutations that appear to be neutral may have subtle effects under stressful conditions. After experiencing heavy DNA damage, bacteria may increase their mutation rates by partially disabling their DNA repair systems in order to generate new genotypes that might be evolutionarily useful (Goodman 1998; Brookes 1998).
Genomes exhibit many diverse phenomena and genetic information is often stored in complex ways. A gene, for example, may be split into exons and introns, the latter being excised as "junk" when the gene is transcribed into messenger RNA. Similarly, some proteins that are produced by ribosomes consists of exteins and inteins, the latter being excised from the polypeptide chain to make the final form of the protein. Wu and others (1998) describe such a protein and its gene in the microbe Synechocystis. An added complication is that the gene itself is split into 2 parts found in 2 different parts of the chromosome. Each part codes for an extein and part of the one intein. Only after the 2 polypeptides are formed do they join to form the complete intein, which then excises itself to form the final protein molecule!
Pennisi (1998b) reviews the ways in which genomes can change, including transposable elements, shuffling or duplication of material, mutational hotspots, and inaccurate copying of 2- and 3- base repeats which may affect the function of neighboring genes. Max (1998) discusses pseudogenes, short and long interspersed elements, retroviruses, and retroposons as evidence for evolution. The numbers of multiple elements are still increasing in mouse species (Anonymous 1998); the house mouse has 3000 of them! Vogel (1998) and Pennisi (1998a) review modern ideas and experiments concerning the evolution of the genetic code. Van den Burg and others (1998) were able to utilize mutations to modify a bacterial enzyme to work at very high temperatures.
Natural SelectionSargent and others (1998) review the phenomenon of industrial melanism. Losos and others (1998) explore the role of historical contingency in influencing adaptive radiation of Anolis on different islands in the Caribbean. A special section of Science (Hines and Culotta 1998) contains a number of papers reviewing hypotheses about the evolution of sex, including the possible adaptive value of sex (Barton and Charlesworth 1998) and tests of the various hypotheses (Wuethrich 1998).
A number of papers dealt with sexual selection. Arnqvist (1998) discusses the possibility that the shape of male genitalia evolved under sexual selection. Evans (1998) tests the hypothesis that sexual selection produced the long tail streamers of male swallows, discovering that the length of the tail is governed by natural selection. Call duration in tree frogs may be used by females to select males with superior genetic quality (Welch and others 1998). In swordtail fish, females prefer larger swords (Rosenthal and Evans 1998). In stalk-eyed flies, females prefer males that have longer stalks (Wilkinson and others 1998). The long eye stalk condition is linked to the possession of a Y chromosome that suppresses the meiotic drive of a "selfish" X chromosome that biases the sex ratio in favor of females.
Designing with EvolutionPetit (1998) gives a popular description of the use in industry of genetic algorithms to design engineering systems, directed (test-tube) evolution to produce new drugs, and genetic programming to evolve computer programs. Taubes (1998) discusses research on FPGA (Field Programmable Gate Array) chips, which allow computer hardware to be programmed by genetic algorithms. Lenski (1998) provides an informative book review on artificial life’s existing and evolving in computers.
Landweber and others (1998) review the successes in ribozyme engineering using test-tube evolution. They list 2 dozen new ribozymes "evolved" either from some precursor RNA or from random sequences of RNA. Macbeath and others (1998) used test-tube evolution to redesign enzyme topology. Crameri and others (1998) describe DNA shuffling, a technique used to speed up test-tube evolution.
GenomesThe genomes of more organisms continue to be sequenced. In 1998, the genomes of 5 microorganisms and 1 multicellular animal were sequenced. These include the hyperthermophilic bacterium Aquifex aeolicus with about 1.5 million base pairs (Mbp; Deckert and others 1998), the tuberculosis microbe Mycobacterium tuberculosis with about 4.4 Mbp and 4000 genes (Cole and others 1998), the syphilis spirochete Treponemas pallidum with about 1.3 Mbp and 1041 genes (Fraser and others 1998), the intracellular human pathogen Chlamydia trachomatis with about 1 Mbp (Stephens and others 1998), the typhus microbe Rickettsia prowazekii with about 1.1 Mbp and 834 genes, many of which are similar to mitochondrial genes (Andersson and others 1998), and the first animal to have its genome completely sequenced, the nematode worm Caenorhabditis elegans with 97 Mbp and 19 000 genes (Hodgkin and others 1998; Hodgkin and Herman 1998). The Drosophila genome sequence will be finished soon. Work continues on sequencing the plant model Arabidopsis (the European Union [EU] Arabidopsis Genome Project 1998; Meinke and others 1998). Huynen and Bork (1998) report on a comparative study of 9 microbial genomes.
It is estimated that vertebrates have between 50 000 and 100 000 genes, while invertebrates have fewer than 25 000. Simmen and others (1998) estimate that the invertebrate chordate Ciona has about 15 000 genes. Evidence indicates that at least 2 rounds of polyploidy occurred in the vertebrate ancestors after the separation of Amphioxus and the craniates (Pebusque and others 1998; Postlethwait and others 1998).
The extensive data on microbial sequences point to the possibility that early in the evolution of life, before the 3 domains (Bacteria, Eukara, and Archaea) emerged, there was much horizontal transfer of genetic material (Pennisi 1998; Koga and others 1998; Woese 1998; Katz 1998). Miller (1998) discusses horizontal gene transfer occurring today, since it could allow genetically engineered microbes to pass their genes to other species in the environment with unintended results. Katz (1998) reviews the latest ideas on the evolution of eukaryotes. She presents evidence that the eukaryote archezoans, which do not possess mitochondria, have secondarily lost those organelles. Aravalli and others (1998) report that Archaea, originally considered to be confined to extreme environments, are much more widespread, being found in soils, lake sediments, marine picoplankton and deep-sea locations. Microbiologists have estimated that there are 5 x 1024 bacteria living on earth in the ocean, in the soil, beneath the surface, in the air, and inside animals. Soil and subsurface habitats account for 94%; the insides of animals account for only a fraction of 1 percent. In the oceans, any given bacterial gene is estimated to undergo an average of 4 mutations every 20 minutes (Anonymous 1998).
Brookes (1998) gives a popular account of the concepts of species and speciation. Orr and Smith (1998) explore the role of ecological divergence in the rise of reproductive isolation and speciation. Galis and Metz (1998) discuss the roles of sexual selection and niche differentiation on the explosive speciation of cichlid fishes in Lake Victoria. Geiser and others (1998) describe cryptic speciation in a fungus.
The Origin of Species
On the basis of computer simulations, Kondrashov and Shpak (1998) report that assortative mating can give rise both to reproductive isolation and to sympatric speciation. Gavrilets and others (1998) report on computer simulations that indicate the possibility of rapid speciation in subdivided populations without the need of founder effects, complete isolation, or the existence of distinct adaptive peaks. Ting and others (1998) investigate the speciation role of a rapidly evolving homeobox found in a male sterility gene in Drosophila. Swanson and Vacquier (1998) investigate gamete interactions in abalone involving egg lock/sperm key proteins that open the vitelline envelope of the egg to allow the sperm to enter, and how these can evolve to produce reproductive isolation and new species. Waugh O'Neal and others (1998) investigate the roles of undermethylation and retroelement activation in chromosome remodeling in interspecific hybrids.