In 1989, Kenyon and Davis published the first edition of Of Pandas and People as a supplementary biology text. In both the first and second editions, the authors claim that there is scientific evidence against evolution in a number of fields of scientific research. Since 1995, I have searched the scientific literature in those fields identified in Pandas as being problematic for evolution and reported on it in our members' publications. As expected, a number of questions in the sciences were unanswered at the time of the original publication of Pandas in 1989. By the publication of the second edition in 1993, more of these issues were resolved, but new questions were also raised.
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.
chapter 1: The Origin of Life
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 Space Connection
Strong 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.
Researchers 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.
Research 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 Eukaryotes
Eukaryotes 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).
chapter 2: Genetics and Evolution
Current 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.
Sargent 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 Evolution
Petit (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.
The 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).
chapter 3: The Origin of Species
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.
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.
chapter 4: The Fossil Record
The Cambrian Explosion
Evidence is accumulating that complex animals evolved long before they appeared as fossils in the "Cambrian explosion". Seilacher and others (1998) report the finding of worm burrows in 1000-Ma-old Precambrian rocks, but there is much controversy over the dating of the rocks and the interpretation of the fossils. Xiao and others (1998; see also Gould 1998) have discovered almost perfectly preserved fossils of algae and animal embryos in 570-Ma-old phosphorites in southern China — 20 Ma before the Cambrian Period. Molecular dating techniques also indicate a much earlier evolution of metazoans (about 680–830 MaBP) in the Precambrian (Gu 1998; Bromham and others 1998). Thomas (1998) reconsiders the Cambrian Explosion in light of these new findings. Cooper and Fortey (1998) review the evidence for metazoan evolution prior to the Cambrian fossil record.
Li and others (1998) report the finding of Precambrian sponges. Moldowan and Talyzina (1998) report biogeochemical evidence for dinoflagellate ancestors in the early Cambrian. Jensen and others (1998) report on the occurrence of Cambrian ediacarans (vendobionts). McMenamin (1998) reports on a new interpretation of ediacarans as a separate "metacellular" kingdom. Morris and Gould (1998) debate the interpretation of the Burgess Shale fauna. Morris (1998) claims that this fauna can be classified into existing phyla. Orr and others (1998) discuss the conditions under which the Burgess Shale animals were preserved. Hecht (1998) discusses the possibility (reported last year) that during Cambrian times, the earth's crust slipped around the core almost 90 degrees. The changing climatic conditions may have spurred rapid evolution. On the other hand, geologists report evidence of long geologically stable periods in the Precambrian (Anonymous 1998). The late Precambrian provides evidence for glaciation in what are now tropical latitudes. Hoffman and others (1998) explain this by a "snowball" earth hypothesis, while Williams and others (1998) prefer to invoke a change in the orientation of the earth's spin axis.
The end-Cretaceous Chicxulub impact event is discussed by Johnson (1998), Cerveny (1998), and Pope and others (1998). Jablow (1998) describes the discovery of the Chicxulub structure. Kyte (1998) reports on the finding of a possible fragment of the asteroid in the sediments of the northern Pacific ocean. Shukolyukov and Lugmair (1998) present geochemical evidence that the asteroid had a carbonaceous chondrite composition. Evidence has been reported (Anonymous 1998a) that the impact fractured the edge of the continent, resulting in gigantic submarine landslides and giant tsunamis.
Cowen (1998) describes the possible causes of a comet shower that may have done in the dinosaurs. Smith and Jeffery (1998) discuss the selectivity of sea-urchin extinction due to this event. Jablonski (1998) discusses the molluscan recovery. Research on plankton extinctions that occurred before the event and of plankton that survived the event is discussed in (Anonymous 1998b). Erwin (1998) discusses recoveries from mass extinctions in general. Spray and others (1998) report evidence of a late Triassic multiple impact event. Bowring and others (1998) report geochronological evidence that the End-Permian extinction event lasted less than 1 million years. Ward (1998) reports evidence that the End-Permian land animals suffered from intense global warming. Schultz and others (1998) report a Pliocene impact event in Argentina. Wynn and Shoemaker (1998) describe an impact in Arabia that occurred in historic times. Gibbs (1998) describes the search for an impact crater in Greenland that formed in December 1997.
New fossil finds include Devonian myriapods from Australia (Edgecombe 1998) and ants in amber from New Jersey 92 MaBP (Agosti and others 1998). Plant fossils include complex rooted plants from the early Devonian 390 MaBP (Jensen 1998), a Jurassic angiosperm (Sun and others 1998), and an upper Cretaceous monocot (Gandolfo and others 1998). The discovery of Late Jurassic pollinating Brachyceran flies (Ren 1998) supports the Jurassic origin of angiosperms. New fish fossils include a lobe-finned fish with "fingers" (Daeschler and Shubin 1998) and a complete primitive rhizodont lobe-finned fish from Australia (Johanson and Ahlberg 1998). New dinosaur fossils include an early Carboniferous tetrapod (Clack 1998), a fish-eating dinosaur from Africa (Sereno and others 1998), sauropod dinosaur eggs and embryos from the upper Cretaceous of Patagonia (Coria and others 1998), a 16-inch–long claw resembling that of Velociraptor from Patagonia (Menon 1998), an early Cretaceous sea turtle (Hirayama 1998), a new species of predatory dinosaur from Madagascar (Sampson and others 1998), a giant Cretaceous dinosaur coprolite (Chin and others 1998), a Jurassic ankylosaur dinosaur (Carpenter and others 1998), and a small theropod dinosaur fossil from Italy with soft tissue preservation (Sasso and Signore 1998). Other new vertebrate fossils include a new Eocene archaeocete whale from India (Bajpai and Gingerich 1998), new specimens of giant armadillo from Florida (Anonymous 1998b), and a 53-Ma-old jaw representing the tiniest known mammal (only 1.3 grams) from Wyoming (Monastersky 1998a).
Adrain and others (1998) discuss Ordovician trilobite diversity. The osteolepiform (lobe-fin fish) ancestors of the tetrapods are discussed by Ahlberg and Johanson (1998). Clark and others (1998) report fossil evidence that early pterosaurs were quadripedal. Evidence that Cretaceous plesiosaurs ate ammonites is reported by Sato and Tanabe (1998). New primitive skeletons from Japan shed light on the origin of ichthyosaurs (Motani and others 1998). Fossils of Cretaceous duck-billed dinosaurs have been found in Antarctica (Monastersky 1998a). Late Cretaceous fossils of champsosaurs, large crocodilelike reptiles, have been found in the high Canadian Arctic (Tarduno and others 1998), suggesting that the poles had a warm climate at that time.
Traces of bone tumors are found in dinosaur vertebrae (Anonymous 1998c). Growth layers in dinosaur bones indicate that large sauropods grew fast and attained their full size in about 10 years (Stokstad 1998). Some Cretaceous sail-backed dinosaurs may have actually been humpbacked (Anonymous 1998a). Studies of the bone growth of high-latitude Australian dinosaur fossils revealed no growth lines, indicating that they might have been endothermic and grown continuously (Monastersky 1998b).
New, more complete specimens of the Late Cretaceous mammal Deltatheridium (Rougier and others 1998) shed light on the evolutionary relations of basal marsupials and early mammals. Flynn and Wyss (1998) review recent knowledge of South American mammal fossils. Meng and McKenna (1998) discuss mammalian faunal turnovers in the early Tertiary. Shoshani (1998) reviews elephant evolution. DNA analysis of the excrement of the extinct ground sloth reveals the plant species in its diet (Poinar and others 1998). Zimmer (1998c) recalls the 19th-century discovery of the early whale Basilosaurus. A new fossil of a mouse-sized flightless animal, Phenocolemur, suggests that the ancestors of bats hung from tree branches by all four legs (Hecht 1998). Zimmer (1998a) discusses bats and their evolution.
Grande (1998) describes the fossil-rich Eocene lake deposits of Wyoming. Zimmer (1998b) gives an in-depth review of the evolution of amphibians from fishes and the evolution of whales from land mammals. Lockley (1998) reviews the data on fossil footprints. Such fossil tracks, found all over the world, are one of the most direct lines of evidence indicating that the geologic strata were not laid down continuously by a giant world-wide flood. Erdmann and others (1998) report on the finding of modern coelacanth populations (Latimeria) off the coast of Indonesia.
Britt and others (1998) have discovered passageways for air sacs in Archaeopteryx specimens, demonstrating that the hollow postcranial bones were pneumatized and reinforcing the idea that they are homologous with similar pneumatized bones in the skeletons of non-avian theropod dinosaurs. Controversy over the dinosaurian origin of birds continues: Padian and Chiappe (1998), Thomas and Garner (1998), and Martin (1998), Ostrom (1998), and Padian (1998) summarize the opposing views; Hicks and others (1998) debate Rubin's 1997 claim that the theropod lung could not have evolved into a bird lung. Questions over whether the 3 digits in a bird's wing are homologous to the 3 digits in a theropod’s arm are discussed in (Anonymous 1998).
A theropod that might have had a feathered crest (Chen and others 1998) and 2 feathered dinosaurs (Ji and others 1998) have been found in the Lower Cretaceous formations in China. Ackerman (1998) summarizes the discovery of these animals in an article with many beautiful illustrations. The early Cretaceous Chinese fossil site yielding these discoveries is described by Wang (1998); Chiappe (1998) describes the Spanish site yielding early Cretaceous birds. The skull of a Late Cretaceous relative of Mononykus has been found in Mongolia (Chiappe and others 1998). The oldest Coelurosaurian theropod (from the Early Jurassic) is reported from China (Zhao and Xu 1998). Forster and others (1998) report on a primitive Late Cretaceous bird with a large sicklelike claw similar to those of dromaeosaurid dinosaurs. Stidham (1998) reports on a Late Cretaceous parrot fossil. Bones of a large (possibly 140 kg) flightless bird of the Late Cretaceous, Gargantuavis, have been found in France. This species may have produced the hundreds of fossil eggs found in the region previously thought to be dinosaur eggs (Holden 1998). Two more books on the origin of birds appeared this year (Dingus and Rowe 1998; Shipman 1998).
Babcock (1998) gives a good introduction to the literature on taphonomy, the science of what happens after an animal dies and under what conditions it will fossilize. Hazard (1998) offers suggestions how to teach about transitional forms.
Two 45-Ma-old primate fossils found in Southeastern China are the smallest known, being less than 1 cm tall (Anonymous 1998a). They may represent the most primitive anthropoids. Gibbons (1998b) suggested that one ape line that returned to Africa from Asia may be the ancestor of the modern apes. New evidence suggests that the Miocene ape Oreopithecus was bipedal (Anonymous 1998b). A recent anatomical study has revealed that the chimpanzee brain exhibits asymmetry similar to that of the human brain in an area associated with language (Bower 1998a).
Several previous finds have been re-evaluated. The purported Neandertal bone flute appears to have been gnawed and punctured by an animal, perhaps a wolf (Bower 1998b). Rock art in Australia previously dated at 50–75 000 years ago has been redated to about 10,000 years by different dating methods (Bird and others 1998).
McKinney (1998) re-evaluates the "neotenic ape" model of the origin of humans. The 117,000–year-old footprints of anatomically modern humans found in 1995 near Langebaan Lagoon in South Africa will be moved to the safety of a museum (MacKenzie 1998). They are no longer the oldest known such footprints. Another set, the Nahoon prints, which have been in a South African museum for the past 34 years, have been dated at 200,000 years (Holden 1998a). Agnew and Demas (1998) discuss the preservation of the Laetoli footprints. The discovery of a complete Australopithecine skull and limb bone material in the Sterkfontein caves of South Africa was announced in December (Gee 1998). Computer simulation of Lucy's legs indicate that she walked in a human manner, not with a chimp-like gait (Lincoln 1998).
Computer imaging techniques have measured the endocranial capacity of a South African Australopithecus africanus specimen at about 515 cc — smaller than previous estimates. The endocranial capacities of other early hominids may also be too large (Conroy and others 1998). New specimens of Australopithecus anamensis confirm its age as intermediate between the older Ardipithecus ramidus and the younger Australopithecus afarensis (Leakey and others 1998). Recent reports suggest that A africanus has more apelike body proportions than A afarensis (Svitil 1999). A 1-Ma-old skull with a mixture of H erectus and H sapiens characters has been found in Eritrea (Albianelli and others 1998). A skeleton of a modern human child has been found in the Nile valley dating from a time (55 000 years) when many anthropologists think modern humans were about to invade Europe and Asia (Copley 1998).
Fission-track dating of stone tools and fossils on the island of Flores date at 900 000 years ago, suggesting that Homo erectus was capable of crossing open water in some kind of watercraft (Morwood and others 1998). Stone tools found in Israel's Hayonim cave have been dated at 200 000 years ago. Similar tools found at 2 other sites date to 250 000 years ago (Bower 1998c). Reexamination of the evidence for fire at Zhoukoudian, China, does not reveal any direct evidence for in situ burning (Weiner and others 1998).
Recent discoveries have led anthropologists to conclude that the New World was invaded by humans long before 11 000 years ago (McDonald 1998). The first humans may have reached the New World 30 000 years ago. They may have included people of European ancestry (Lewin 1998a). Last year's analysis of Neandertal DNA indicated that they were not directly ancestral to modern Homo sapiens, but some anthropologists, such as Milford Wolpoff, question that conclusion (see Holden 1998b and related readings). The replacement of Neandertals by modern Cro-Magnons is discussed by Mellars (1998). The June 1998 issue of Current Anthropology (vol 39, supplement) has several articles on Neandertals and early modern humans (Brainard 1998).
The anatomical requirements for language are discussed by Cartmill (1998). Investigations on the size of the hypoglossal canal, which transmits the nerves of the tongue, have led some authorities to conclude that Neandertals could talk as well as modern humans do (Kay and others 1998). According to Lieberman (1998), the origin of the cranial features characteristic of modern humans are related to reduction of the sphenoid bone. That ancient humans practiced cannibalism has been controversial. New evidence indicates that it occurred in the prehistoric American southwest and among the Aztecs, Maoris, and people in England 12 000 years ago (McKie 1998).
Analysis of human Y chromosomes supports the "out-of-Africa" hypothesis but also indicates that subsequently some populations returned to Africa (Hammer and others 1998). Patterns of mitochondrial genes and the non-recombining part of the Y chromosome suggest that humans had a small effective population size (about 10 000) during the Pleistocene (Harpending and others 1998). This same evidence rules out the multiregional hypothesis. Similar results come from studies of variation in the human dystrophin gene (Zietkiewicz and others 1998). This bottleneck may have been caused by climate changes caused by the eruption of Mount Toba in Sumatra about 71 000 years ago. This eruption was about 4000 more severe than the recent Mount St Helens eruption (Anonymous 1998c).
Although the apparent continuity of fossil and modern anatomy in China appears to support the multiregional hypothesis, a recent genetic study of Chinese populations (Chu and others 1998) does not. Rather, it indicates that the ancestors of East Asia entered from Southeast Asia. Comparison of mtDNA and Y chromosome data seems to indicate that women had a migration rate 8 times that of men (Boyce 1998).
With the Human Genome Project in full swing, some researchers are beginning to look for the genes that distinguish us from apes. One such difference, in the human CMP-sialic acid hydroxylase enzyme (Gibbons 1998a), involves a 92–base-pair deletion, which also causes a frame shift. This finding has relevance for the argument of anti-evolutionists that although humans and apes differ in only 1% of their genome, this amounts to 1 million base pairs and hence 1 million favorable point mutations would have had to occur (Schroeder 1997: 120) Obviously, point mutations are not the only way in which 1 million base-pair differences could have occurred.
Problems with calibrating mtDNA mutation rates are reviewed by Gibbons (1998b). Recent forensic work (such as identifying the recently discovered bodies of Tsar Nicholas and his family) has discovered many cases of heteroplasmy — instances where an individual has more than one mtDNA sequence. More than one type of mitochondrion can be inherited from a person's mother because the egg contains hundreds of these bodies. Such differences arose by mutation, and their occurrence suggests much higher mutation rates than previously thought.
A special section on archaeology in the November 20, 1998, issue of Science (Appenzeller and others 1998) reviews the latest ideas and information on the origin of art (Appenzeller 1998), the development of communities (Balter 1998), the birth of agriculture (Pringle 1998), and the origin of language (Holden 1998c). Lewin's human evolution textbook (Lewin 1998b) provides an up-to-date exposition of all aspects of human evolution.
chapter 5: Homology
Richardson and others (1997) published a paper that compared many vertebrate embryos to investigate the validity of the phylotype concept and, as an aside, claimed that Haeckel's figures illustrating recapitulation were inaccurate to the point of being fraudulent — a point not overlooked by anti-evolutionists. This paper produced a series of letters in Science in 1998 (Hanken and Richardson 1998; Richardson and others 1998). The authors of the original paper say that Haeckel was essentially correct: his drawings enhanced superficial similarities — mainly of the general outlines of the various embryos — but certainly did not concoct the similarities of pharyngeal slits, and so on, that were, in fact, known to all other 19th-century anatomists, including Haeckel's enemies. (The few illustrations of recapitulation that Darwin used in The Descent of Man were taken from other sources). The "fraud" has been fully exploited by anti-evolutionists in their attempts to discredit evolution (Behe and others 1998).
Gilbert (1998) summarizes recent conceptual breakthroughs in developmental biology. These include the ideas that genetic and biological mechanisms can indeed explain development, that the core of development involves various signal transduction mechanisms, that homologous genes and pathways exist among distantly related phyla, and that modularity in development and developmental changes can result in major evolutionary changes. Modern findings on signaling molecules in development are summarized by Strauss (1998). Transmembrane receptors including olfactory receptors may function as a cell surface code for assembling embryos (Dreyer 1998).
A number of papers document new homeobox genes and their role in macroevolution. Wray and Raff (1998) report that echinoderms use the same regulatory genes as other animals to make both their bilateral larvae and their radial adults. The expression pattern of AmphiEn, which initiates certain repeated body segments in vertebrates, is similar to that of engrailed in invertebrates. Hox genes in ribbonworms (Nemerteans) consist of 1 cluster of 6 genes (Kmita-Cunisse and others 1998), and their most closely related orthologs are found in the mouse or Amphioxus. This finding indicates that ribbonworms have diverged relatively little from the last common ancestor of protostomes and deuterostomes.
Martinez and others (1998) report that coelenterates do not possess a full complement of Hox genes. A new cluster of 3 Hox-like genes (the ParaHox cluster) has been found in Amphioxus (Brooke and others 1998). Henry (1998) reports on a Hox gene needed for endoderm development.
The general role of homeobox genes in evolution and the Cambrian explosion is discussed in a number of papers (Cameron and others 1998; Pendick 1998; Meyer 1998). The discovery of 7 Hox clusters in modern fish (tetrapods have only 4) may account for the wide diversity displayed by modern fishes (Amores and others 1998). Hox genes and their role in vertebrate hindbrain segmentation are discussed by Prince (1998). Holland and Holland (1998) report on the expression patterns of 5 Hox genes in Amphioxus, which indicate the presence of a forebrain.
Martindale and Henry (1998) discuss the evolution of bilaterality. Several papers summarize our knowledge of limb development (Gardiner and others 1998; Schwabe and others 1998). The wide variability in tetrapod limb morphology is probably due to the timing and sequence of expression of Hox genes. Duboule and Wilkins (1998) point out that most of our genes are shared with other organisms, so phylogenetic diversity depends not on evolution of new genes, but on differential use of the same component genes. Evolutionary "bricolage" (that is, tinkering) with the developmental system is very conservative.
Tautz (1998) and Lee (1998) explore the use of the concept of homology in comparative and evolutionary studies. Modern techniques for reconstructing evolutionary trees are summarized by Lewin (1998). Hall (1998) presents a review of historical and recent research bearing on the germ-layer theory.
chapter 6: Biochemical Similarities
Molecular taxonomy is changing our conception of the relationships of the animal phyla. Maley and Marshall (1998) provide a brief summary of molecular systematics and some of the outstanding issues in the field. Collins (1998) compares hypotheses concerning the evolution of the Bilateria based on ribosomal RNA data. Bilaterians seem to be closely related to placozoans and cnidarians. Balavoine and Adoutte (1998) review the evidence from ribosomal RNA data for grouping the triploblastic phyla into 3 large groups; Anderson and others (1998) report Hox gene data that may indicate that the protozoan Myzozoa may be a degenerate metazoan.
Several molecular studies appear to conflict with morphological and paleontological data. Sequencing of the mitochondrial genome suggests that turtles may be more closely related to diapsid than to anapsid reptiles (Zardoya and Meyer 1998). Another mitochondrial genome study suggests a closer-than-expected relationship between hippopotamus and whale clades (Ursing and Arnason 1998), but these findings are not consistent with other studies. The most newly discovered ancient whale fossils weaken the link to mesonychids and make the artiodactyl connection more plausible (Normile 1998). A molecular time scale for vertebrate evolution (Kumar and Hedges 1998) indicates that many modern mammalian orders diverged in the Cretaceous rather than the Tertiary, yet the latest fossil evidence (Normile 1998) disputes this hypothesis. Gaut (1998) reviews the research done on molecular clocks using plant data.
Study of mitochondrial introns suggests the liverworts were the earliest land plants (Qiu and others 1998). De Ley and others (1998) use ribosomal DNA data to classify the nematodes. Springer and others (1998) use both mitochondrial and nuclear gene data to resolve ambiguities in the relationships of the marsupials. The studies have confirmed that the marsupials are a natural grouping. Schubart and others (1998) studied the mitochondrial genes of Jamaican land crabs and concluded that they are descended from one marine ancestor about 4 MaBP.
Astronomers continue to find evidence of extrasolar planetary systems. More genomes are being completely sequenced, including the first genome to be sequenced of an animal, the nematode Caenorhabditis elegans, which has about 19, 000 genes. Darwinian evolutionary paradigms, in the form of genetic algorithms and test-tube evolution, are being used more and more to design engineering systems and to produce new enzymes, many of medical importance. Traces of animals that preceded the Cambrian explosion have been found, as have been feathered dinosaurs. New human fossils are being found that add variety and depth to the human family tree. The discovery of new homeobox-type genes are helping to elucidate developmental systems.
All these new findings are supportive of evolution and advance our knowledge of the history and variety of life beyond what we knew in 1989 when Of Pandas and People was first published. By contrast, the "intelligent design" theory presented in the pages of Pandas has yet to produce any scientific advances in the main areas of study laid out in the 6 chapters of the original (and revised) textbook.
Chapter 1: The Origin of Life
Holmes B. Life is... New Scientist 1998 Jun 13; 158 (2138): 38–42.
Joyce GF, Orgel LE. The origins of life — A status report. The American Biology Teacher 1998 Jan; 60 (1): 10–2.
Radetsky P. Life's crucible. Earth 1998 Feb; 7 (1): 34–41.
The Space Connection
Bada JL, Glavin DP, McDonald GD, Becker L. A search for endogenous amino acids in Martian meteorite ALH84001. Science 1998 Jan 16; 279: 362–5. Related reading: Cowen R. Reports raise questions about Martian rock. Science News 1998 Jan 24 (4); 153: 54. Jull AJT, Courtney C, Jeffrey DA, Beck JW. Isotopic evidence for a terrestrial source of organic compounds found in Martian meteorites Allan Hills 84001 and Elephant Moraine 79001. Science 1998 Jan 16; 279: 366–9.
Bailey J, Chrysostomou A, Hough JH, Gledhill TM, McCall A, Clark S, Ménard F, Tamura M. Circular polarization in star-formation regions: Implications for biomolecular homochirality. Science 1998 Jul 31; 281: 672–4. Related reading: Cowen R. Starlight shows life the right path. Science News 1998 Aug 1; 154 (5): 68. Green MM, Selinger JV. Cosmic chirality [letter]. Science 1998 Oct 30; 282: 880–1. Guterman L. Why life on earth leans to the left. New Scientist 1998 Dec 12; 160 (2164): 16. Hecht J. Inner circles. New Scientist 1998 Aug 8; 159 (2146): 11. Irion R. Did twisty starlight set stage for life? Science 1998 Jul 31; 281: 626–7. Schneider D. Polarized life. Scientific American 1998 Oct 24; 279 (3): 24.
Brainard J. Any Mars life would be hard to find. Science News 1998 Aug 29; 154 (9): 135. Related reading: Hecht J. Mission impossible. New Scientist 1998 Aug 29; 159 (2149): 20.
Cowen R. Exploring new worlds. Science News 1998a Aug 1; 154 (6): 88–90. Related reading: Cowen R. A dozen new planets ... and still counting. Science News 1998 Sep 26; 154 (13): 197. Cowen R. Star motions yield four more planets. Science News 1998 Dec 5; 154 (23): 362.
Cowen R. Epsilon Eridani: An early solar system? Science News 1998b Aug 8; 154 (6): 91. Related reading: Schilling G. Hints of a nearby solar system? Science 1998 Jul 10; 281: 152–3.
Gibbs WW. Endangered. Scientific American 1998 Apr; 278 (4): 19–21.
Holden C. Ocean sighting confirmed. Science 1998 Mar 13; 279: 1639. Related reading: [Anonymous]. Planets, moons, a supernova, and more. Discover 1999 Jan; 20 (1): 74. [Anonymous]. A world of ice. Discover 1998 Mar; 19 (3): 22. [Anonymous]. Slush on Europa? Discover 1998 May; 19 (5): 16. Cowen R. Craft eyes new evidence of a slushy Europa. Science News 1998 Mar 7; 153 (10): 149. Hecht J. Galileo gets slushy with Europa. New Scientist 1998 Mar 7; 157 (2124): 5. Seife C. To the iceworld. New Scientist 1998 Feb 14; 157 (2121): 20.
Kalas P. Dusty disks and planet mania. Science 1998 Jul 10; 281: 182–3
Kerr RA. Requiem for life on Mars? Support for microbes fades. Science 1998a Nov 20; 282: 1398–1400. Related reading: Cowen R. Fossils from Mars: Point, counterpoint. Science News 1998 Jan 3; 153 (1): 11.
Kerr RA. Planetary scientists sample ice, fire, and dust in Houston. Science 1998b Apr 3; 280: 38–9.
Kivelson MG, Stevenson DJ, Schubert G, Russell CT, Walker RJ, Polanskey C, Khurana KK. Induced magnetic fields as evidence for subsurface oceans in Europa and Callisto. Nature 1998 Oct 22; 395: 777–80. Related reading: [Anonymous]. Other worlds, other oceans. Discover 1998 Sep; 19 (9): 20. Cowen R. An ocean for Callisto? Science News 1998 Nov 7; 154 (19): 296. Kerr RA. Geophysicists ponder hints of otherworldly water. Science 1998 Jan 2; 279: 30–1. Neubauer F. Oceans inside Jupiter's moons. Nature 1998 Oct 22; 395: 749–51.
Leutwyler K. New planet? Scientific American 1998 Aug; 279 (2): 22. Related reading: [Anonymous]. Planet poseur? Discovery 1998 Aug; 19 (8): 24.
McCord TB, Hansen GB, Fanale FP, Carlson RW, Matson DL, Johnson TV, Smythe WD, Crowley JK, Martin PD, Ocampo A, Hibbitts CA, Granahan JC, and the NIMS Team. Salts on Europa's surface detected by Galileo's near infrared mapping spectrometer. Science 1998 May 22; 280: 1242–5. Related reading: [Anonymous]. Salty moon. New Scientist 1998 Mar 28; 157 (2127): 23. Cowen R. Europa's salty surface. Science News 1998 Jan 3; 153 (1): 11. Kargel JS. The salt of Europa. Science 1998 May 22; 280: 1211–2.
Pizzarello S, Cronin JR. Alanine enantiomers in the Murchison meteorite. Nature 1998 Jul 16; 394: 236.
Schueller G. Stuff of life. New Scientist 1998 Sep 12; 159 (2151): 30–5.
Semeniuk I. Real worlds of other suns. SkyNews 1998 Nov/Dec; 4 (4): 12–5.
Svitil KA. Hot times on Titan. Discover 1998 Mar; 19 (3): 29.
Cary SC, Shank T, Stein J. Worms bask in extreme temperatures. Nature 1998 Feb 5; 391: 545–6. Related reading: Jensen M. Worms' hot ends set thermal record. Science News 1998 Feb 21; 153 (8): 126.
Cossins AR. Some like it hot. Nature 1998 May 21; 393: 227–8.
DeLong E. Archeal means and extremes. Science 1998 Apr 24; 280: 542–3.
Gross M. Life on the Edge: Amazing Creatures Thriving in Extreme Environments. New York: Plenum Press 1998.
Kajander EO, Ciftcioglu N. Nanobacteria: An alternative mechanism for pathogenic intra- and extracellular calcification and stone formation. Proceedings of the National Academy of Sciences 1998 Jul 7; 95 (14): 8274–9. Related reading: Folk RL. Life in miniature [letter]. Science News 1998 Sep 12; 154 (11): 163, 169. Travis J. The bacteria in the stone. Science News 1998 Aug 1; 154 (5): 75–7. Vogel G. Bacteria to blame for kidney stones? Science 1998 Jul 10; 281: 153.
Pain S. Extremeworms. New Scientist 1998a Jul 25; 159 (2144): 48–50.
Pain S. The intraterrestrials. New Scientist 1998b Mar 7; 157 (2124): 28–32.
Priscu JC, Fritsen CH, Adams EE, Giovannoni SJ, Paerl HW, McKay CP, Doran PT, Gordon DA, Lanoil BD, Pinckney JL. Perennial Antarctic lake ice: An oasis for life in a polar desert. Science 1998 Jun 26; 280: 2095–8. Related reading: Knight J. On thin ice. New Scientist 1998 Jul 4; 159 (2141): 13. Milius S. Looking for life in all the worst places. Science News 1998 Jul 11; 154 (2): 27. Svitil KA. Life on ice. Discover 1998 Oct; 19 (10): 38.
Vogel G. Finding life's limits. Science 1998 Nov 20; 282: 1399.
Balter M. Did life begin in hot water? Science 1998 Apr 3; 280: 31.
Boctor NZ, Cody GD, Cooper BA, Hazen RM, Yoder HS, Brandes JA. Abiotic nitrogen reduction on the early earth. Nature 1998 Sep 24; 395: 365–7. Related reading: Chyba C. Buried beginnings. Nature 1998 Sep 24; 395: 329–30.
Canfield DE. A new model for Proterozoic ocean chemistry. Nature 1998; 450–453.
Carmi N, Balkhi SR, Breaker RR. Cleaving DNA with DNA. Proceedings of the National Academy of Sciences 1998 Mar 3; 95 (5): 2233–7. Related reading: Wu C. DNA scissors cleave their comrades. Science News 1998 Apr 4; 153 (14): 223.
Cleaves HJ, Miller SL. Oceanic protection of prebiotic organic compounds from UV radiation. Proceedings of the National Academy of Sciences 1998 Jun 23; 95 (13): 7260–3. Related reading: Brainard J. What was life's first sunblock? Science News 1998 Jul 11; 154 (2): 31.
Cohen P. Molecules of ancient life are born again. New Scientist 1998 Oct 17; 160 (2156): 10. Related reading: Zhang B, Cech TR. Peptide bond formation by in vitro selected ribozymes. Nature 1997 Nov 6; 390: 96–100.
Edwards MR. From a soup or a seed? Pyritic metabolic complexes in the origin of life. Trends in Ecology and Evolution 1998 May; 13 (5): 178–81.
Huber C, Wachtershauser G. Peptides by activation of amino acids with CO on (Ni,Fe)S surfaces: Implications for the origin of life. Science 1998 Jul 31; 281: 670–2. Related reading: Vogel G. A sulfurous start for protein synthesis? Science 1998 July 31; 281: 627–9.
Jeffares DC, Poole AM, Penny D. Relics from the RNA world. Journal of Molecular Evolution 1998 Jan; 46: 18–36.
Levy M, Miller SL. The stability of the RNA bases: Implications for the origin of life. Proceedings of the National Academy of Sciences 1998 Jul 7; 95 (14): 7933–8. Related reading: Knight J. Cold start. New Scientist 1998 Jul 11; 159 (2142): 10.
Luther A, Brandsch R, von Kiedrowski G. Surface-promoted replication and exponential amplification of DNA analogues. Nature 1998 Nov 19; 396: 245–8. Related reading: Day M. Did stones nurture the first life on Earth? New Scientist 1998 Nov 21; 160 (2161): 6.
Nitta I, Kamada Y, Noda H, Ueda T, Watanabe K. Reconstitution of peptide bond formation with Escherischia coli 23s ribosomal RNA domains. Science 1998 Jul 31; 281: 666–9. Related reading: Schimmel P, Alexander R. All you need is RNA. Science 1998 Jul 31; 281: 658–9.
Parsons I, Lee MR, Smith JV. Biochemical evolution II: Origin of life in tubular microstructures on weathered feldspar surfaces. Proceedings of the National Academy of Sciences 1998 Dec 22; 95 (26): 15173–6.
Poole AM, Jeffares DC, Penny D. The path from the RNA world. Journal of Molecular Evolution 1998 Jan; 46: 1–17.
Smith JV. Biochemical evolution. I. Polymerization on internal, organophilic silica surfaces of dealuminated zeolites and feldspars. Proceedings of the National Academy of Sciences 1998 Mar 31; 95 (7): 3370–5.
Unrau PJ, Bartel DP. RNA-catalysed nucleotide synthesis. Nature 1998 Sep 17; 395: 260–3. Related reading: [Anonymous]. Dawn of life. New Scientist 1998 Sep 19; 159 (2152): 27. Robertson MP, Ellington AD. How to make a nucleotide. Nature 1998 Sep 17; 395: 223–5.
The Rise of Eukaryotes
Blackman S. Safety in numbers. New Scientist 1998 Mar 14; 157 (2125): 15.
Martin W, Muller M. The hydrogen hypothesis for the first eukaryote. Nature 1998 Mar 5; 392: 37–41. Related reading: Doolittle WF. A paradigm gets shifty. Nature 1998 Mar 5; 392: 15–6. Sandman K, Reeve JN. Origin of the eukaryotic nucleus [letter]. Science 1998 Apr 24; 280: 501–2. Travis J. The hydrogen hypothesis. Science News 1998 Apr 18; 153 (16): 253–5. Vogel G. Did the first complex cell eat hydrogen? Science 1998 Mar 13; 279: 1633–4.
Monastersky R. Fossil soil has the dirt on early microbes. Science News 1998a Mar 7; 153 (10): 151. Related reading: [Anonymous]. Getting the dirt on land life. Earth 1998 Aug; 7 (4): 14.
Monastersky R. Arctic fossils record evolutionary burst. Science News 1998b Nov 7; 154 (19): 294.
Chapter 2: Genetics and Evolution
[Anonymous]. Still jumping. New Scientist 1998 Nov 14; 160 (2160): 30.
Boyce N. Good for nothing. New Scientist 1998 Jan 17; 157 (2117): 7.
Brookes M. Day of the mutators. New Scientist 1998 Feb 14; 157 (2121): 38–42.
Max EE. "New" persuasive evidence for evolution. The American Biology Teacher 1998 Nov/Dec; 60 (9): 662–70.
Pennisi E. The first codon and its descendents. Science 1998a Jul 17; 281: 330.
Pennisi E. How the genome readies itself for evolution. Science 1998b Aug 21; 281: 1131–4.
Rainey PB, Travisano M. Adaptive radiation in a heterogeneous environment. Nature 1998 Jul 2; 394: 69–72.
Van den Burg B, Vriend G, Veltman OR, Venema G, Eijsink VGH. Engineering an enzyme to resist boiling. Proceedings of the National Academy of Sciences 1998 Mar 3; 95 (5): 2056–60. Related reading: Seife C. Designer enzymes enjoy life in the hot seat. New Scientist 1998 Mar 7; 157 (2124): 10.
Vogel G. Tracking the history of the genetic code. Science 1998 Jul 17; 281: 329–31.
Wu H, Hu Z, Liu X-Q. Protein trans-splicing by a split intein encoded in a split DnaE gene of Synechocystis sp. PCC6803. Proceedings of the National Academy of Sciences 1998 Aug 4; 95 (16): 9226–31. Related reading: Vogel G. A two-piece protein assembles itself. Science 1998 Aug 7; 281: 763.
Arnqvist G. Comparative evidence for the evolution of genitalia by sexual selection. Nature 1998 Jun 25; 393: 784–6. Related reading: Gwynne DT. Genitally does it. Nature 1998 June 25; 393: 734–5. Milius S. Why guys get fancy. Science News 1998 Aug 29; 154 (9): 140–1.
Barton NH, Charlesworth B. Why sex and recombination? Science 1998 Sep 25; 281: 1986–90.
Evans MRJ. Selection on swallow tail streamers. Nature 1998 Jul 16; 394: 233–4. Related reading: Hedenstrom A, Moller AP. Length of tail streamers in barn swallows. Nature 1999 Jan 14; 397: 115.
Hines P, Culotta E. The evolution of sex. Science 1998 Sep 25; 281: 1979.
Losos JB, Jackman TR, Larson A, de Queiroz K, Rodriguez-Schettino L. Contingency and determinism in replicated adaptive radiations of island lizards. Science 1998 Mar 27; 279: 2115–8. Related reading: Vogel G. For island lizards, history repeats itself. Science 1998 Mar 27; 279: 2043.
Rosenthal GG, Evans CS. Female preference for swords in Xiphophorus helleri reflects a bias for large apparent size. Proceedings of the National Academy of Sciences 1998 Apr 14; 95 (8): 4431–6.
Sargent TD, Millar CD, Lambert DM. The "classical" explanation of industrial melanism: Assessing the evidence. Evolutionary Biology 1998; 30: 299–322.
Welch AM, Semlitsch RD, Gerhardt HC. Call duration as an indicator of genetic quality in male gray tree frogs. Science 1998; 280: 1928–30. Related reading: Pennisi E. Females pick good genes in frogs, flies. Science 1998 Jun 19; 280: 1837–8.
Wilkinson GS, Presgraves DC, Crymes L. Male eye span in stalk-eyed flies indicates genetic quality by meiotic drive suppression. Nature 1998 Jan 15; 391: 276–9. Related reading: Hurst LD, Pomlankowski A. The eyes have it. Nature 1998 Jan 15; 391: 223–4. Milius S. Female flies pick mates with sexy eyes. Science News 1998 Jan 17; 153 (3): 36.
Wuethrich B. Why sex? Putting theory to the test. Science 1998; 281: 1980–2.
Designing with Evolution
Crameri A, Raillard S-A, Bermudez E, Stemmer WPC. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 1998 Jan 15; 391: 288–91.
Landweber LF, Simon PJ, Wagner TA. Ribozyme engineering and early evolution. BioScience 1998 Feb; 48 (2): 94–103.
Lenski RE. Get a life. Science 1998 May 8; 280: 849–50.
MacBeath G, Kast P, Hilvert D. Redesigning enzyme topology by directed evolution. Science 1998 Mar 20; 279: 1958–61.
Petit CW. Touched by nature: Putting evolution to work on the assembly line. U.S. News & World Report 1998 Jul 27; 125 (4): 43–5.
Taubes G. Evolving a conscious machine. Discover 1998 Jun; 19 (6): 72–9.
Andersson SGE, Zomorodipour A, Andersson JO, Sicheritz-Pont[eacute]n T, Alsmark UCM, Podowski RM, N[auml]slund AK, Eriksson A-S, Winkler HH, Kurland CG. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 1998 Nov 12; 396: 133–40. Related reading: Gray MW. Rickettsia, typhus and the mitochondrial connection. Nature 1998; 396: 109–10. Pennisi E. Genome links typhus bug to mitochondrion. Science 1998 Nov 13; 282: 1243.
Aravalli RN, She Q, Garrett RA. Archaea and the new age of microorganisms. Trends in Ecology and Evolution. 1998 May; 13 (5): 190–4.
Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, R Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quai MA, Rajandream M-A, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998 Jun 11; 393: 537–3. Related reading: Young DB. Blueprint for the white plague. Nature 1998 Jun 11; 393: 515–6.
Deckert G, Warren PV; Gaasterland T; Young WG; Lenox AL; Graham DE; Overbeek R; Snead MA; Keller M; Aujay M; Feldman RA; Short JM; Olsen GJ; Huber R; Swanson RV. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 1998 Mar 26; 392: 353–8. Related reading: Doolittle RF. Microbial genomes opened up. Nature 1998 Mar 26; 392: 339–42.
The EU Arabidopsis Genome Project. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 1998 Jan 29; 391:485–8. Related reading: Ecker JR. Genes blossom from a weed. Nature 1998 Jan 29; 391: 438.
Fraser CM, Norris SJ, Weinstock JM, White O, Sutton GG, Dodson R, Gwinn M, Hickey EK, Clayton R, Ketchum KA, Sodergren E, Hardham JM, McLeod MP, Salzberg S, Peterson J, Khalak H, Richardson D, Howell JK, Chidambaram M, Utterback T, McDonald L, Artiach P, Bowman C, Cotton MD, Fujii C, Garland S, Hatch B, Horst K, Roberts K, Sandusky M, Weidman J, Smith HO, Venter JC. Complete genome sequence of Treponema pallidum, the syphilis spirochaete. Science 1998 Jul 17; 281: 375–88. Related reading: Pennisi E. Genome reveals wiles and weak points of syphilis. Science 1998 Jul 17; 281: 324–5. Seppa N. Reseachers solve syphilis genome. Science News 1998 Aug 11; 154 (5): 79.
Hodgkin J, Herman RK. Changing styles in C. elegans genetics. Trends in Genetics 1998 Sep; 14 (9): 352–7.
Hodgkin J, Horvitz HR, Jasny BR, Kimble J. C. elegans: Sequence to biology. Science 1998 Dec 11; 282: 2011. Related reading: Chalfie M. The worm revealed. Nature 1998 Dec 17; 396: 620–1. Ferry G. The human worm. New Scientist 1998 Dec 5; 160 (2163): 33–5. Pennisi E. Worming secrets from the C. elegans genome. Science 1998 Dec 11; 282: 1972–5. Travis J. Worm offers the first animal genome. Science News 1998 Dec 12; 154 (24): 372. Yam P. Worm genome project. Scientific American 1999 Feb; 87 (2): 26.
Huynen MA, Bork P. Measuring genome evolution. Proceedings of the National Academy of Sciences 1998 May 26; 95 (11): 5849–56.
Katz LA. Changing perspectives on the origin of eukaryotes. Trends in Ecology and Evolution 1998 Dec; 13 (12): 493–7.
Koga Y, Kyuragi T, Nishihara M, Sone N. Did archaeal and bacterial cells arise independently from noncellular precursors? A hypothesis stating that the advent of membrane phospholipid with enantiomeric glycerophosphate backbones caused the separation of the two lines of descent. Journal of Molecular Biology 1998 Jan; 46 (1): 54–63. Related reading: Barnett A. The second coming. New Scientist 1998 Feb 14; 157 (2121): 19.
Meinke DW, Cherry JM, Dean C, Rounsley SD, Koornneef M. Arabidopsis thaliana: A model plant for genome analysis. Science 1998 Oct 23; 282: 662–81.
Miller RV. Bacterial gene swapping in nature. Scientific American 1998 Jan; 278 (1): 66–71.
Pebusque M-J, Coulier F, Birnbaum D, Pontarotti P. Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution. Molecular Biology and Evolution 1998; 15 (9): 1145–59.
Pennisi E. Genome data shake tree of life. Science 1998 May 1; 280: 672, –4.
Postlethwait JH, Yan Y-L, Gates M, Horne S, Amores A, Brownlie A, Donovan A, Egan E, Force A, Gong Z, Goutel C, Fritz A, Kelsh R, Knapik E, Liao E, Paw B, Ransom D, Singer A, Thomson M, Abduljabbar T, Yelick P, Beier D, Joly L, Larhammar D, Rosa F, Westerfield M, Zon L, Johnson S, Talbot W. Vertebrate genome evolution and the zebrafish gene map. Nature Genetics 1998 Apr; 18: 345–9. Related reading: Aparicio S. Exploding vertebrate genomes. Nature Genetics 1998 Apr; 18: 301–3.
Simmen MW, Leitgeb S, Clark VH, Jones SJM, Bird A. Gene number in an invertebrate chordate, Ciona intestinalis. Proceedings of the National Academy of Sciences 1998 Apr 14; 95: 4437–40.
Stephens RS, Kalman S, Lammel C, Fan J, Marathe R, Aravind L, Mitchell W, Olinger L, Tatusov RL, Zhao Q, Koonin EV, Davis RW. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 1998 Oct 23; 282: 754–9. Related reading: Hatch T. Chlamydia: Old ideas crushed, new mysteries bared. Science 1998 Oct 23; 282: 638–9.
Woese C. The universal ancestor. Proceedings of the National Academy of Sciences 1998 Jun 9; 95 (12): 6854–9.
Chapter 3: The Origin of Species
Brookes M. The species enigma. New Scientist 1998 Jun 13; 158 (2138). Inside Science supplement nr. 111.
Galis F, Metz JAJ. Why are there so many cichlid species? Trends in Ecology and Evolution 1998 Jan; 13 (1): 1–2.
Gavrilets S, Li H, Vose MD. Rapid parapatric speciation on holey adaptive landscapes. Proceedings of the Royal Society of London Series B 1998; 265: 1483–9.
Geiser DM, Pitt JI, Taylor JW. Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus. Proceedings of the National Academy of Sciences 1998 Jan 3; 95: 388–93.
Kondrashov AS, Shpak M. On the origin of species by means of assortative mating. Proceedings of the Royal Society of London Series B 1998 Dec 7; 265 (1412): 2273–8.
Orr MR, Smith TB. Ecology and speciation. Trends in Ecology and Evolution. 1998 Dec; 13 (12): 502–6.
Swanson WJ, Vacquier VD. Concerted evolution in an egg receptor for a rapidly evolving abalone sperm protein. Science 1998 Jul 31; 281: 710–2. Related reading: Cohen P. Promiscuity helps the abalone evolve into a new species. New Scientist 1998 Aug 8; 159 (2146): 19.
Ting C-T, Tsaur S-C, Wu M-L, Wu C-I. A rapidly evolving homeobox at the site of a hybrid sterility gene. Science 1998 Nov 20; 282; 1501–4. Related reading: Cohen P. Splitting heirs. New Scientist 1998 Nov 28; 160 (2162): 11.Nei M, Zhang J. Molecular origin of species. Science 1998 Nov 20; 282: 1428–9.
Waugh O'Neill RJ, O'Neill MJ, and Marshall Graves JA. Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature 1998 May 7; 393: 68–72.
Chapter 4: The Fossil Record
The Cambrian Explosion
[Anonymous]. A billion years of stability. Discover 1998 Sep; 19 (9): 19.
Bromham L, Rambaut A, Fortey R, Cooper A, Penny D. Testing the Cambrian explosion hypothesis by using a molecular dating technique. Proceedings of the National Academy of Sciences 1998 Oct 3; 95 (21): 12386–9.
Cooper A, Fortey R. Evolutionary explosions and the phylogenetic fuse. Trends in Ecology and Evolution 1998 Apr; 13 (4): 151–6. Related reading: Lee MSY. Similarity, parsimony and conjecture of homology: The chelonian shoulder girdle revisited. Journal of Evolutionary Biology 1998 May; 11: 379–87.
Gould SJ. On embryos and ancestors. Natural History 1998 Jul/Aug 8; 107 (6): 20–2, 58–65.
Gu X. Early metazoan divergence was about 830 million years ago. Journal of Molecular Evolution 1998 Sep; 47 (3): 369–71.
Hecht J. Tilt-a-world. Earth 1998 Jun; 7 (3): 34–7. Related reading: Kirschvink JL, Ripperdan RL, Evans DA. Evidence for a large-scale reorganization of early Cambrian continental masses by inertial interchange true polar wander. Science 1997 Jul 25; 277: 541–5.
Hoffman PF, Kaufman AJ, Halverson GP, Schrag DP. A neoproterozoic snowball earth. Science 1998 Aug 28; 281: 1342–6. Related reading: Jenkins GS, Scotese CR. An early snowball earth? [letter] Science 282 Nov 27: 1644–6. Kerr RA. Did an ancient deep freeze nearly doom life? Science 1998 Aug 28; 281: 1259–60; Monastersky R. Popsicle Planet. Science News 1998 Aug 29; 154 (9): 137–9.
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Chapter 5. Homology
Amores A, Force A, Yan Y-L, Joly L, Amemiya C, Fritz A, Ho RK, Langeland J, Prince V, Wang Y-L, Westerfield M, Ekker M, Postlethwait JH. Zebrafish hox clusters and vertebrate genome evolution. Science 1998 Nov 27; 282: 1711–4. Related reading: Vogel G. Doubled genes may explain fish diversity. Science 1998 Aug 21; 281: 1119–21.
Behe MJ, Sander K, Bender R. Embryology and evolution [letters]. Science 1998 Jul 17; 281: 348–9. Related reading: Richardson MK. Haeckel's embryos, continued [letter]. Science 1998 Aug 28; 281: 1289.
Brooke NM, Garcia-Fernandez J, Holland PWH. The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster. Nature 1998 Apr 20; 392: 920–2.
Cameron RA, Peterson KJ, Davidson EH. Developmental gene regulation and the evolution of large animal body plans. American Zoologist 1998; 38 (4): 609–20.
Dreyer WJ. The area code hypothesis revisited: Olfactory receptors and other related transmembrane receptors may function as the last digits in a cell surface code for assembling embryos. Proceedings of the National Academy of Sciences 1998 Aug 4; 95 (16): 9072–7.
Duboule D, Wilkins AS. The evolution of bricolage. Trends in Genetics 1998 Feb; 14 (2): 54–9.
Gardner DM, Torok MA, Mullen LM, Bryant SV. Evolution of vertebrate limbs: Robust morphology and flexible development. American Zoologist 1998; 38 (4): 659–71.
Gilbert SF. Conceptual breakthroughs in development biology. Journal of Biosciences 1998 Sep; 23 (3): 169–76.
Hall BK. Germ layers and the germ-layer theory revisited: Primary and secondary germ layers, neural crest as a fourth germ layer, homology, and demise of the germ-layer theory. Evolutionary Biology 1998; 30: 121–86.
Henry GL, Melton DA. Mixer, a homeobox gene required for endoderm development. Science 1998 Jun 26; 281: 91–6.
Holland LZ, Holland ND. Developmental gene expression in Amphioxus: New insights into the evolutionary origin of vertebrate brain regions, neural crest, and rostrocaudal segmentation. American Zoologist 1998; 38 (4): 647–58.
Kmita-Cunisse M, Loosli F, Bierne J, Gehring WJ. Homeobox genes in the ribbonworm Linea sanguineus: Evolutionary implications. Proceedings of the National Academy of Sciences 1998 Mar 17; 95 (6): 3030–5.
Lee MSY. Similarity, parsimony and conjecture of homology: The chelonian shoulder girdle revisited. Journal of Evolutionary Biology 1998 May; 11: 379–87.
Lewin R. Family feuds. New Scientist 1998 Jan 24; 157 (2118): 36–40.
Martindale MQ, Henry JQ. The development of radial and biradial symmetry: The evolution of bilaterality. American Zoologist 1998; 38 (4): 672–84.
Martinez DE, Bridge D, Masuda-Nakagawa LM, Cartwright P. Cnidarian homeoboxes and the zootype. Nature 1998 Jun 25; 393: 748–9.
Meyer A. Hox gene variation and evolution. Nature 1998 Jan 15; 225–8.
Pendick D. When life got legs. Earth 1998 Aug; 7 (4): 26–33.
Prince VE. Hox genes and segmental patterning of the vertebrate hindbrain. American Zoologist 1998; 38 (4): 634–6.
Richardson MK, Hanken J, Gooneratne ML, Pieau C, Raynaud A, Selwood L, Wright GM. There is no highly conserved embryonic stage in the vertebrates: Implications for current theories of evolution and development. Anatomy and Embryology 1997; 196: 91–106.
Richardson MK, Hanken J, Selwood L, Wright GM, Richards RJ, Pieau C, Raynaud A. Haeckel, embryos, and evolution [letter]. Science 1998 May 15; 280: 983–5.
Schwabe JWR, Rodriguez-Esteban C, Belmonte JCI. Limbs are moving: where are they going? Trends in Genetics 1998 Jun; 14 (6): 229–35.
Strauss E. How embryos shape up. Science 1998 Jul 10; 281: 166–7.
Tautz D. Debatable homologies. Nature 1998 Sep 3; 395: 17–18.
Wray GA, Raff RA. Body builders of the sea. Natural History 1998 Dec/Jan; 107 (10): 38–47.
Chapter 6: Biochemistry
Anderson CL, Canning EU, Okamura B. A triploblast origin for Myxozoa? Nature 1998 Mar 26; 392: 346.
Balavoine G, Adoutte A. One or three Cambrian radiations? Science 1998 Apr 17; 280: 397–8.
Collins AG. Evaluation multiple alternative hypotheses for the origin of Bilateria: An analysis of 18S rRNA molecular evidence. Proceedings of the National Academy of Sciences 1998 Dec 22; 95 (26): 15458–63.
De Ley P, Garey JR, Liu LX, Scheldeman P, Vierstraete A, Vanfleteren JR, Mackey LY, Dorris M, Frisse LM, Vida JT, Thomas WK, Blaxter ML. A molecular evolutionary framework for the phylum Nematoda. Nature 1998 Mar 5; 392: 71–6. Related reading: Anderson RC. Out of order [letter]. Nature 1998 May 14; 393: 10. Nielsen C. Sequences lead to tree of worms. Nature 1998 Mar 5; 392: 25–6.
Gaut BS. Molecular clocks and nucleotide substitution rates in higher plants. Evolutionary Biology 1998; 30: 93–120.
Kumar S, Hedges SB. A molecular timescale for vertebrate evolution. Nature 1998 Apr 30; 392: 917–20. Related reading: Gibbons A. Genes put mammals in age of dinosaurs. Science 1998 May 1; 280: 675–6. McDonald KA. Mammals diversified earlier than believed. The Chronicle of Higher Education 1998 May 29; 44 (38): A21.
Maley LE, Marshall CR. The coming of age of molecular systematics. Science 1998 Jan 23; 279: 505–6.
Normile D. New views of the origins of mammals. Science 1998 Aug 7; 281: 774–5. Related reading: Wong K. Cetacean creation. Scientific American 1999 Jan; 87 (1): 26–30.
Qiu Y-L, Cho Y, Cox JC, Palmer JD. The gain of three mitochondrial introns identifies liverworts as the earliest land plants. Nature 1998 Aug 13; 394: 671–4. Related reading: [Anonymous]. The Ur-plant. Discover 1998 Nov; 19 (11): 26.
Schubart CD, Diesel R, Blair-Hedges S. Rapid evolution to terrestrial life in Jamaican crabs. Nature 1998 May 28; 363–5. Related reading: Tromans A. Land-loving crabs. Nature 1998 May 28; 393: 305.
Springer MS, Westerman M, Kavanagh JR, Burk A, Woodburne MO, Kao DJ, Krajewski C. The origin of the Australasian marsupial fauna and the phyogenetic affinities of the enigmatic monito del monte and marsupial mole. Proceedings of the Royal Society of London Series B 1998 Dec 22; 265 (1413): 2381–6.
Ursing BM, Arnason U. Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade. Proceedings of the Royal Society of London Series B 1998 Dec 7; 265 (1412): 2251–5.
Zardoya R, Meyer A. Complete mitochondrial genome suggests diapsid affinities of turtles. Proceedings of the National Academy of Sciences 1998 Nov 24; 95 (24): 14226–31. Related reading: [Anonymous]. Don't mess with me — my cousin's a dinosaur. New Scientist 1998 Nov 28; 160 (2162): 25. Monastersky R. Turtle genes upset reptilian family tree. Science News 1998 Dec 5; 154 (23): 358.
About the Author(s):
Frank J Sonleitner
Department of Zoology
University of Oklahoma
Norman, OK 73019